ChemWiki - User contributions [en]

Rep:Mod:szd2810

2013-03-12T12:40:06Z

Sd2810: /* frequency analysis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

===frequency analysis===

[[File:Convergence.png]]

[[file:Low_freq.png]]

===IR analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

===charge distribution===

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

===frequency analysis===

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

===charge distribution===
[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

==pyridinium==

[[File:Pyridine.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

===frequency analysis===

[[file:Pyridium_conv.png]]
[[file:Pyr_low_freq.png]]

=== charge distribution===
[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]
===orbitals analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

==borazine==

[[File:Borazine2.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

===frequency analysis===

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

===charge distribution===

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

===MO diagram of borazine===
[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Pyr low freq.png

2013-03-12T12:39:53Z

Sd2810: uploaded a new version of "File:Pyr low freq.png"

Rep:Mod:szd2810

2013-03-12T12:39:29Z

Sd2810: /* pyridinium */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

===frequency analysis===

[[File:Convergence.png]]

[[file:Low_freq.png]]

===IR analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

===charge distribution===

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

===frequency analysis===

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

===charge distribution===
[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

==pyridinium==

[[File:Pyridine.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

===frequency analysis===

[[file:Pyridium_conv.png]]
[[file:Pyridium_low_freq.png]]

=== charge distribution===
[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]
===orbitals analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

==borazine==

[[File:Borazine2.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

===frequency analysis===

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

===charge distribution===

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

===MO diagram of borazine===
[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Pyridium conv.png

2013-03-12T12:38:56Z

Sd2810:

File:Pyr low freq.png

2013-03-12T12:38:08Z

Sd2810:

File:Pyr covergence.png

2013-03-12T12:38:07Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T12:31:33Z

Sd2810: /* borazine */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

===frequency analysis===

[[File:Convergence.png]]

[[file:Low_freq.png]]

===IR analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

===charge distribution===

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

===frequency analysis===

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

===charge distribution===
[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

==pyridinium==

[[File:Pyridine.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

=== charge distribution===
[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]
===orbitals analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

==borazine==

[[File:Borazine2.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

===frequency analysis===

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

===charge distribution===

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

===MO diagram of borazine===
[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T12:30:02Z

Sd2810: /* pyridinium */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

===frequency analysis===

[[File:Convergence.png]]

[[file:Low_freq.png]]

===IR analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

===charge distribution===

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

===frequency analysis===

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

===charge distribution===
[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

==pyridinium==

[[File:Pyridine.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

=== charge distribution===
[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]
===orbitals analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T12:28:56Z

Sd2810: /* boratabenzene */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

===frequency analysis===

[[File:Convergence.png]]

[[file:Low_freq.png]]

===IR analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

===charge distribution===

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

===frequency analysis===

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

===charge distribution===
[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T12:27:41Z

Sd2810: /* benzene */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

===frequency analysis===

[[File:Convergence.png]]

[[file:Low_freq.png]]

===IR analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

===charge distribution===

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

===orbital analysis===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T12:05:32Z

Sd2810: /* NH3 molecule */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

N-H bond distance before the optimization = 1.0000A
N-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T12:02:59Z

Sd2810: /* NH3 orbitals */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

===NH3 charge distribution===
[[file:Nh3_charge_no..png|250px]]
[[file:Nh3_charge.png|250px]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T12:02:06Z

Sd2810: /* NH3 molecule */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

===frequency analysis===
[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

===vibrational analysis of NH3===
{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

===NH3 orbitals===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:55:21Z

Sd2810: /* IR analysis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:47:43Z

Sd2810: /* BBr3 optimisation */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:47:02Z

Sd2810: /* BBr3 optimisation */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-Br bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ BBr3 optimisation
! file name !! heading
|-
| file type || .log
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || Gen
|-
| charge || 0
|-
| spin || singlet -64.43645296 a.u.
|-
| total energy || 0.00000382 a.u.
|-
| RMS gradient norm ||
|-
| dipole moment || 0.0000 Debye
|-
| point group || D3H
|-
| job cpu time || 0 days 0 hours 0 minutes 10.0 seconds.
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:21:44Z

Sd2810: /* IR analysis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

===BBr3 frequency analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:21:21Z

Sd2810: /* BH3 frequency analysis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BBr3 optimisation===

to determine if the optimisation of the BBr3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:20:50Z

Sd2810: /* TlBr3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

===TlBr3 optimisation===

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:13:11Z

Sd2810: /* TlBr3 optimisation and frequency analysis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency analysis===

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:12:35Z

Sd2810: /* TlBr3 optimisation and frequency analysis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis
Filename = \\ic.ac.uk\homes\sd2810\COMPUTATION\TlBr3\TlBr3_optimisation.chk

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || .chk
|-
| calulation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient norm || 0.00000090 a.u.
|-
| dipole moment || 0.0000 Debye
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:09:46Z

Sd2810: /* TlBr3 optimisation */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 ==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:09:23Z

Sd2810: /* TlBr3 frequency anaylsis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:05:24Z

Sd2810: /* comparison of BH3 BBr3 and TlBr3 bondlengths */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3==

===comparison of BH3 BBr3 and TlBr3 bondlengths===

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:04:33Z

Sd2810: /* BH3 BBr3 and TlBr3 vibrational modes comparison */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T11:03:55Z

Sd2810: /* comparison of BH3 BBr3 and TlBr3 bondlengths */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:59:10Z

Sd2810: /* BH3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:58:52Z

Sd2810: /* virational modes of BH3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:58:25Z

Sd2810:

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

===TlBr3 vibrational analysis===

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:57:51Z

Sd2810: /* BH3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

{| class="wikitable" border="1"
|+ orbitals of BH3
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:57:24Z

Sd2810: /* molecular orbitals of BH3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:49:57Z

Sd2810: /* NH3 molecule */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[file:Nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:49:05Z

Sd2810: /* NH3 molecule */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]
[[fileNh3_low_freq.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Nh3 low freq.png

2013-03-12T10:48:43Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T10:45:05Z

Sd2810: /* NH3 molecule */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]
[[file:Nh3_charge.png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Nh3 charge.png

2013-03-12T10:44:45Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T10:44:27Z

Sd2810: /* NH3 molecule */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

[[file:Nh3_charge_no..png]]

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Nh3 charge no..png

2013-03-12T10:44:09Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T10:24:29Z

Sd2810: /* TlBr3 frequency anaylsis */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 optimisation and frequency analysis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:17:26Z

Sd2810: /* BBr3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[file:Bbr3_conv.png]]
[[file:BBr3_low_freq.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:BBr3 low freq.png

2013-03-12T10:17:03Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T10:16:41Z

Sd2810: /* BBr3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

[[Bbr3_conv.png]]

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Bbr3 conv.png

2013-03-12T10:16:15Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T10:15:39Z

Sd2810: /* BBr3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png|250px]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:15:14Z

Sd2810: /* BBr3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

[[file:Bbr3.png]]

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:Bbr3.png

2013-03-12T10:14:18Z

Sd2810:

Rep:Mod:szd2810

2013-03-12T10:07:34Z

Sd2810: /* basis set 6-31G */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:07:15Z

Sd2810: /* basis set 6-31G */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

[[File:6-31G_summary.png|350px|thumb| picture showing the converge table is correct]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

Rep:Mod:szd2810

2013-03-12T10:06:49Z

Sd2810: /* frequency analysis of BH3 */

==introduction==

In this study Gaussview is used to simulate a varitey of inorganic molecules and to the then probe them using a variety of basis sets and methods. the NBO's and MO's of the molecules where also investigated. Gaussview would then give predicted information on the molecules bonds and its IR's, along with any bonding interactions.

== '''BH3 '''==
=== optimistation of the bond lengths in BH3 ===
The bond lengths of the intial generated molecule where changed to 1.500A from the intal value of 1.18A

[[File:Untitled.png|250px]]

===basis set 3-21G===
The BH3 molecule was then optimized using the following method illustrated

{| class="wikitable" border="1"
|+ '''Method of optimization'''
! method || ground state || DFT || default spin || B3LYP
|-
| basis set || 3-21G || -- || -- || --
|-
| charge || 0 || spin || singlet || --
|}

B-H bond distance before the optimization = 1.500A
B-H distance after optimization method = 1.194539A
the bond angle remained constant throughout the optimization = 120.0000

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || 3-21G
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -26.46226433 a.u.
|-
| rms gradient || 0.00004507 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

[[File:BH3_summary.txt‎]] - this is a link to the above table

[[ File:Summary.png|350px|thumb| A picture showing the converge. note - in the converge all boxes are yes]]

[[File:BH3_optimisation_note_pad.txt‎]] - link to the original convergence document

===basis set 6-31G===
The molecule was further optimized via the 6-31G basis as this is a higher level basis and hence a better overall basis

{| class="wikitable" border="1"
|+ method of 6-31G basis
! method !! Ground state ||DFT||default spin||B3LYP
|-
| basis set || 6-31G ||d ||p
|-
| charge || 0 ||spin ||singlet
|}

B-H bond distance before the optimization = 1.19453A
B-H bond distance after the 6-31G optimization method = 1.19231A

the bond angle renamed constant throughout the optimization

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -26.61532225 a.u.
|-
| RMS gradient norm || 0.00024090 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0000 debye
|-
| point group || D3h
|-
| Job cpu time || 0 days 0 hours 0 minutes 4.0 seconds.
|}

[[File:BH3_optimisation_6-31g_summary.txt]] - link to the above table

[[File:6-31G_graph.png|350px|thumb| graphic analysis of the two basis]]

[[File:6-31G_summary.png|350px|thumb| picture showing the converge table is correct]]

[[File:BH3_OPTIMISATION_6-31G2_summary_convergence_yes.txt]]

=== frequency analysis of BH3===

[[FILE:6-31G_summary.png]]

[[FILE:BH3_low_freq.png]]

==TlBr3 optimisation==

the TlBr3 molecule was simulated on Gaussview with tight symmetry restrictions of a tolerance of 0.0001 then optimisied under these restrictions using a LanL2DZ basis

[[File:TlBr3.png|250px]]

{| class="wikitable" border="1"
|+ method
! method !! ground state ||DFT ||default spin ||B3LYP
|-https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:szd2810&action=edit
| basis set || LanL2DZ
|-
| charge || 0 ||spin ||singlet
|}

{| class="wikitable" border="1"
|+ BH3 optimization
|-
| file name || BH3_optimisation
|-
| file type || .chk
|-
| calculation type || FOPT
|-
| calculation method || RB3LYP
|-
| basis set || LANL2DZ
|-
| charge || 0
|-
| spin || singlet
|-
| total energy || -91.21812851 a.u.
|-
| rms gradient || 0.00000090 a.u.
|-
| imaginary freq ||
|-
| dipole moment || 0.000 debye
|-
| point group || --
|}

Tl-Br bond distance before the optimization = xxxxx
Tl-Br bond distance after the optimization = 2.65095A

the bond angle remained constant throughout the optimization

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = xxxx
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

[[File:TlBr_convergence.png]]

==TlBr3 vibrational analysis==

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration !! frequency !! infra red
|-
| 1 || [[File:Tl_1.gif|200px]] || wagging motion with all H atoms moving in the opposite direction of the B atom || 46.43 || 3.6867 || E'
|-
| 2 || [[File:Tl_2.gif|200px]] || scissoring motion || 46.43 || 3.6867 || E'
|-
| 3 || [[File:Tl_3.gif|200px]] || rocking motion || 52.14 || 5.6466 || A2"
|-
| 4 || [[File:Tl_4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 165.27 || 0.0000 || A1
|-
| 5 || [[File:Tl_5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 210.69 || 25.4830 || E'
|-
| 6 || [[File:Tl_6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 210.69 || 25.4797 ||E'
|}

[[file:TlBr_IR.png||250px]]

3 peaks are seen since only 5 are ir active with 4 being degenerate. mode 4 isnt active since it has no dipole moment

==BBr3==

bond length before optimisation = 2.0000A
bond length after optimisation = 1.93396A

==comparison of BH3 BBr3 and TlBr3 bondlengths==

{| class="wikitable" border="1"
|+ optimized bond lengths
! molecule !! bond length (A)
|-
| BH3 || 1.19231
|-
| BBr3 || 1.93396
|-
| TlBr3 || 2.65095
|}

the bond length orders are then seen (with decreasing value) TlBr3,BBr3,BH3
BH3 is smaller than BBr3 due to the smaller atomic radii of the H atom compared to Br, with a value of 53ppm compared to 120ppm. this means a larger molecule since the central Boron atom doesn't change in atomic radii. both molecules are bonded covalently, though the presence of the lone pairs on bromine allows for donation into the orthogonal P orbital of the boron atom. this would consequently shorten the B-Br bond since there is better overlap between the orbitals, however this decrease in bond length is relatively small compared to the increased size due to the bromine being a larger atom.

the increased size of the TlBr3 atom compared to the BBr3 molecule is due to the increased size of the central atom (since in this case it is the bromine atoms that stay constant in atomic radii length B=90ppm Tl=190ppm). it is the increase in size of the Tl orbitals (S and P) that result in a poorer overlap in the Tl-Br bond compared to the B-Br bond. as with before both bonds are also covalent.

The gaussview program however will form bonds between 2 atoms if the bond distance is small enough for orbital interactions. this will sometimes result in the formation of bonds in gaussview that wouldn't be expected, since bonds are the interaction between two (or more is relevant)atoms and their filled bonding orbitals. however gaussviews definition of bonds are the interaction between electrons and atoms, not filled bonding orbital interactions.

===BH3 frequency analysis===

to determine if the optimisation of the BH3 molecule was correct a frequency analysis of the molecule must be undertaken

B-H bond length = 1.19231
bond angle remained constant throughout analysis at 1200

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calculation type || FREQ
|-
| calculation method || FREQ
|-
| basis set || 6-31G
|-
| charge || 0
|-
| spin || singet
|-
| total energy ||
|-
| RMS gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

this was taken from the frequency analysis and shows that the molecule was correctly optimized since the low frequency is XXXX. it is also seen that the molecule has been optimized to a minimum due to the presence of a energy minima.

=== IR analysis===

in the IR spectrum 3 peaks are visible, though there are predicted 6 peaks. the reason for this is only 5 of the modes are IR active with the with the other 2 modes being degenerate. the mode NUMBER is also inactive since is doesnt have a dipole moment, with the final modes NUMBERS having the same symmetry (E') and hence seen as one peak due to them being degenerate.

=== virational modes of BH3===

{| class="wikitable" border="1"
|+ caption
! vibrational number!! visulisation of vibration!! description of
vibration!! frequency!! intensity!! symetry point group
|-
| 1 || [[File:BH3_1_moving.gif|200px]]||wagging motion with all H atoms moving in the opposite direction of the B atom || 1162.98 || 92.5496 || A2"
|-
| 2 || [[File:BH3_2_moving.gif|200px]] || scissoring motion || 1213.17 || 14.0545 || E'
|-
| 3 || [[File:BH3_3_moving.gif|200px]] || rocking motion || 1213.18 || 14.0581 || E'
|-
| 4 || [[File:BH3_4_moving.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom stationary || 2582.32 || 0.0000 || A1'
|-
| 5 || [[fILE:BH3_5_moving.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically with the final H stationary || 2715.50 || 126.3285 || E'
|-
| 6 || [[File:BH3_6_moving.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H assymetically to the other 2 H atoms || 2715.5 || 126.3189 || E'
|}

[[file:Bh3_ir.png|350px]]

===TlBr3 frequency anaylsis===

Tl-Br bond length before analysis = XXXX
Tl-Br bond length after analysis = 2.65095
the bond angles remained constant throughout the analysis

{| class="wikitable" border="1"
|+ caption
! file name !! heading
|-
| file type || cell
|-
| calulation type || cell
|-
| calculation method ||
|-
| basis set ||
|-
| charge ||
|-
| spin ||
|-
| E(RB3YLP) ||
|-
| rms gradient norm ||
|-
| dipole moment ||
|-
| point group ||
|-
| job cpu time ||
|}

https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/23582 - this is the link to the completed BBr3 optimization file

=== IR analysis ===

as with the BH3 molecule there will be 6 expected peaks, however since 5 modes are IR active and 4 of the modes being of the same symmetry are degenerate. since modes NUMBER have a dipole moment they are IR active, giving a peak.

===BH3 BBr3 and TlBr3 vibrational modes comparison===

the use of the 6-31G basis gives a more accurate potential energy of the molecules surface. This is due to the basis being a larger set. since different energy potentials of the molecules surfaces mean that a comparison cannot be undertaken, and give respectable and fair results, different methods of optimizations will give different potentials. This will mean the energy minima will be nonequivalent for the two differing optimized molecules. this is why frequency analysis is used, since it will allow us to see whether or not the molecule was correctly optimized.

the reason that the BBR3 AND TLBr3 molecule have much lower values is since they are much more massive than the BH3 molecule and this means that their reduced mass will much greater in turn lowering the wavenumbers. the poorer overlap of orbitals between the B-Br bond and Tl-Br bonds also accounts for them being weaker than the B-H bond, and this is seen by the Tl-Br bond being much longer than the others, with the B-H bond being much shorter.

all the molecules have 3 IR peaks with 5 peaks being IR active, with 2 degenerate E' modes 1 inactive A' mode and one A2" mode, with the E' and A' mode being relatively simular in energy.

===molecular orbitals of BH3===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:Nh3_1.png|200px]]
|-
| 2 || [[file:Nh3_2.png|200px]]
|-
| 3 || [[file:Nh3_3.png|200px]]
|-
| 4|| [[file:Nh3_4.png|200px]]
|-
| 5 || [[file:Nh3_5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|-
| 7 || [[file:Nh3_7.png|200px]]
|-
| 8|| [[file:Nh3_8.png|200px]]
|}

===inserts.===

both the molecules have D3h symetry labels and hence are triagonal plance, so using the 3N-6 rule this gives 6 modes of vibration. since the energies of the symmerteies are the same (this is seen by the equal intesities and frequencyts for the symmerty) the modes of vibration are equal. the molecules all have 3 peaks as explained by the 5 modes being active with the symmetry labels of E,A'1 and A"2. since the B-H bonds are shorter than the Tl-Br bonds due to better orbital overlap the BH3 molecule has a larger range of motions relative to the TlBr3 molecule since the B-H bonds are stronger.

since the B-H bonds are shorter, a larger energy is needed for the same vibrational energy to result in a equivelent motion. this is seen by the frequencts for the intensties of the same symmerty vibrations are of a higher value for the BH3, relative to TlBr3.

since the Tl and Br atoms have larger more diffuse electron clouds thhis means the intensites are much lower for the TlBr3 molecule with the peaks in the same place (relatively) for the two molecules.

the A'1 and E' are both strech motions and these are of a higher energy than the scissorting and wagging motions of the E and A"2. this explains why the A"2 and E' vibrations are similar and the E' and A'1 vibrations are close. the reason for the larger energy of the stretches is because they require a change of electron density.

as the mode number increases the frequency is also seen to increase for both molecules, though due to the increased mass difference between the Tl and Br relative to B and H this makes the A"2 labelled mode more energic reltive to the E', for the TlBr3 molecule. this accounts for the movement of the central atom in the molecule.

==NH3 molecule==

the ammonia molecule was optimised using gaussview to generate an optimised molecule with a changed bond lenth

B-H bond distance before the optimization = 1.0000A
B-H bond distance after the 6-31G optimization method = 1.01797A

the bond angle renamed constant throughout the optimization

[[File:NH3.png|250px|thumb| A gaussvuew image of the NH molecule. this has a bond length of 1.01797A]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! BH3 optimisation 6-31G
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -56.55776856 a.u.
|-
| RMS gradient norm || 0.00000885 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8464 Debye
|-
| point group ||
|}

[[File:NH3_conv.png]]

{| class="wikitable" border="1"
|+ vibrational modes of NH3
! vibrational number !! visulisation of vibration !! description of
vibration
|-
| 1 || [[File:1.gif|200px]] || wagging motion with all H atoms moving in the opposite
direction of the B atom || 1089.55 || 145.4401 || A
|-
| 2 || [[File:2.gif|200px]] || scissoring motion || 1694.12 || 13.5558 || A
|-
| 3 || [[File:3.gif|200px]] || rocking motion || 1694.19 || 13.5560 || A
|-
| 4 || [[File:4.gif|200px]] || stretching (symmetric) all H atoms moves with central B atom
stationary || 3460.98 || 1.0593 || A
|-
| 5 || [[File:5.gif|200px]] || stretching (antisymetric) 2 H atoms moving non symetrically
with the final H stationary || 3589.40 || 0.2700 || A
|-
| 6 || [[File:6.gif|200px]] || stretching (antisymetric) 3 H atoms moving with the final H
assymetically to the other 2 H atoms || 3589.52 || 0.2709 ||A
|}

[[file:Nh3_ir.png]]

Nh3_8.png

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[file:N1.png|200px]]
|-
| 2 || [[file:N2.png|200px]]
|-
| 3 || [[file:N3.png|200px]]
|-
| 4|| [[file:N4.png|200px]]
|-
| 5 || [[file:N5.png|200px]]
|-
| 6|| [[file:Nh3_6.png|200px]]
|}

==NH3BH3==

[[File:Bh3nh3.png|250px]]

===optimisation===

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -83.22468918 a.u.
|-
| RMS gradient norm || 0.00006806 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 5.5655 Debye
|}

===frequency analysis===

[[File:Bh3nh3_convergence.png]]

[[file:Bh3nh3_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! NH3BH3_optimisation
|-
| 1 || 265.98 || 0.000 || A
|-
| 2|| 632.38 || 13.9923 || A
|-
| 3 || 639.08 || 3.5550 || A
|-
| 4 || 640.21 || 3.5556 || A
|-
| 5 || 1069.12 || 40.4878 || A
|-
| 6|| 1069.58 || 40.5609 || A
|-
| 7 || 1169.58 || 108.8541 || A
|-
| 8 || 1203.63 || 3.5164 || A
|-
| 9 || 1203.96 || 2.4878 || A
|-
| 10 || 1329.72 || 113.7031 || A
|-
| 11 || 1676.2 || 27.5551 || A
|-
| 12|| 1676.32 || 27.5393 || A
|-
| 13 || 2470.21 || 67.2475 || A
|-
| 14 || 2530.04 || 231.3619 || A
|-
| 15 || 2530.30 || 231.3495 || A
|-
| 16|| 3462.41 || 2.5098 || A
|-
| 17 || 3579.19 || 27.9254 || A
|-
| 18 || 3579.27 || 27.9208 || A
|}

[[file:Nh3bh3_ir.png]]

==energy of association of NH3 and BH3 molecule==

E of BH3 = -26.4623
E of NH3 = -56.5578
E of NH3BH3 = -83.2247

change in energy = E of NH3BH3 - [(E OF NH3) +E of BH3)]
= -0.02439a.u
since 1 a.u = 2625.5 kjmol-1
enthalpy of formation = 64.035945

==aromacity==
this was futher investigatied using aromatic cmpaunds as a basis

===benzene===

[[File:Benzene.png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 0
|-
| spin || singlet
|-
| total energy|| -232.25820551 a.u.
|-
| RMS gradient norm || 0.00009549 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0001 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Convergence.png]]

[[file:Low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimization
|-
| 1 || 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 2|| 0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 3 || 0.0000 || c-c bond bending into the plane
|-
| 4|| 0.0000 || c-c bond bending into the plane
|-
| 5 || 74.2532 || c-h wagging in and out of the plane
|-
| 6||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 7 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 8||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 9 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 10 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating
|-
| 11 ||0.0000 || c-h wagging in and out of the plane
|-
| 12||0.0000 || c-c bond stretching into the plane (asymmetric and alternating)
|-
| 13 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 14||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 15 ||3.3878 || c-c bond stretching into the plane (asymmetric)
|-
| 16||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 17 ||0.0000 || 2 opposite H pairs wagging in and out of the plane alternating (asymmetric)
|-
| 18||0.0000 || c-c bond bending into the plane (asymmetric)
|-
| 19 ||0.0000 || c-c bond stretching into the plane (asymmetric)
|-
| 20 ||0.0000 ||c-c bond bending into the plane (asymmetric)
|-
| 21 ||6.6362 || c-c and c-h bond stretching into the plane (alternating)
|-
| 22||6.6274 || c-c and c-h bond stretching into the plane (alternating)
|-
| 23 ||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 24||0.0000 || c-c stretching into the plane (asymmetric alternating)
|-
| 25 ||0.0030 || c-h stretching into the plane
|-
| 26||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric)
|-
| 27 ||0.0001 || 2 opposite H pairs stretching into the plane (asymmetric alternating)
|-
| 28||46.6015 || 2 opposite H pairs stretching (asymmetric alternating)
|-
| 29 ||46.5711 || 3 C-H stretching (half of the ring) into the plane
|-
| 30 ||0.0003 || All 6 C-H stretching (symmetrically)
|}

[[file:Benzene_IR.png|250px]]

[[file:Charge_benzene.png|250px]]

[[file:Charge_benzene_no..png|250px]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 1 || [[File:1.png|200px]]
|-
| 2 || [[File:2.png|200px]]
|-
| 3 || [[File:3.png|200px]]
|-
| 4|| [[File:4.png|200px]]
|-
| 5 || [[File:5.png|200px]]
|-
| 6|| [[File:6.png|200px]]
|-
| 7 || [[File:7.png|200px]]
|-
| 8|| [[File:8.png|200px]]
|-
| 9 || [[File:9.png|200px]]
|-
| 10 || [[File:10.png|200px]]
|-
| 11 || [[File:11.png|200px]]
|-
| 12 || [[File:12.png|200px]]
|-
| 13 || [[File:13.png|200px]]
|-
| 14|| [[File:14.png|200px]]
|-
| 15 || [[File:15.png|200px]]
|-
| 16|| [[File:16.png|200px]]
|-
| 17 || [[File:17.png|200px]]
|-
| 18|| [[File:18.png|200px]]
|-
| 19 || [[File:19.png|200px]]
|-
| 20 || [[File:20.png|200px]]
|-
| 21|| [[File:21.png|200px]]
|}

==boratabenzene==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| -1
|-
| spin || singlet
|-
| total energy|| -219.02052962 a.u
|-
| RMS gradient norm || 0.00016251 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 2.8446 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 1 minutes 7.0 seconds.
|}

[[File:Borazine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:7'.png|200px]]
|-
| 8|| [[File:8'.png|200px]]
|-
| 9 || [[File:9'.png|200px]]
|-
| 10 || [[File:10'.png|200px]]
|-
| 11 || [[File:11'.png|200px]]
|-
| 12 || [[File:12'.png|200px]]
|-
| 13 || [[File:13'.png|200px]]
|-
| 14|| [[File:14'.png|200px]]
|-
| 15 || [[File:15'.png|200px]]
|-
| 16|| [[File:16'.png|200px]]
|-
| 17 || [[File:17'.png|200px]]
|-
| 18|| [[File:18'.png|200px]]
|-
| 19 || [[File:19'.png|200px]]
|-
| 20 || [[File:20'.png|200px]]
|-
| 21|| [[File:21'.png|200px]]
|}

[[File:Coverge.png]]
[[File:Boratabenzene_low_freq.png]]

[[file:Bb_charge.png]]

[[file:Bb_charge_no..png]]

==pyridinium==

[[File:Pyridine.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| UB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -248.66807401 a.u.
|-
| RMS gradient norm || 0.00002449 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 1.8724 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 13 minutes 12.0 seconds.
|}

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:PRYIDINE_7.png|200px]]
|-
| 8|| [[File:PRYIDINE_8.png|200px]]
|-
| 9 || [[File:PRYIDINE_9.png|200px]]
|-
| 10 || [[File:PRYIDINE_10.png|200px]]
|-
| 11 || [[File:PRYIDINE_11.png|200px]]
|-
| 12 || [[File:PRYIDINE_12.png|200px]]
|-
| 13 || [[File:PRYIDINE_13.png|200px]]
|-
| 14|| [[File:PRYIDINE_14.png|200px]]
|-
| 15 || [[File:PRYIDINE_15.png|200px]]
|-
| 16|| [[File:PRYIDINE_16.png|200px]]
|-
| 17 || [[File:PRYIDINE_17.png|200px]]
|-
| 18|| [[File:PRYIDINE_18.png|200px]]
|-
| 19 || [[File:PRYIDINE_19.png|200px]]
|-
| 20 || [[File:PRYIDINE_20.png|200px]]
|-
| 21|| [[File:PRYIDINE_21.png|200px]]
|}

[[file:Pyr_charge.png]]

[[file:Pyr_charge_no..png]]

==borazine==

[[File:Borazine2.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! File name !! benzene_optimisation
|-
| file type || .chk
|-
| calculation type|| FOPT
|-
| file type || FOPT
|-
| calculation method|| RB3LYP
|-
| basis set || 6-31G (d,p)
|-
| charge|| 1
|-
| spin || singlet
|-
| total energy|| -242.68459789 a.u.
|-
| RMS gradient norm || 0.00007128 a.u.
|-
| imaginary frequency || --
|-
| dipole moment || 0.0003 Debye
|-
| Point Group || C1
|-
| Job cpu time || 0 days 0 hours 2 minutes 37.0 seconds.
|}

the borazines N-B bond length is longer than a B=N bond yet shorter than a B-N bond indicating delocalisation across the bond

[[file:Charge_borazine.png|250px]]

[[file:Charge_borazine_no..png|250px]]

[[file:Borazine_convergence.png|250px]]

[[file:Borazine_low_freq.png]]

{| class="wikitable" border="1"
|+ method of 6-31G basis
! orbital number !! visulisation
|-
| 7 || [[File:Borazine7.png|200px]]
|-
| 8|| [[File:Borazine8.png|200px]]
|-
| 9 || [[File:Borazine9.png|200px]]
|-
| 10 || [[File:Borazine10.png|200px]]
|-
| 11 || [[File:Borazine11.png|200px]]
|-
| 12 || [[File:Borazine12.png|200px]]
|-
| 13 || [[File:Borazine13.png|200px]]
|-
| 14|| [[File:Borazine14.png|200px]]
|-
| 15 || [[File:Borazine15.png|200px]]
|-
| 16|| [[File:Borazine16.png|200px]]
|-
| 17 || [[File:Borazine17.png|200px]]
|-
| 18|| [[File:Borazine18.png|200px]]
|-
| 19 || [[File:Borazine19.png|200px]]
|-
| 20 || [[File:Borazine20.png|200px]]
|-
| 21|| [[File:Borazine21.png|200px]]
|}

[[file:MO3.png]]
[[file:MO2.png]]
[[File:MO1.png]]

==comparison of the molecular orbitals of benzene, boratabenzene, pyrdine and borazine==

{| class="wikitable" border="1"
|+ method of 6-31G basis
! benzene charge !! boratabenzene charge !! pyridium charge !! borazine charge
|-
| [[file:Charge_benzene_no..png|150px]] ||[[file:Bb_charge_no..png|150px]] ||[[file:Pyr_charge_no..png|150px]] || [[file:Charge_borazine_no..png|150px]]
|-
|[[file:Charge_benzene.png|150px]] ||[[file:Bb_charge.png|150px]] ||[[file:Pyr_charge.png|150px]] || [[file:Charge_borazine.png|150px]]
|-
|}

all the four molecules have a delocalised pi bond with a nodal plane through the plane of the molecule. the filled Pz orbital in the boratabenzene molecule allows for a full delcocalised electron ring. in pyrdine the lone pair on the nitrogen isnt participating in the electron overlap.

pyrdinium is the lowest energy orbitsl. this is expected since the nitrogen is much more electronegative comapared to the carbon and boron, and this lowers the energy of all the pyrdinium orbtals. conversly the boratabenzene molecule is the hghest energy due to the boron being highly electropostive. the intermedate energy region for the borazine and benzene is due to benzene being composed solely of carbon and hydrogen, wheras the electrongatvity of the nirogens is offset by the electoposvty of the boron in borazine

pyridium's non contributiing nitrogen orbital therefore has a stabilising affect compared to benzene since it is a antibonding orbital, and since it is playing no part in the bonding this makes it more stable, the boron however contributes to the antibonding significantly so is a higher energy than the benzene.

the molecules HOMO's and HOMO-1 have nodal planes into the ring and a nodal plane perpendicular to the ring. the benzene molecule has a double degenerate HOMO as does the borazine since they both have the same symmetry. since the symmetry changed with boratabenzene and pryidium this becomes no longer true since the boron atom subsitution raises the moecules energy in boratabenzene and the subsiution of nitrogen in pyridum lowers the enrgy.

boratabenzene's HOMO-1 orbital is higher in energy than the HOMO since it has a node in the boron atom and electron density across the boron atom in the HOMO, this makes it destabiised since boron is an electropostive atom. the negative charge assigned to the boratabenzene means that there is a high electron density near the boron atom in the HOMO. the reasoning behind the negative charges on the carbon atoms in the ring are due to borons electron donating ability, meaning the carbons closest to the boron will have a greater electron density giving a asymetric distrubtion of elecron density.

for pyridium the HOMO-1 is lower in enrgy than the HOMO since there is a high amount of electron denisty at the nitrogen atom and the nitrogen is electronegative. the nitrogen will then draw electron density from the carbons closest to it (opposite of the boratabenzene) and this is seen the LCAO

borazines electrongeative nitrogens mean that the orbital with the largest nitrogen contribution will be larger (seen in the HOMO as illistrated) and vice versa with the orbital with 2 boron atoms and 1 nitrogen being smaller.

this is all totally rationalised by comapring the electronegativites of the atoms on the molecule. since the boratabenzene has a electropostive atom it is destabilised and so is higher in energy. the pyridium nitrogen stabilises the molecule since it is electronegatie.

File:6-31G summary.png

2013-03-12T10:06:29Z

Sd2810: uploaded a new version of "File:6-31G summary.png"