Rep:Mod:EFC18

2019-03-01T14:38:55Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000323 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database<ref name="NH3 db" /> value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.745 [°] (database<ref name="NH3 db" /> value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000014 0.001800 YES
RMS Displacement 0.000009 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database<ref name="N2 db" /> value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database<ref name="H2 db" /> value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database<ref name="NF3 db" /> value 1.365 [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database<ref name="NF3 db" /> value 102.37 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/7/7c/EWAN_NF3_OPTF_POPP.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 6.]]This MO has energy -1.23341 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2s orbitals of two of the fluorine atoms.

[[File:ewan_mo_c.jpg|thumb|none|300px|Image showing computed MO 17.]]This MO has energy -0.35162 [a.u.]. This essentially non bonding MO is the result of 2p orbital from all the nitrogen and fluorine atoms, resulting in an orbital resembling a lone pair of electrons on nitrogen, which is in agreement with this molecule reacting as a lewis base and nucleophile through nitrogen.

[[File:ewan_mo_d.jpg|thumb|none|300px|Image showing computed MO 11.]]This MO has energy -0.57102 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2p orbitals of nitrogen and fluorine.

[[File:ewan_mo_e.jpg|thumb|none|300px|Image showing computed MO 16.]]This MO has energy -0.42224 [a.u.]. This anti-bonding MO is the result of a complete out-of phase combination of the atomic 2p orbitals of the 3 fluorines.

==References==

<references>

<ref name="NH3 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7664417, (accessed Feb 2019). </ref>

<ref name="N2 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7727379, (accessed Feb 2019). </ref>

<ref name="H2 db">http://www.millsian.com/summarytables/SummaryTables022709S.pdf, (accessed Feb 2019). </ref>

<ref name="NF3 db">Computational Chemistry Comparison and Benchmark DataBase, https://cccbdb.nist.gov/expgeom2.asp?casno=7783542&charge=0, (accessed Feb 2019). </ref>

Rep:Mod:EFC18

2019-03-01T14:34:47Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database<ref name="NH3 db" /> value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database<ref name="NH3 db" /> value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database<ref name="N2 db" /> value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database<ref name="H2 db" /> value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database<ref name="NF3 db" /> value 1.365 [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database<ref name="NF3 db" /> value 102.37 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/7/7c/EWAN_NF3_OPTF_POPP.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 6.]]This MO has energy -1.23341 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2s orbitals of two of the fluorine atoms.

[[File:ewan_mo_c.jpg|thumb|none|300px|Image showing computed MO 17.]]This MO has energy -0.35162 [a.u.]. This essentially non bonding MO is the result of 2p orbital from all the nitrogen and fluorine atoms, resulting in an orbital resembling a lone pair of electrons on nitrogen, which is in agreement with this molecule reacting as a lewis base and nucleophile through nitrogen.

[[File:ewan_mo_d.jpg|thumb|none|300px|Image showing computed MO 11.]]This MO has energy -0.57102 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2p orbitals of nitrogen and fluorine.

[[File:ewan_mo_e.jpg|thumb|none|300px|Image showing computed MO 16.]]This MO has energy -0.42224 [a.u.]. This anti-bonding MO is the result of a complete out-of phase combination of the atomic 2p orbitals of the 3 fluorines.

==References==

<references>

<ref name="NH3 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7664417, (accessed Feb 2019). </ref>

<ref name="N2 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7727379, (accessed Feb 2019). </ref>

<ref name="H2 db">http://www.millsian.com/summarytables/SummaryTables022709S.pdf, (accessed Feb 2019). </ref>

<ref name="NF3 db">Computational Chemistry Comparison and Benchmark DataBase, https://cccbdb.nist.gov/expgeom2.asp?casno=7783542&charge=0, (accessed Feb 2019). </ref>

Rep:Mod:EFC18

2019-03-01T13:14:58Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

<jmol>

<jmolApplet>
<script>frame 1.16;</script>
<color>white</color>
<size>300</size>
<uploadedFileContents>EWAN_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 16; rotate x -20; frank off; zoom 150</script>
<name>ammonia</name>
</jmolApplet>
<jmolbutton>
<script>measure 1 2</script>
<text>N-H bond length</text>
<target>ammonia</target>
</jmolbutton>
<jmolbutton>
<script>measure 4 1 3</script>
<text>H-N-H bond angle</text>
<target>ammonia</target>
</jmolbutton>
</jmol>

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database<ref name="NH3 db" /> value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database<ref name="NH3 db" /> value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

<jmol>

<jmolApplet>
<script>frame 1.4;</script>
<color>white</color>
<size>300</size>
<uploadedFileContents>EWAN_N2_OPT.LOG</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 4; rotate x -90; frank off; zoom 200</script>
<name>nitrogen</name>
</jmolApplet>
<jmolbutton>
<script>measure 1 2</script>
<text>N-N bond length</text>
<target>nitrogen</target>
</jmolbutton>

</jmol>

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database<ref name="N2 db" /> value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

<jmol>

<jmolApplet>
<script>frame 1.4;</script>
<color>white</color>
<size>300</size>
<uploadedFileContents>efc18_h2_optpop.LOG</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 4; rotate x -90; frank off; zoom 200</script>
<name>nitrogen</name>
</jmolApplet>
<jmolbutton>
<script>measure 1 2</script>
<text>H-H bond length</text>
<target>nitrogen</target>
</jmolbutton>

</jmol>

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database<ref name="H2 db" /> value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

<jmol>

<jmolApplet>
<script>frame 1.16;</script>
<color>white</color>
<size>300</size>
<uploadedFileContents>EWAN_NF3_OPTF_POPP.LOG</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 16; rotate x -20; frank off; zoom 150</script>
<name>ammonia</name>
</jmolApplet>
<jmolbutton>
<script>measure 1 2</script>
<text>N-F bond length</text>
<target>ammonia</target>
</jmolbutton>
<jmolbutton>
<script>measure 4 1 3</script>
<text>F-N-F bond angle</text>
<target>ammonia</target>
</jmolbutton>
</jmol>

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database<ref name="NF3 db" /> value 1.365 [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database<ref name="NF3 db" /> value 102.37 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/7/7c/EWAN_NF3_OPTF_POPP.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 6.]]This MO has energy -1.23341 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2s orbitals of two of the fluorine atoms.

[[File:ewan_mo_c.jpg|thumb|none|300px|Image showing computed MO 17.]]This MO has energy -0.35162 [a.u.]. This essentially non bonding MO is the result of 2p orbital from all the nitrogen and fluorine atoms, resulting in an orbital resembling a lone pair of electrons on nitrogen, which is in agreement with this molecule reacting as a lewis base and nucleophile through nitrogen.

[[File:ewan_mo_d.jpg|thumb|none|300px|Image showing computed MO 11.]]This MO has energy -0.57102 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2p orbitals of nitrogen and fluorine.

[[File:ewan_mo_e.jpg|thumb|none|300px|Image showing computed MO 16.]]This MO has energy -0.42224 [a.u.]. This anti-bonding MO is the result of a complete out-of phase combination of the atomic 2p orbitals of the 3 fluorines.

==References==

<references>

<ref name="NH3 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7664417, (accessed Feb 2019). </ref>

<ref name="N2 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7727379, (accessed Feb 2019). </ref>

<ref name="H2 db">http://www.millsian.com/summarytables/SummaryTables022709S.pdf, (accessed Feb 2019). </ref>

<ref name="NF3 db">Computational Chemistry Comparison and Benchmark DataBase, https://cccbdb.nist.gov/expgeom2.asp?casno=7783542&charge=0, (accessed Feb 2019). </ref>

Rep:Mod:EFC18

2019-03-01T13:12:21Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database<ref name="NH3 db" /> value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database<ref name="NH3 db" /> value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database<ref name="N2 db" /> value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database<ref name="H2 db" /> value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database<ref name="NF3 db" /> value 1.365 [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database<ref name="NF3 db" /> value 102.37 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/7/7c/EWAN_NF3_OPTF_POPP.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 6.]]This MO has energy -1.23341 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2s orbitals of two of the fluorine atoms.

[[File:ewan_mo_c.jpg|thumb|none|300px|Image showing computed MO 17.]]This MO has energy -0.35162 [a.u.]. This essentially non bonding MO is the result of 2p orbital from all the nitrogen and fluorine atoms, resulting in an orbital resembling a lone pair of electrons on nitrogen, which is in agreement with this molecule reacting as a lewis base and nucleophile through nitrogen.

[[File:ewan_mo_d.jpg|thumb|none|300px|Image showing computed MO 11.]]This MO has energy -0.57102 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2p orbitals of nitrogen and fluorine.

[[File:ewan_mo_e.jpg|thumb|none|300px|Image showing computed MO 16.]]This MO has energy -0.42224 [a.u.]. This anti-bonding MO is the result of a complete out-of phase combination of the atomic 2p orbitals of the 3 fluorines.

==References==

<references>

<ref name="NH3 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7664417, (accessed Feb 2019). </ref>

<ref name="N2 db">Computational Chemistry Comparison and Benchmark DataBase, http://cccbdb.nist.gov/exp2x.asp?casno=7727379, (accessed Feb 2019). </ref>

<ref name="H2 db">http://www.millsian.com/summarytables/SummaryTables022709S.pdf, (accessed Feb 2019). </ref>

<ref name="NF3 db">Computational Chemistry Comparison and Benchmark DataBase, https://cccbdb.nist.gov/expgeom2.asp?casno=7783542&charge=0, (accessed Feb 2019). </ref>

2019-03-01T12:35:17Z

Efc18:

Rep:Mod:EFC18

2019-03-01T12:30:53Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 6.]]This MO has energy -1.23341 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2s orbitals of two of the fluorine atoms.

[[File:ewan_mo_c.jpg|thumb|none|300px|Image showing computed MO 17.]]This MO has energy -0.35162 [a.u.]. This essentially non bonding MO is the result of 2p orbital from all the nitrogen and fluorine atoms, resulting in an orbital resembling a lone pair of electrons on nitrogen, which is in agreement with this molecule reacting as a lewis base and nucleophile through nitrogen.

[[File:ewan_mo_d.jpg|thumb|none|300px|Image showing computed MO 11.]]This MO has energy -0.57102 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic 2p orbitals of nitrogen and fluorine.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

2019-03-01T12:20:12Z

Efc18:

Rep:Mod:EFC18

2019-03-01T12:01:46Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 6.]]This MO has energy -1.23341 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic s orbitals of two of the fluorine atoms.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

Rep:Mod:EFC18

2019-03-01T12:00:48Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in-phase combination of the atomic s orbitals of nitrogen and fluorine.

[[File:ewan_mo_b.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This anti-bonding MO is the result of an out-of-phase combination of the atomic s orbitals of two of the fluorine atoms.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

[[File:ewan_mo_a.jpg|thumb|none|300px|Image showing computed MO 5.]]This MO has energy -1.35870 [a.u.]. This bonding MO is the result of a complete in phase combination of the atomic 2s orbitals of nitrogen and fluorine.

2019-03-01T11:50:50Z

Efc18:

Rep:Mod:EFC18

2019-03-01T11:32:35Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

====Molecular orbitals of NF3====

Rep:Mod:EFC18

2019-03-01T11:18:10Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=blue, F=turquoise]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

Rep:Mod:EFC18

2019-03-01T11:17:04Z

Efc18: /* Charge Analysis */

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is 0.660 and the charge on each fluorine atom is -0.220. The fact that the sum of the charges equals zero is promising because NF3 is a neutral species overall. Another good sign is that the fluorine atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be +3 and the charge on each fluorine would be -1, but this basic model doesn't agree with the computed results.

Rep:Mod:EFC18

2019-03-01T11:14:16Z

Efc18:

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''F-N-F bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NF3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NF3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_nf3_charge.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

File:Ewan nf3 charge.jpg

2019-03-01T11:12:25Z

Efc18:

Rep:Mod:EFC18

2019-03-01T11:08:31Z

Efc18: /* Questions about vibrations of NH3 */

==efc18 wiki==

===NH3===

====Interactive 3D viewer====

====Summary table for optimised NH3 molecule====
{| class="wikitable"
|'''Molecule'''
|NH3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-56.55776873 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000485 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-H bond length'''
|1.01798 [Å] (database value 1.0124 [Å])
|-
|'''H-N-H bond angle'''
|105.741 [°] (database value 106.670 [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7412 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7412 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7412 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8571 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/b/be/EWAN_NH3_OPTF_POP.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nh3_vibrations.jpg|frame|none|This image shows the 6 unique vibrations for ammonia.]]

====NH3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|1090
|1694
|1694
|3461
|3590
|3590
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|145
|14
|14
|1
|0
|0
|-
|Image
|[[File:ewan_1090.jpg|150px]]
|[[File:ewan_1694first.jpg|150px]]
|[[File:ewan_1694second.jpg|150px]]
|[[File:ewan_3461.jpg|150px]]
|[[File:ewan_3590first.jpg|150px]]
|[[File:ewan_3590second.jpg|150px]]
|-
|
|
|
|
|
|
|
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 1,2 and 3 are "bending" vibrations and modes 4,5 and 6 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric but mode 1 is also rather symmetric.
; One mode is known as the "umbrella" mode, which one is this?: Mode 1.
; How many bands would you expect to see in an experimental spectrum of gaseous ammonia?: 2 bands: one at frequency ~1700cm-1 due to H-N-H scissoring and another more intense band at frequency ~1100cm-1 due to N-H wagging.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.

===N2===

====Interactive 3D viewer====

====Summary table for optimised N2 molecule====
{| class="wikitable"
|'''Molecule'''
|N2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-109.52412868 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000060 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''N-N bond length'''
|1.106 [Å] (database value 1.098 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/c/ca/EWAN_N2_OPT.LOG N2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_n2_vibrationswindow.jpg|frame|none|This image shows the single vibration for nitrogen.]]

====N2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|2457
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_n2_onlyvibration.jpg|150px]]
|-
|
|
|}
====N2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous N2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_n2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each nitrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===H2===

====Interactive 3D viewer====

====Summary table for optimised H2 molecule====
{| class="wikitable"
|'''Molecule'''
|H2
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-1.17853936 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00000017 [a.u.]
|-
|'''Point group'''
|D∞h
|-
|'''H-H bond length'''
|0.743 [Å] (database value 0.741 [Å])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/6/69/Efc18_h2_optpop.LOG H2 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_h2_vibration.jpg|frame|none|This image shows the single vibration for hydrogen.]]

====H2 vibrations data table====
{| class="wikitable"
|Vibration
|1
|-
|Wavenumber/cm-1
|4466
|-
|Symmetry
|A1g
|-
|Intensity/arbitrary units
|0
|-
|Image
|[[File:ewan_h2_vibration1.jpg|150px]]
|-
|
|
|}

====H2 vibrations====
I expect there to be only 1 vibrational mode for this linear molecule using the 3N-5 rule and the fact that there are 2 atoms (N=2). This mode is evidently a "bond stretch" vibration however we would not expect to observe this band in an experimental spectrum of gaseous H2 because this vibration doesn't induce a change in the molecule's dipole moment - something that is required of a vibration to make a molecule IR active (Δμ ≠ 0).

====Charge Analysis====

[[File:ewan_h2_charge.jpg|thumb|none|300px|Image showing computed charges on atoms.]]

The charge on each hydrogen atom is 0 which is expected of this homonuclear diatomic molecule in its elemental form.

===Transition metal complex with N2 ===
Unique REFCODE: BOWVUG

[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BOWVUG&DatabaseToSearch=Published Transition metal complex with N2]

Measured N-N bond length in complex: 1.125 [Å].

The two equivalent N-N bond lengths of 1.125 [Å] in this transition metal complex are both larger than that measured in elemental N2 (1.106 [Å]). This agrees with the fact that the N-N triple bond is partially weakened through coordination with the central metal ion and this results in a weaker, longer N-N triple bond in the complex.

===Haber-Bosch calculations===
{| class="wikitable"
|'''Energies'''
|'''Value in [a.u]'''
|-
|E(NH3)
|<nowiki>-56.55776873</nowiki>
|-
|2*E(NH3)
|<nowiki>-113.11553746</nowiki>
|-
|E(N2)
|<nowiki>-109.52412868</nowiki>
|-
|E(H2)
|<nowiki>-1.17853936</nowiki>
|-
|3*E(H2)
|<nowiki>-3.53561808</nowiki>
|-
|ΔE
|<nowiki>-0.0557907</nowiki>
|}
Converting the energy difference from Hartrees [a.u] to kJmol-1 we obtain a ΔE''' '''value of -146.48 kJmol-1, which reveals that the product ammonia is more stable than the reactants hydrogen and nitrogen in the Haber-Bosch process.

===NF3===

====Interactive 3D viewer====

====Summary table for optimised NF3 molecule====
{| class="wikitable"
|'''Molecule'''
|NF3
|-
|'''Calculation method'''
|RB3LYP
|-
|'''Basis set'''
|6-31G(d,p)
|-
|'''Job type'''
|Opt+Freq
|-
|'''E(RB3LYP)'''
|<nowiki>-354.07131058 [a.u.]</nowiki>
|-
|'''RMS Gradient Norm'''
|0.00010257 [a.u.]
|-
|'''Point group'''
|C3v
|-
|'''N-F bond length'''
|1.38404 [Å] (database value XXXX [Å])
|-
|'''H-N-H bond angle'''
|101.830 [°] (database value XXX [°])
|}

====Item table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000108 0.000300 YES
Maximum Displacement 0.000613 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
====Parameters being optimised====
<pre>
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.384 -DE/DX = 0.0 !
! R2 R(1,3) 1.384 -DE/DX = 0.0 !
! R3 R(1,4) 1.384 -DE/DX = 0.0 !
! A1 A(2,1,3) 101.8302 -DE/DX = 0.0001 !
! A2 A(2,1,4) 101.8302 -DE/DX = 0.0002 !
! A3 A(3,1,4) 101.8302 -DE/DX = 0.0002 !
! D1 D(2,1,4,3) -104.9443 -DE/DX = -0.0001 !

</pre> [https://wiki.ch.ic.ac.uk/wiki/images/d/d7/EWAN_NF3_OPTF_POP.LOG.LOG NH3 optimisation *.log file]

====Display Vibrations window====

[[File:ewan_nf3_vibrationwindow.jpg|frame|none|This image shows the 6 unique vibrations for NF3 .]]

====NF3 vibrations data table====
{| class="wikitable"
|Vibration
|1
|2
|3
|4
|5
|6
|-
|Wavenumber/cm-1
|644
|482
|482
|1062
|930
|930
|-
|Symmetry
|A1
|E
|E
|A1
|E
|E
|-
|Intensity/arbitrary units
|3
|1
|1
|40
|208
|208
|}

====Questions about vibrations of NH3====

; How many modes do you expect from the 3N-6 rule?: I expect there to be 6 modes of vibration for this non-linear molecule using the 3N-6 rule and the fact that there are 4 atoms (N=4).
; Which modes are degenerate?: Modes 2 and 3 have the same energy. Modes 5 and 6 also have the same energy, but this energy differs to that of modes 2 and 3
; Which modes are "bending" vibrations and which are "bond stretch" vibrations?: Modes 2, 3, 5 and 6 are "bending" vibrations and modes 1 and 4 are "bond stretch" vibrations.
; Which mode is highly symmetric?: Mode 4 is the most symmetric.
====Charge Analysis====

[[File:ewan_chargeanalysis_nh3.jpg|thumb|none|300px|Image showing computed charges on atoms. N=red, H=green]]

The charge on the nitrogen atom is -1.125 and the charge on each hydrogen atom is +0.375. The fact that the sum of the charges equals zero is promising because ammonia is a neutral species overall. Another good sign is that the hydrogen atoms all have the same charge due to the C3 symmetry. However one might expect that the charge on nitrogen would be -3 and the charge on each hydrogen would be +1, but this basic model doesn't agree with the computed results.