ChemWiki - User contributions [en]

Rep:Mod:ssv15

2018-05-24T08:53:26Z

Ssv15:

== BH3 ==

=== B3LYP/ 6-31G (d,p) ===

[[File:Ssv15 summary table for optimised bh3.PNG|left|thumb|Summary table for optimised BH3]]

[[File:Ssv15 item table for bh3 optimised.PNG|left|thumb|500x500px|Item table for BH3]]

Completed BH3 frequency log file link: [[Media:SSV15_BH3_FREQ_631G.LOG]]

<pre>
Low frequencies --- -0.2456 -0.1129 -0.0055 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951
</pre>

The frequencies observed above are unusually high, however after checking the frequency analysis lined up with the optimised BH3 molecule in terms of energy and whether the calculation converged, it was concluded that this due to inaccuracy of the software and computers running these simulations. This was also checked and confirmed by a demonstrator.

<jmol><jmolApplet>
<title>ssv15 BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SSV15_BH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ Vibrational modes of BH3
! Wavenumber (cm-1) !! Intensity (arbitrary units)!! Symmetry !! IR active? !! Type
|-
| 1164 || 92 || A2" || yes || bend ||
|-
| 1214 || 14 || E' || slightly || bend ||
|-
| 1214 || 14 || E' || slightly || bend ||
|-
| 2580 || 0 || A1' || no || symmetric stretch ||
|-
| 2713 || 126 || E' || yes || asymmetric stretch ||
|-
| 2713 || 126 || E' || yes || asymmetric stretch ||
|}

[[File:ssv15 spectrum for bh3.PNG|left|Spectrum for BH3]]

In the IR spectrum above there are 3 distinct peaks shows despite there being 6 vibrational modes. The vibration at wavenumber (2580 cm-1) is IR inactive due to there being no change in dipole moment during the symmetric stretch. There are also 2 degenerate pairs of vibrations, one set at 1214 cm-1 and the other at 2713 cm-1, therefore we only observe 2 peaks for these 4 vibrational modes. This leaves one mode at 1164 cm-1 which produces its own peak. In total we witness 3 peaks in the IR spectrum.

[[File:Full mo diagram bh3.PNG|left|thumb|MO diagram of BH3<ref name= "MO diagram" />]]

The above diagram shows there are no significant differences between the LCAO MO's and the real ones, therefore one can accurately predict the shapes of MO's using qualitative MO theory.

== NH3 ==

=== B3LYP/ 6-31G (d,p)===

[[File:Nh3_optimisation_summary_table.PNG|left|thumb|Summary table for optimised NH3]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844515D-11
Optimization completed.
-- Stationary point found.
</pre>

Frequency NH3 log file: [[Media:SSV15_NH3_FREQ_631G.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

<jmol><jmolApplet>
<title>ssv15 NH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SSV15_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

== BH3NH3 ==

=== B3LYP/ 6-31G (d,p)===

[[File:Ssv15_bh3nh3_summary_table.PNG|left|thumb|Summary table for optimised BH3NH3]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000035 0.000300 YES
Maximum Displacement 0.000780 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
Predicted change in Energy=-1.113039D-07
Optimization completed.
-- Stationary point found.
</pre>

Frequency BH3NH3 log file [[Media:SSV15_BH3NH3_FREQ_631G.LOG]]

<pre>
Low frequencies --- -19.3181 -0.0151 -0.0035 0.0170 9.1260 9.1294
Low frequencies --- 262.5021 631.2247 637.8482
</pre>

<jmol><jmolApplet>
<title>ssv15 BH3NH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SSV15 BH3NH3 FREQ 631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

BH3NH3 association energies

E(BH3) = -26.61532 au (5 d.p.)
E(NH3) = -56.55777 au (5 d.p.)
E(BH3NH3) = -83.22469 au (5 d.p.)

ΔE = E(BH3NH3) - [E(NH3) + E(BH3)]
ΔE = -0.0516 au = 135 kJ/mol

Based on the information above the B-N dative bond is weak. Comparing it to the dissociation energy of C-H (337.2 kJmol<ref name= "bond length" />), a known strong bond, B-H has a much lower dissociation energy (135 kJ/mol).

== BBr3 ==

=== B3LYP/ 6-31G (d,p) ===

[[File:Sum_table_bbr3.PNG|left|thumb|Summary table for optimised BBr3]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.027061D-10
Optimization completed.
-- Stationary point found.
</pre>

Frequency BBr3 log file: [[Media:Ssv15_bbr3_freq.log]]

<pre>
Low frequencies --- -0.0137 -0.0064 -0.0046 2.4315 2.4315 4.8421
Low frequencies --- 155.9631 155.9651 267.7052
</pre>

<jmol><jmolApplet>
<title>ssv15 BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Ssv15 bbr3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

DSpace link: http://hdl.handle.net/10042/202459

{{DOI|10042/202459}}

== Aromaticity ==

=== Benzene ===

==== B3LYP/ 6-31G (d,p) ====

[[File:Benzene sum table 2.PNG|left|thumb|Summary table for optimised benzene]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
</pre>

Completed benzene frequency log file link: [[Media: SSV15_BENZENE_FREQ_AND_MOS2.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>ssv15 benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SSV15_BENZENE_FREQ_AND_MOS2.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== Borazine ===

==== B3LYP/ 6-31G (d,p) ====

[[File:Borazine_sum_table.PNG|left|thumb|Summary table for optimised borazine]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000064 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-3.183408D-09
Optimization completed.
-- Stationary point found.
</pre>

Completed borazine frequency log file link: [[Media: SSV15_BORAZINE_FREQ_AND_MOS.LOG]]

<pre>
Low frequencies --- -9.5469 -0.0004 0.0007 0.0010 4.2777 11.8176
Low frequencies --- 288.5478 290.5350 404.2742
</pre>

<jmol><jmolApplet>
<title>ssv15 borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SSV15_BORAZINE_FREQ_AND_MOS.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NBO charge distribution analysis ===

[[File:Benzene nbo charge.PNG|left|thumb|NBO charge distribution in benzene]]

{| class="wikitable" border="1"
|+ Benzene charge distribution
! Atom !! Charge value
|-
| Carbon || -0.239 ||
|-
| Hydrogen || 0.239 ||
|}

[[File:Ssv15_borazine_nbo_charge.PNG|left|thumb|NBO charge distribution in borazine]]

{| class="wikitable" border="1"
|+ Borazine charge distribution
! Atom !! Charge value
|-
| Nitrogen || -1.102 ||
|-
| Boron || 0.747 ||
|-
| Hydrogen (N-H) || 0.432 ||
|-
| Hydrogen (B-H) || -0.077 ||
|-

|}

From the data above, it can be seen that borazine has a more complex charge distribution than benzene. Benzene is a highly symmetric structure where majority of the charge is located in the delocalised pi ring. The carbon atoms in the ring have a charge of -0.239 whereas the terminal hydrogens have a more positive charge of 0.239. In borazine, the nitrogen atoms have the greatest electronegativity and so hold the most negative charge of -1.102 therefore implying the highest electron density is found at the nitrogen atoms in the molecule. The hydrogens attached to the nitrogen have the most postive charge of 0.432 due to the polarised bond that forms between them, due to the difference in electronegativity. Hydrogen is slightly more electronegative than boron, therefore the hydrogens attached to boron hold a slight negative charge and the borons a positive charge of 0.747.

=== Comparable MO's of Benzene and Borazine ===

[[File:Mo_9_benzene.PNG|left|thumb|Benzene MO 9]]
[[File:Borazine_mo_9.PNG|left|thumb|Borazine MO 9]]

MO 9 of benzene and borazine are the lowest in energy that has been picked to compare. Benzene is a highly symmetric molecule causing an even split of phase and one nodal plane running through the centre of the molecule. Borazine has a much lower degree of symmetry due to the alternating boron and nitrogen atoms around the ring. The electronegative nitrogen atoms pull in electron density, therefore distorting the two phases present in MO 9 of borazine. There is also limited contribution from some terminal hydrogens.

[[File:MO_13_BENZENE.PNG|left|thumb|Benzene MO 13]]
[[File:MO_16_BORAZINE.PNG|left|thumb|Borazine MO 16]]

Antibonding character is displayed by MO's 13 and 16 between orbitals. The orbitals form around individual atoms in the ring structure forming 6 orbitals in both borazine and benzene. In benzene these orbitals are symmetric and evenly sized as benzene has an even charge distribution. As we know from the MO diagram, boron is less electronegative than hydrogen and so the boron orbitals lie higher in energy and therefore contribute more character to the antibonding orbitals. Therefore we see larger antibonding orbitals around the boron atoms in MO 16 of borazine.

[[File:Benzene_mo_17.PNG|left|thumb|Benzene MO 17]]
[[File:Borazine_mo_17.PNG|left|thumb|Borazine MO 17]]

Both MO 17's of benzene and borazine display the pi orbitals above and below the delocalised ring structure, formed from the filled Pz orbitals on each atom in the ring structure interacting with one another. Both molecules display the same symmetry in these pi clouds despite having different symmetries otherwise.

=== Qualitative discussion of Aromaticity ===

Aromaticity is used to describe planar molecules with a delocalised electron pi system that exhibit more stability than other cyclic molecules that do not exhibit resonance. Bond lengths can give hints as to whether a molecule has a delocalised electron system as the bond length is in between the length of a single and double bond. Aromatic compounds play important roles in natural products and biochemistry of living organisms especially.

Hückel's rule can be used to determine whether a molecule classifies as aromatic. Hückel's rule states that a molecule must have a continuous ring a of p orbitals which can bond together to form a fully conjugated system of p orbitals, the molecule must be cyclic and planar and have 4n + 2 electrons (where n=integer value).

Molecules can have conjugation from overlapping pz orbitals, however this does not necessarily mean the molecule exhibits aromatic properties. Therefore overlapping pz orbitals alone is not a good description or criteria for aromaticity. Aromatic structures must all exhibit properties of resonance, however this does not imply that all molecules with resonance are aromatic structures. The real MO's portrayed above of benzene and borazine show sigma and pi bonding orbitals and thorough orbital combinations that surpass just pz orbitals overlapping.

== References ==

<ref name= "MO diagram">http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf
</ref>
<ref name= "bond length">https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf
</ref>

Rep:Mod:ssv15

2018-05-24T08:50:14Z

Ssv15: /* References */

2018-05-23T14:16:52Z

Ssv15: