ChemWiki - User contributions [en]

CHEMIMM2P

2019-03-15T14:24:37Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CObondlength" />,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.

<references>
<ref name="CObondlength"> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:23:17Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CObondlength" />,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name="CObondlength"> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:21:01Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CObondlength"/>,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name="CObondlength"> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:20:36Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name='CObondlength'/>,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name='CObondlength'> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:19:59Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name='CObond'/>,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name='CObond'> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:19:24Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name=CObond/>,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name=CObond> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:17:47Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CObond"/>,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name="CObond"> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:14:35Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CObond" />,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

<references>
<ref name="CObond"> Gilliam, O. R.; Johnson, C. M.; Gordy, W. (1950). "Microwave Spectroscopy in the Region from Two to Three Millimeters". Physical Review. 78 (2): 140–144. Bibcode:1950PhRv...78..140G. doi:10.1103/PhysRev.78.140.</ref>
</references>

CHEMIMM2P

2019-03-15T14:13:16Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CO"/>,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

CHEMIMM2P

2019-03-15T14:12:12Z

Rj218: /* Comparison of bond length */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, occupied, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital. Since it has such high energy, it doesn't participate in any reaction.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, occupied, it has energy -10.30433 au.
This is the 1σ* orbital formed from the 1s atomic orbital. This molecular orbital doesn't participate in any reaction as well.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 2σ orbital formed from 2s atomic orbital, occupied, energy level -1.15790
</pre>

[[File:2pi_MO.PNG]]
<pre>
This is the 1π Molecular orbital, occupied, formed from 2px and 2py atomic orbital. It has energy level -0.46743 au.
</pre>

[[File:RjHOMO.PNG]]
<pre>
This is the HOMO (Highest Occupied Molecular Orbital), 3σ orbital formed from 2pz atomic orbital. It has the lowest energy of -0.37145 au.
</pre>

=== Comparison of bond length ===

<pre>
The actual bond length between Carbon and Oxygen in carbon monoxide is 1.128Å <ref name="CO" />,
compare to our calculated bond length 1.13794Å, there is a slight difference. This is most likely caused
by the ionic character in carbon monoxide molecule that attract the two particles closer to each other.
</pre>

CHEMIMM2P

2019-03-15T14:04:34Z

Rj218: /* CO Molecule */

CHEMIMM2P

2019-03-15T14:03:41Z

Rj218: /* CO Molecular Oribital */

File:RjHOMO.PNG

2019-03-15T14:01:39Z

Rj218:

File:HOMO.PNG

2019-03-15T14:00:59Z

Rj218: Rj218 uploaded a new version of File:HOMO.PNG

File:2piab MO.PNG

2019-03-15T13:57:40Z

Rj218:

File:2pi MO.PNG

2019-03-15T13:51:00Z

Rj218:

CHEMIMM2P

2019-03-15T13:49:15Z

Rj218: /* CO Molecular Oribital */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has energy -19.25805 au.
This is the 1σ orbital formed from the 1s atomic orbital.
</pre>

[[File:1sab_MO..PNG]]
<pre>
This is the second deepest molecular orbital of carbon monoxide, it has energy -10.30433 au.
This is the 2σ orbital formed from the 1s atomic orbital.
</pre>

[[File:2s_MO.PNG]]
<pre>
This is the 3σ orbital formed from 2s atomic orbital, energy level -1.15790
</pre>

File:2s MO.PNG

2019-03-15T13:47:09Z

Rj218:

File:1sab MO..PNG

2019-03-15T13:45:25Z

Rj218:

CHEMIMM2P

2019-03-15T13:36:12Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_CO_OPTF_POP.LOG]] CO Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

File:RJIA CO OPTF POP.LOG

2019-03-15T13:35:56Z

Rj218: Rj218 uploaded a new version of File:RJIA CO OPTF POP.LOG

CHEMIMM2P

2019-03-15T13:35:39Z

Rj218: /* N2 Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] N2 Log File

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

File:RJIA N2 OPTF POP.LOG

2019-03-15T13:35:09Z

Rj218: Rj218 uploaded a new version of File:RJIA N2 OPTF POP.LOG

CHEMIMM2P

2019-03-15T13:34:46Z

Rj218: /* H2 and N2 Molecules */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_N2_OPTF_POP.LOG]] H2 Log File

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

File:RJIA N2 OPTF POP.LOG

2019-03-15T13:34:10Z

Rj218: Rj218 uploaded a new version of File:RJIA N2 OPTF POP.LOG

CHEMIMM2P

2019-03-15T13:33:41Z

Rj218: /* NH3 Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]] NH3 Log File
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T13:33:10Z

Rj218:

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:RJIA_NH3_OPTF_POP.LOG]]
<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

File:RJIA NH3 OPTF POP.LOG

2019-03-15T13:32:45Z

Rj218: Rj218 uploaded a new version of File:RJIA NH3 OPTF POP.LOG

CHEMIMM2P

2019-03-15T13:28:34Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.
</pre>

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T13:28:13Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''

|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]
<pre>
Oxygen (Red atom) is more electro-negative than Carbon (Green), thus it is expect to have a δ- on oxygen and a δ+ on Carbon which is correctly shown above.

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T13:23:27Z

Rj218: /* Haber Process */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.0557907*2625.5 = -146.48 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T13:22:02Z

Rj218: /* N2 Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[File:Investigation_molecule_diagram.PNG]]
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

File:Investigation molecule diagram.PNG

2019-03-15T13:21:46Z

Rj218:

CHEMIMM2P

2019-03-15T13:20:23Z

Rj218:

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VECXEJ&Doi=doi%3A10.1139%2FV05-236&Year=2006&Volume=84&SPage=164&DatabaseToSearch=Published]]
<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T13:17:54Z

Rj218:

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate (Mode 2 and 3). Wavenumber 3589 and 3589 are degenerate (Mode 5 and 6).
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693 (Mode 1, 2, 3). Bond stretch vibration : 3461, 3589, 3589(Mode 4, 5, 6).
which mode is highly symmetric? Answer : 3461 (Mode 4)
one mode is known as the "umbrella" mode, which one is this? Answer : 1089 (Mode 1)
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]
<pre>
The electron-negativity of Hydrogen atoms are identical, thus it will not have a intermolecular charge within the H2 molecule as expected.
</pre>

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]
<pre>
The electron-negativity for both Nitrogen atoms are identical, thus it is expected to not have an intermolecular charge.
</pre>

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
[[https://pubs.acs.org/doi/abs/10.1021/acs.organomet.7b00445]]
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T11:58:24Z

Rj218: /* CO Molecular Oribital */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===
[[File:1s_MO.PNG]]
<pre>
This is the the deepest molecular orbital of carbon monoxide, it has the energy -19.25805 au.
This is the 1s bonding orbital formed from the 1s atomic orbital of the carbon and oxygen.
</pre>

CHEMIMM2P

2019-03-15T11:47:37Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
=== CO Molecule ===
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===

CHEMIMM2P

2019-03-15T11:46:25Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

===CO Molecular Oribital===

File:1s MO.PNG

2019-03-15T11:46:01Z

Rj218: Rj218 uploaded a new version of File:1s MO.PNG

CHEMIMM2P

2019-03-15T11:42:05Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

CHEMIMM2P

2019-03-15T11:37:59Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:Calculated_CO_Spectrum.PNG]]
<pre>
[[File:Actual_CO_Spectrum.PNG]]
Picture From: Coblentz Society, Inc., "Evaluated Infrared Reference Spectra" in NIST Chemistry WebBook, NIST Standard Reference Database Number 69, Eds. P.J. Linstrom and W.G. Mallard, National Institute of Standards and Technology, Gaithersburg MD, 20899, https://doi.org/10.18434/T4D303, (retrieved March 15, 2019).
</pre>
In Comparison to actual literature for the wavenumber of the Carbon Monoxide,

[[File:CO_Charge.PNG]]

CHEMIMM2P

2019-03-15T11:36:05Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:Calculated_CO_Spectrum.PNG]]
[[File:Actual_CO_Spectrum.PNG]]
<pre>
In Comparison to actual literature for the wavenumber of the Carbon Monoxide,

[[File:CO_Charge.PNG]]

File:Actual CO Spectrum.PNG

2019-03-15T11:35:48Z

Rj218:

File:Calculated CO Spectrum.PNG

2019-03-15T11:35:23Z

Rj218:

CHEMIMM2P

2019-03-15T11:27:00Z

Rj218: /* CO Molecule */

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

[[File:CO_Charge.PNG]]

File:CO Charge.PNG

2019-03-15T11:26:47Z

Rj218:

File:CO Vibration.PNG

2019-03-15T11:26:34Z

Rj218: Rj218 uploaded a new version of File:CO Vibration.PNG

CHEMIMM2P

2019-03-15T11:24:21Z

Rj218:

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2209

|-
!Symmetry
|SG

|-
!Intensity (arbitary unit)
|67

|}

CHEMIMM2P

2019-03-15T11:22:53Z

Rj218:

== '''NH3 Molecule''' ==
{| class="wikitable"
!Molecule
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-56.55776873(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000485(a.u.)
|-
!Point Group
|C3V
|-
!N-H Bond Length
|1.01798('''Å)'''
|-
!N-H-N Bond Angle
|105.741o
|}

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-5.986287D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
[[File:Rjia_Vibration.PNG]]
{| class="wikitable"
!Wavenumber (cm-1)
|1089
|1693
|1693
|3461
|3589
|3589
|-
!Symmetry
|A1
|E
|E
|A1
|E
|E
|-
!Intensity (arbitary unit)
|145
|13
|13
|1
|0
|0
|}
<pre>
Answer the following questions in your wiki refer to the vibrations by their wavenumber not their order number!:
how many modes do you expect from the 3N-6 rule? Answer : 3*4 - 6 = 6, 6 modes.
which modes are degenerate (ie have the same energy)? Answer : Wavenumber 1693 and 1693 are degenerate. Wavenumber 3589 and 3589 are degenerate.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer : Bending vibration: 1089, 1693 and 1693. Bond stretch vibration : 3461, 3589, 3589.
which mode is highly symmetric? Answer : 1089, 3461
one mode is known as the "umbrella" mode, which one is this? Answer : 3461
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer : two bands
</pre>
[[File:rjia_charge.PNG]]
<pre>
Nitrogen is more electron-negative than hydrogen, which we should expect a negative charge on N atom and positive charge on H atoms.
</pre>

= '''H2 and N2 Molecules''' =
=== H2 Molecule ===
{| class="wikitable"
!Molecule
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-1.17853936(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000017(a.u.)
|-
!Point Group
|D*H
|-
!H-H Bond Length
|0.74279('''Å)'''
|-
!H-H Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>H2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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
Predicted change in Energy=-1.164080D-13
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 0.7428 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:RJia_H2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|4465

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:H2_Charge.PNG]]

=== N2 Molecule ===
{| class="wikitable"
!Molecule
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-109.52412868(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000001(a.u.)
|-
!Point Group
|D*H
|-
!N-N Bond Length
|1.1055('''Å)'''
|-
!N-N Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>N2 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-9.720915D-17
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1055 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:N2_Vibration.PNG]]

{| class="wikitable"
!Wavenumber (cm-1)
|2457

|-
!Symmetry
|SGG

|-
!Intensity (arbitary unit)
|0

|}

[[File:RJIA_N2_Charge.PNG]]

<pre>
Molecule Identifier : VECXEJ
Molecule Name : tris(μ-N-(3,5-dimethylphenyl)di(propan-2-yl)phosphanaminido)-(diphenylmethanone)-dinitrogen-titanium-cobalt pentane solvate
Link : 10.1021/acs.organomet.7b00445
N-N bond length : 1.101 Å
The bond length for my computational result and actual result are very much identical. In the molecule I found, nitrogen had only involved as a ligand,
there was no other atoms to have an influence on nitrogen's intermolecular bonding thus it should be very close to the theoretical result. In fact,
computational result is calculated based on the theory, and it explains why they have such similar bond length.
</pre>

=== Haber Process ===
<pre>
E(NH3)= -56.5577687 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.5241287 au
E(H2)= -1.17853936 au
3*E(H2)= -3.5356181 au
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au
-0.00557907*2625.5 = -14.648 kJ/mol
As energy is being released from the reaction, product is in lower energy state than reactants, thus ammonia product is more stable.
</pre>

= '''CO Molecule''' =
{| class="wikitable"
!Molecule
|CO
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!E(RB3LYP)
|<nowiki>-113.30945314(a.u.)</nowiki>
|-
!RMS Gradient
|0.00000002(a.u.)
|-
!Point Group
|C*V
|-
!C-O Bond Length
|1.13794('''Å)'''
|-
!C-O Bond Angle
|180o
|}

<jmol><jmolApplet>
<title>CO Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>RJIA_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

<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 0.000000 0.001200 YES
Predicted change in Energy=-6.433359D-16
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1379 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

[[File:CO_Vibration.PNG]]

File:CO Vibration.PNG

2019-03-15T11:21:10Z

Rj218: