==NH3 Molecule==
===NH3 Molecule Calculation parameters===
Calculations for an ammonia molecule (NH3). Following parameters were used to carry out the optimisation
<ul>
<li>Calculation Method = RB3LYP
<li>Calculation Type = OPT+FREQ
<li>Basis Set = 6-31G(d,p)
</ul>

===NH3 Molecule results===

<ul>
<li>E(RB3LYP) = -56.55776873 a.u.
<li>RMS Gradient Norm = 0.00000485 a.u.
<li>Point Group = C3V
</ul>
N-H bond length 1.01798 angstroms 
H-N-H bond angle 105.741 degrees

====NH3 Jmol picture====

[[media:MS8017_NH3_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_NH3_OPTFRQ.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

====NH3 Vibrations====
6 Vibrational modes were expected according to the 3n-6 rule (4 atoms). 
4 vibrational modes were found to be degenerate (2 bending modes and 2 stretching modes). 
Bending modes are numbere 1,2 and 3. Stretching modes are numbered 4,5 and 6. 
The modes with highest symmetries were 1 (bending) and 4 (stretching). Hydrogen atoms in these cases were performing the same motion relative to the nitrogen atom. 
The vibrational mode designated as 1 is the "umbrella" mode as it is mimicking the folding and unfolding of an umbrella. 
2 peaks would be expected in a IR spectral analysis of gaseous ammonia

[[File:MS8017 NH3 VIB.PNG]]
[[File:MS8017_NH3_IR.PNG]]

====NH3 Charge distribution====

Nitrogen is known to have higher electronegativity compared to hydrogen therefore we expect to see more electrons on the nitrogen atom. A negative number higher in magnitude is expected on the nitrogen atom compared to the hydrogen atoms.

[[File:MS8017 NH3 CHRG.PNG]]
===Haber-Bosch process===
[[File:MS8017_N2_MOL.PNG|right|thumb|Nitrogen molecule]] 
[[File:MS8017_H2_MOL.PNG|right|thumb|Hydrogen moleucle]] 
<ul>
<li>E(NH3)=-56.55776873 a.u.
<li>2*E(NH3)=-113.11553746 a.u.
<li>E(N2)=-109.52412868 a.u.
<li>E(H2)=-1.17853936 a.u.
<li>3*E(H2)=-3.53561808 a.u.
<li>ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907 a.u. = 146.45 kJ.mol-1
</ul>
This reaciton tells us that the ammonia gas is more stable as thermodynamically it is an exothermic reaction.

==Molecule of choice PH5==
<ul>
<li>Charge = 0
<li>E(RB3LYP) = -344.25491049 a.u.
<li>RMS Gradient Norm = 0.00000471 a.u.
<li>Dipole Moment = 0.0000 Debye
<li>Point Group = D3H
</ul>
[[media:MS8017_PH5_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>PH5 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_PH5_OPTFRQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Charge Distribution on PH5====
[[File:MS8017_PH5_OPTFRQ.PNG]] 
The values obtained form GaussView (their signs) are same as expected. Hydrogen should have a negative charge as it is more electronegative in comparison to phosphorus. As observed there is a discrepancy between the charge on the axial hydrogen copared to equatoreal charge. This is due to Jahn Teller distortion and it can also be observed in bond lengths. H (axial) = 1.496Å and H (equatoreal) = 1.433Å
<ul>
<li> P = 0.412e
<li> H (axial) = -0.183
<li> H (equatoreal) = -0.015
</ul>
====Vibrations within PH5====
PH5 is not a linear molecule so we expect it to have 12 vibrational modes (3N-6).
[[File:MS8017_PH5_VIB.PNGthumb]] 
4 vibrations (No. 6,7,8 and 10) do not produce any peaks in the IR spectra as they have no change in the dipole moment. These vibrations are highly symmetrical. 
Multiple degenerate vibrational modes are present (No. 1 and 2, 4 and 5, 6 and 7, 11 and 12).
Only 4 peaks would be observed as multiple of these peaks are degenerate and some vibraitons are not IR active (No change in dipole)
[[File:MS8017_PH5_IR.PNG]]
====PH5 Molecular orbitals====
[[File:MS8017_PH5_HOMOLUMO.PNG]] 
The lowest energy orbital is a 1s orbital at the phosphorus atom. Then follow the 2s, 2p orbitals. 
[[File:ENERGY_MS8017_PH5_3S.PNG|600px]] 
Orbital formed by combining the 3s orbital of P and 1s orbital of H. Bonding orbital. Occupied. 
[[File:ENERGY_MS8017_PH5_3SANTI.PNG|600px]] 
Antibonding 3s orbital. Antibonding orbital. Vacant. 
[[File:ENERGY_MS8017_PH5_HOMO.PNG|600px]] 
HOMO orbital of PH5. Formed by combining a 3dz2 (P) with a 1s of H. Bonding orbital. Occupied 
[[File:ENERGY_MS8017_PH5_LUMO.PNG|600px]] 
LUMO orbital of PH5. Contribution from 3d orbital of P and 1s orbital of H. Vacant 
[[File:ENERGY_MS8017_PH5_3PANTI.PNG|600px]] 
Antibonding orbital formed by combining 3p orbital of P with 1s orbital of H. Vacant 
These orbitals can be found in the HOMO/LUMO energy region. We can see the orbitals 1-5 are in the core band. They are the non bonding 1s, 2s and 2p orbitals of the P. 
==Optimisation, Log Files, Results==
====NH3====
<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=-5.986279D-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>
<pre>
nh3 optimisation
File Name = MS8017_NH3_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8466 Debye
Point Group = C3V
</pre>
[[media:MS8017_NH3_OPTFRQ.LOG]]
====N2 Optimization====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401057D-13
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>
<pre>
N2 optimization
File Name = MS8017_N2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_N2_OPTFRQ.LOG]]
====H2 Optimization====
<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>
<pre>
H2 optimisation
File Name = MS8017_H2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_H2_OPTFRQ.LOG]]
====PH5 Optimisation====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000055 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-1.032823D-09
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.4332 -DE/DX = 0.0 !
! R2 R(1,3) 1.4869 -DE/DX = 0.0 !
! R3 R(1,4) 1.4869 -DE/DX = 0.0 !
! R4 R(1,5) 1.4332 -DE/DX = 0.0 !
! R5 R(1,6) 1.4332 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 90.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A5 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,6) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 90.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 120.0 -DE/DX = 0.0 !
! A10 L(3,1,4,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,4,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D2 D(2,1,6,3) -90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) -90.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) 90.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 180.0 -DE/DX = 0.0 !
! D6 D(3,1,6,5) -90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) 90.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
<pre>
PH5 optimisation
File Name = MS8017_PH5_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -344.25491049 a.u.
RMS Gradient Norm = 0.00000471 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
</pre>
[[media:MS8017_PH5_OPTFRQ.LOG]]

Rep:Mod:MS8017

2018-03-16T10:33:09Z

Ms8017:

==NH3 Molecule==
===NH3 Molecule Calculation parameters===
Calculations for an ammonia molecule (NH3). Following parameters were used to carry out the optimisation
<ul>
<li>Calculation Method = RB3LYP
<li>Calculation Type = OPT+FREQ
<li>Basis Set = 6-31G(d,p)
</ul>

===NH3 Molecule results===

<ul>
<li>E(RB3LYP) = -56.55776873 a.u.
<li>RMS Gradient Norm = 0.00000485 a.u.
<li>Point Group = C3V
</ul>
N-H bond length 1.01798 angstroms 
H-N-H bond angle 105.741 degrees

====NH3 Jmol picture====

[[media:MS8017_NH3_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_NH3_OPTFRQ.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

====NH3 Vibrations====
6 Vibrational modes were expected according to the 3n-6 rule (4 atoms). 
4 vibrational modes were found to be degenerate (2 bending modes and 2 stretching modes). 
Bending modes are numbere 1,2 and 3. Stretching modes are numbered 4,5 and 6. 
The modes with highest symmetries were 1 (bending) and 4 (stretching). Hydrogen atoms in these cases were performing the same motion relative to the nitrogen atom. 
The vibrational mode designated as 1 is the "umbrella" mode as it is mimicking the folding and unfolding of an umbrella. 
2 peaks would be expected in a IR spectral analysis of gaseous ammonia

[[File:MS8017 NH3 VIB.PNG]]
[[File:MS8017_NH3_IR.PNG]]

====NH3 Charge distribution====

Nitrogen is known to have higher electronegativity compared to hydrogen therefore we expect to see more electrons on the nitrogen atom. A negative number higher in magnitude is expected on the nitrogen atom compared to the hydrogen atoms.

[[File:MS8017 NH3 CHRG.PNG]]
===Haber-Bosch process===
[[File:MS8017_N2_MOL.PNG|right|thumb|Nitrogen molecule]] 
[[File:MS8017_H2_MOL.PNG|right|thumb|Hydrogen moleucle]] 
<ul>
<li>E(NH3)=-56.55776873 a.u.
<li>2*E(NH3)=-113.11553746 a.u.
<li>E(N2)=-109.52412868 a.u.
<li>E(H2)=-1.17853936 a.u.
<li>3*E(H2)=-3.53561808 a.u.
<li>ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907 a.u. = 146.45 kJ.mol-1
</ul>
This reaciton tells us that the ammonia gas is more stable as thermodynamically it is an exothermic reaction.

===Molecule of choice PH5===
<ul>
<li>Charge = 0
<li>E(RB3LYP) = -344.25491049 a.u.
<li>RMS Gradient Norm = 0.00000471 a.u.
<li>Dipole Moment = 0.0000 Debye
<li>Point Group = D3H
</ul>
[[media:MS8017_PH5_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>PH5 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_PH5_OPTFRQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Charge Distribution on PH5====
[[File:MS8017_PH5_OPTFRQ.PNG]] 
The values obtained form GaussView (their signs) are same as expected. Hydrogen should have a negative charge as it is more electronegative in comparison to phosphorus. As observed there is a discrepancy between the charge on the axial hydrogen copared to equatoreal charge. This is due to Jahn Teller distortion and it can also be observed in bond lengths. H (axial) = 1.496Å and H (equatoreal) = 1.433Å
<ul>
<li> P = 0.412e
<li> H (axial) = -0.183
<li> H (equatoreal) = -0.015
</ul>
====Vibrations within PH5====
PH5 is not a linear molecule so we expect it to have 12 vibrational modes (3N-6).
[[File:MS8017_PH5_VIB.PNGthumb]] 
4 vibrations (No. 6,7,8 and 10) do not produce any peaks in the IR spectra as they have no change in the dipole moment. These vibrations are highly symmetrical. 
Multiple degenerate vibrational modes are present (No. 1 and 2, 4 and 5, 6 and 7, 11 and 12).
Only 4 peaks would be observed as multiple of these peaks are degenerate and some vibraitons are not IR active (No change in dipole)
[[File:MS8017_PH5_IR.PNG]]
====PH5 Molecular orbitals====
[[File:MS8017_PH5_HOMOLUMO.PNG]] 
The lowest energy orbital is a 1s orbital at the phosphorus atom. Then follow the 2s, 2p orbitals. 
[[File:ENERGY_MS8017_PH5_3S.PNG|600px]] 
Orbital formed by combining the 3s orbital of P and 1s orbital of H. Bonding orbital. Occupied. 
[[File:ENERGY_MS8017_PH5_3SANTI.PNG|600px]] 
Antibonding 3s orbital. Antibonding orbital. Vacant. 
[[File:ENERGY_MS8017_PH5_HOMO.PNG|600px]] 
HOMO orbital of PH5. Formed by combining a 3dz2 (P) with a 1s of H. Bonding orbital. Occupied 
[[File:ENERGY_MS8017_PH5_LUMO.PNG|600px]] 
LUMO orbital of PH5. Contribution from 3d orbital of P and 1s orbital of H. Vacant 
[[File:ENERGY_MS8017_PH5_3PANTI.PNG|600px]] 
Antibonding orbital formed by combining 3p orbital of P with 1s orbital of H. Vacant 
These orbitals can be found in the HOMO/LUMO energy region. We can see the orbitals 1-5 are in the core band. They are the non bonding 1s, 2s and 2p orbitals of the P. 
===Optimisation, Log Files, Results===
====NH3====
<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=-5.986279D-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>
<pre>
nh3 optimisation
File Name = MS8017_NH3_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8466 Debye
Point Group = C3V
</pre>
[[media:MS8017_NH3_OPTFRQ.LOG]]
====N2 Optimization====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401057D-13
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>
<pre>
N2 optimization
File Name = MS8017_N2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_N2_OPTFRQ.LOG]]
====H2 Optimization====
<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>
<pre>
H2 optimisation
File Name = MS8017_H2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_H2_OPTFRQ.LOG]]
====PH5 Optimisation====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000055 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-1.032823D-09
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.4332 -DE/DX = 0.0 !
! R2 R(1,3) 1.4869 -DE/DX = 0.0 !
! R3 R(1,4) 1.4869 -DE/DX = 0.0 !
! R4 R(1,5) 1.4332 -DE/DX = 0.0 !
! R5 R(1,6) 1.4332 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 90.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A5 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,6) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 90.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 120.0 -DE/DX = 0.0 !
! A10 L(3,1,4,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,4,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D2 D(2,1,6,3) -90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) -90.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) 90.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 180.0 -DE/DX = 0.0 !
! D6 D(3,1,6,5) -90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) 90.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
<pre>
PH5 optimisation
File Name = MS8017_PH5_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -344.25491049 a.u.
RMS Gradient Norm = 0.00000471 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
</pre>
[[media:MS8017_PH5_OPTFRQ.LOG]]

File:MS8017 PH5 OPTFRQ.LOG

2018-03-16T10:32:28Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 OPTFRQ.LOG

File:MS8017 NH3 OPTFRQ.LOG

2018-03-16T10:31:16Z

File:MS8017 PH5 3PANTIn.PNG

2018-03-16T10:18:02Z

Ms8017:

File:MS8017 PH5 3PANTI.PNG

2018-03-16T10:14:08Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 3PANTI.PNG

File:MS8017 PH5 3PANTI.PNG

2018-03-16T10:13:28Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 3PANTI.PNG

File:MS8017 PH5 3PANTI.PNG

2018-03-16T10:11:53Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 3PANTI.PNG

Rep:Mod:MS8017

2018-03-16T10:10:06Z

Ms8017:

==NH3 Molecule==
===NH3 Molecule Calculation parameters===
Calculations for an ammonia molecule (NH3). Following parameters were used to carry out the optimisation
<ul>
<li>Calculation Method = RB3LYP
<li>Calculation Type = OPT+FREQ
<li>Basis Set = 6-31G(d,p)
</ul>

===NH3 Molecule results===

<ul>
<li>E(RB3LYP) = -56.55776873 a.u.
<li>RMS Gradient Norm = 0.00000485 a.u.
<li>Point Group = C3V
</ul>
N-H bond length 1.01798 angstroms 
H-N-H bond angle 105.741 degrees

====NH3 Jmol picture====

[[media:MS8017_NH3_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_NH3_OPTFRQ.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

====NH3 Vibrations====
6 Vibrational modes were expected according to the 3n-6 rule (4 atoms). 
4 vibrational modes were found to be degenerate (2 bending modes and 2 stretching modes). 
Bending modes are numbere 1,2 and 3. Stretching modes are numbered 4,5 and 6. 
The modes with highest symmetries were 1 (bending) and 4 (stretching). Hydrogen atoms in these cases were performing the same motion relative to the nitrogen atom. 
The vibrational mode designated as 1 is the "umbrella" mode as it is mimicking the folding and unfolding of an umbrella. 
2 peaks would be expected in a IR spectral analysis of gaseous ammonia

[[File:MS8017 NH3 VIB.PNG]]
[[File:MS8017_NH3_IR.PNG]]

====NH3 Charge distribution====

Nitrogen is known to have higher electronegativity compared to hydrogen therefore we expect to see more electrons on the nitrogen atom. A negative number higher in magnitude is expected on the nitrogen atom compared to the hydrogen atoms.

[[File:MS8017 NH3 CHRG.PNG]]
===Haber-Bosch process===
[[File:MS8017_N2_MOL.PNG|right|thumb|Nitrogen molecule]] 
[[File:MS8017_H2_MOL.PNG|right|thumb|Hydrogen moleucle]] 
<ul>
<li>E(NH3)=-56.55776873 a.u.
<li>2*E(NH3)=-113.11553746 a.u.
<li>E(N2)=-109.52412868 a.u.
<li>E(H2)=-1.17853936 a.u.
<li>3*E(H2)=-3.53561808 a.u.
<li>ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907 a.u. = 146.45 kJ.mol-1
</ul>
This reaciton tells us that the ammonia gas is more stable as thermodynamically it is an exothermic reaction.

===Molecule of choice PH5===
<ul>
<li>Charge = 0
<li>E(RB3LYP) = -344.25491049 a.u.
<li>RMS Gradient Norm = 0.00000471 a.u.
<li>Dipole Moment = 0.0000 Debye
<li>Point Group = D3H
</ul>
[[media:MS8017_PH5_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>PH5 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_PH5_OPTFRQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Charge Distribution on PH5====
[[File:MS8017_PH5_OPTFRQ.PNG]] 
The values obtained form GaussView (their signs) are same as expected. Hydrogen should have a negative charge as it is more electronegative in comparison to phosphorus. As observed there is a discrepancy between the charge on the axial hydrogen copared to equatoreal charge. This is due to Jahn Teller distortion and it can also be observed in bond lengths. H (axial) = 1.496Å and H (equatoreal) = 1.433Å
<ul>
<li> P = 0.412e
<li> H (axial) = -0.183
<li> H (equatoreal) = -0.015
</ul>
====Vibrations within PH5====
PH5 is not a linear molecule so we expect it to have 12 vibrational modes (3N-6).
[[File:MS8017_PH5_VIB.PNGthumb]] 
4 vibrations (No. 6,7,8 and 10) do not produce any peaks in the IR spectra as they have no change in the dipole moment. These vibrations are highly symmetrical. 
Multiple degenerate vibrational modes are present (No. 1 and 2, 4 and 5, 6 and 7, 11 and 12).
Only 4 peaks would be observed as multiple of these peaks are degenerate and some vibraitons are not IR active (No change in dipole)
[[File:MS8017_PH5_IR.PNG]]
====PH5 Molecular orbitals====
[[File:MS8017_PH5_HOMOLUMO.PNG]] 
The lowest energy orbital is a 1s orbital at the phosphorus atom. Then follow the 2s, 2p orbitals. 
[[File:MS8017_PH5_3S.PNG|400px]] 
Orbital formed by combining the 3s orbital of P and 1s orbital of H. Bonding orbital. Occupied. 
[[File:MS8017_PH5_3SANTI.PNG|400px]] 
Antibonding 3s orbital. Antibonding orbital. Vacant. 
[[File:MS8017_PH5_HOMO.PNG|400px]] 
HOMO orbital of PH5. Formed by combining a 3dz2 (P) with a 1s of H. Bonding orbital. Occupied 
[[File:MS8017_PH5_LUMO.PNG|400px]] 
LUMO orbital of PH5. Contribution from 3d orbital of P and 1s orbital of H. Vacant 
[[File:MS8017_PH5_3PANTI.PNG|400px]] 
Antibonding orbital formed by combining 3p orbital of P with 1s orbital of H. Vacant 
These orbitals can be found in the HOMO/LUMO energy region. We can see the orbitals 1-5 are in the core band. They are the non bonding 1s, 2s and 2p orbitals of the P. 
===Optimisation, Log Files, Results===
====NH3====
<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=-5.986279D-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>
<pre>
nh3 optimisation
File Name = MS8017_NH3_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8466 Debye
Point Group = C3V
</pre>
====N2 Optimization====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401057D-13
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>
<pre>
N2 optimization
File Name = MS8017_N2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_N2_OPTFRQ.LOG]]
====H2 Optimization====
<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>
<pre>
H2 optimisation
File Name = MS8017_H2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_H2_OPTFRQ.LOG]]
====PH5====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000055 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-1.032823D-09
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.4332 -DE/DX = 0.0 !
! R2 R(1,3) 1.4869 -DE/DX = 0.0 !
! R3 R(1,4) 1.4869 -DE/DX = 0.0 !
! R4 R(1,5) 1.4332 -DE/DX = 0.0 !
! R5 R(1,6) 1.4332 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 90.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A5 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,6) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 90.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 120.0 -DE/DX = 0.0 !
! A10 L(3,1,4,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,4,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D2 D(2,1,6,3) -90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) -90.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) 90.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 180.0 -DE/DX = 0.0 !
! D6 D(3,1,6,5) -90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) 90.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
<pre>
PH5 optimisation
File Name = MS8017_PH5_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -344.25491049 a.u.
RMS Gradient Norm = 0.00000471 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
</pre>

File:MS8017 PH5 3PANTI.PNG

2018-03-16T10:05:13Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 3PANTI.PNG

File:MS8017 PH5 3S.PNG

2018-03-16T10:04:56Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 3S.PNG

File:MS8017 PH5 3SANTI.PNG

2018-03-16T10:04:36Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 3SANTI.PNG

File:MS8017 PH5 HOMO.PNG

2018-03-16T10:04:12Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 HOMO.PNG

File:MS8017 PH5 LUMO.PNG

2018-03-16T10:03:56Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 LUMO.PNG

File:MS8017 PH5 LUMO.PNG

2018-03-16T10:02:58Z

Ms8017: Ms8017 uploaded a new version of File:MS8017 PH5 LUMO.PNG

Rep:Mod:MS8017

2018-03-16T10:02:39Z

Ms8017:

==NH3 Molecule==
===NH3 Molecule Calculation parameters===
Calculations for an ammonia molecule (NH3). Following parameters were used to carry out the optimisation
<ul>
<li>Calculation Method = RB3LYP
<li>Calculation Type = OPT+FREQ
<li>Basis Set = 6-31G(d,p)
</ul>

===NH3 Molecule results===

<ul>
<li>E(RB3LYP) = -56.55776873 a.u.
<li>RMS Gradient Norm = 0.00000485 a.u.
<li>Point Group = C3V
</ul>
N-H bond length 1.01798 angstroms 
H-N-H bond angle 105.741 degrees

====NH3 Jmol picture====

[[media:MS8017_NH3_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_NH3_OPTFRQ.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

====NH3 Vibrations====
6 Vibrational modes were expected according to the 3n-6 rule (4 atoms). 
4 vibrational modes were found to be degenerate (2 bending modes and 2 stretching modes). 
Bending modes are numbere 1,2 and 3. Stretching modes are numbered 4,5 and 6. 
The modes with highest symmetries were 1 (bending) and 4 (stretching). Hydrogen atoms in these cases were performing the same motion relative to the nitrogen atom. 
The vibrational mode designated as 1 is the "umbrella" mode as it is mimicking the folding and unfolding of an umbrella. 
2 peaks would be expected in a IR spectral analysis of gaseous ammonia

[[File:MS8017 NH3 VIB.PNG]]
[[File:MS8017_NH3_IR.PNG]]

====NH3 Charge distribution====

Nitrogen is known to have higher electronegativity compared to hydrogen therefore we expect to see more electrons on the nitrogen atom. A negative number higher in magnitude is expected on the nitrogen atom compared to the hydrogen atoms.

[[File:MS8017 NH3 CHRG.PNG]]
===Haber-Bosch process===
[[File:MS8017_N2_MOL.PNG|right|thumb|Nitrogen molecule]] 
[[File:MS8017_H2_MOL.PNG|right|thumb|Hydrogen moleucle]] 
<ul>
<li>E(NH3)=-56.55776873 a.u.
<li>2*E(NH3)=-113.11553746 a.u.
<li>E(N2)=-109.52412868 a.u.
<li>E(H2)=-1.17853936 a.u.
<li>3*E(H2)=-3.53561808 a.u.
<li>ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907 a.u. = 146.45 kJ.mol-1
</ul>
This reaciton tells us that the ammonia gas is more stable as thermodynamically it is an exothermic reaction.

===Molecule of choice PH5===
<ul>
<li>Charge = 0
<li>E(RB3LYP) = -344.25491049 a.u.
<li>RMS Gradient Norm = 0.00000471 a.u.
<li>Dipole Moment = 0.0000 Debye
<li>Point Group = D3H
</ul>
[[media:MS8017_PH5_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>PH5 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_PH5_OPTFRQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Charge Distribution on PH5====
[[File:MS8017_PH5_OPTFRQ.PNG]] 
The values obtained form GaussView (their signs) are same as expected. Hydrogen should have a negative charge as it is more electronegative in comparison to phosphorus. As observed there is a discrepancy between the charge on the axial hydrogen copared to equatoreal charge. This is due to Jahn Teller distortion and it can also be observed in bond lengths. H (axial) = 1.496Å and H (equatoreal) = 1.433Å
<ul>
<li> P = 0.412e
<li> H (axial) = -0.183
<li> H (equatoreal) = -0.015
</ul>
====Vibrations within PH5====
PH5 is not a linear molecule so we expect it to have 12 vibrational modes (3N-6).
[[File:MS8017_PH5_VIB.PNGthumb]] 
4 vibrations (No. 6,7,8 and 10) do not produce any peaks in the IR spectra as they have no change in the dipole moment. These vibrations are highly symmetrical. 
Multiple degenerate vibrational modes are present (No. 1 and 2, 4 and 5, 6 and 7, 11 and 12).
Only 4 peaks would be observed as multiple of these peaks are degenerate and some vibraitons are not IR active (No change in dipole)
[[File:MS8017_PH5_IR.PNG]]
====PH5 Molecular orbitals====
[[File:MS8017_PH5_HOMOLUMO.PNG|thumb|The lowest energy orbital is a 1s orbital at the phosphorus atom. Then follow the 2s, 2p orbitals.]] 
[[File:MS8017_PH5_3S.PNG|thumb|Orbital formed by combining the 3s orbital of P and 1s orbital of H. Bonding orbital. Occupied]] 
[[File:MS8017_PH5_3SANTI.PNG|thumb|Antibonding 3s orbital. Antibonding orbital. Vacant]] 
[[File:MS8017_PH5_HOMO.PNG|thumb|HOMO orbital of PH5. Formed by combining a 3dz2 (P) with a 1s of H. Bonding orbital. Occupied]] 
[[File:MS8017_PH5_LUMO.PNG|thumb|LUMO orbital of PH5. Contribution from 3d orbital of P and 1s orbital of H. Vacant]] 
[[File:MS8017_PH5_3PANTI.PNG|thumb|Antibonding orbital formed by combining 3p orbital of P with 1s orbital of H. Vacant]] 
These orbitals can be found in the HOMO/LUMO energy region. We can see the orbitals 1-5 are in the core band. They are the non bonding 1s, 2s and 2p orbitals of the P. 
===Optimisation, Log Files, Results===
====NH3====
<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=-5.986279D-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>
<pre>
nh3 optimisation
File Name = MS8017_NH3_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8466 Debye
Point Group = C3V
</pre>
====N2 Optimization====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401057D-13
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>
<pre>
N2 optimization
File Name = MS8017_N2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_N2_OPTFRQ.LOG]]
====H2 Optimization====
<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>
<pre>
H2 optimisation
File Name = MS8017_H2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_H2_OPTFRQ.LOG]]
====PH5====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000055 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-1.032823D-09
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.4332 -DE/DX = 0.0 !
! R2 R(1,3) 1.4869 -DE/DX = 0.0 !
! R3 R(1,4) 1.4869 -DE/DX = 0.0 !
! R4 R(1,5) 1.4332 -DE/DX = 0.0 !
! R5 R(1,6) 1.4332 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 90.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A5 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,6) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 90.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 120.0 -DE/DX = 0.0 !
! A10 L(3,1,4,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,4,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D2 D(2,1,6,3) -90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) -90.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) 90.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 180.0 -DE/DX = 0.0 !
! D6 D(3,1,6,5) -90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) 90.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
<pre>
PH5 optimisation
File Name = MS8017_PH5_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -344.25491049 a.u.
RMS Gradient Norm = 0.00000471 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
</pre>

File:MS8017 N2 MOL.PNG

2018-03-16T09:15:07Z

Ms8017:

2018-03-15T11:21:48Z

Ms8017:

Rep:Mod:MS8017

2018-03-15T11:20:15Z

Ms8017:

==NH3 Molecule==
===NH3 Molecule Calculation parameters===
Calculations for an ammonia molecule (NH3). Following parameters were used to carry out the optimisation
<ul>
<li>Calculation Method = RB3LYP
<li>Calculation Type = FREQ
<li>Basis Set = 6-31G(d,p)
</ul>

===NH3 Molecule results===

<ul>
<li>E(RB3LYP) = -56.55776873 a.u.
<li>RMS Gradient Norm = 0.00000485 a.u.
<li>Point Group = C3V
</ul>
N-H bond length 1.01798 angstroms 
H-N-H bond angle 105.741 degrees

====NH3 Jmol picture====

[[media:MS8017_NH3_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_NH3_OPTFRQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====NH3 Vibrations====
6 Vibrational modes were expected according to the 3n-6 rule (4 atoms). 
4 vibrational modes were found to be degenerate (2 bending modes and 2 stretching modes). 
Bending modes are numbere 1,2 and 3. Stretching modes are numbered 4,5 and 6. 
The modes with highest symmetries were 1 (bending) and 4 (stretching). Hydrogen atoms in these cases were performing the same motion relative to the nitrogen atom. 
The vibrational mode designated as 1 is the "umbrella" mode as it is mimicking the folding and unfolding of an umbrella. 
4 bands would be expected in a IR spectral analysis of gaseous ammonia

[[File:MS8017 NH3 VIB.PNG]]

====NH3 Charge distribution====

Nitrogen is known to have higher electronegativity compared to hydrogen therefore we expect to see more electrons on the nitrogen atom. A negative number higher in magnitude is expected on the nitrogen atom compared to the hydrogen atoms.

[[File:MS8017 NH3 CHRG.PNG]]

<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=-5.986279D-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>
<pre>
nh3 optimisation
File Name = MS8017_NH3_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8466 Debye
Point Group = C3V
</pre>

===Haber-Bosch process===
<ul>
<li>E(NH3)=-56.55776873 a.u.
<li>2*E(NH3)=-113.11553746 a.u.
<li>E(N2)=-109.52412868 a.u.
<li>E(H2)=-1.17853936 a.u.
<li>3*E(H2)=-3.53561808 a.u.
<li>ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907 a.u.
</ul>
This reaciton tells us that the ammonia gas is more stable as thermodynamically it is an exothermic reaction.
====N2 Optimization====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.401057D-13
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>
<pre>
N2 optimization
File Name = MS8017_N2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -109.52412868 a.u.
RMS Gradient Norm = 0.00000060 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_N2_OPTFRQ.LOG]]

====H2 Optimization====
<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>
<pre>
H2 optimisation
File Name = MS8017_H2_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -1.17853936 a.u.
RMS Gradient Norm = 0.00000017 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D*H
</pre>
[[media:MS8017_H2_OPTFRQ.LOG]]

===Molecule of choice PH5===
<ul>
<li>Charge = 0
<li>E(RB3LYP) = -344.25491049 a.u.
<li>RMS Gradient Norm = 0.00000471 a.u.
<li>Dipole Moment = 0.0000 Debye
<li>Point Group = D3H
</ul>
[[media:MS8017_PH5_OPTFRQ.LOG]]

<jmol><jmolApplet>
<title>PH5 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MS8017_PH5_OPTFRQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Charge Distribution on PH5====
[[File:MS8017_PH5_OPTFRQ.PNG]] 
The values obtained form GaussView (their signs) are same as expected. Hydrogen should have a negative charge as it is more electronegative in comparison to phosphorus.
<ul>
<li> P = 0.412e
<li> H (axial) = -0.183
<li> H (equatoreal) = -0.015
</ul>
====Vibrations within PH5====
PH5 is not a linear molecule so we expect it to have 12 vibrational modes (3N-6).
[[File:MS8017_PH5_VIB.PNG]] 
4 vibrations (No. 6,7,8 and 10) do not produce any peaks in the IR spectra as they have no change in the dipole moment. These vibrations are highly symmetrical. 
Multiple degenerate vibrational modes are present (No. 1 and 2, 4 and 5, 6 and 7, 11 and 12).
Only 4 peaks would be observed as multiple of these peaks are degenerate and some vibraitons are not IR active (No change in dipole)
[[File:MS8017_PH5_IR.PNG]]
====PH5 Molecular orbitals====
[[File:MS8017_PH5_HOMOLUMO.PNG]] 
The lowest energy orbital is a 1s orbital at the phosphorus atom. Then follow the 2s, 2p orbitals.
[[File:MS8017_PH5_3S.PNG]] 
Orbital formed by combining the 3s orbital of P and 1s orbital of H. Bonding orbital. Occupied 
[[File:MS8017_PH5_3SANTI.PNG]] 
Antibonding 3s orbital. Antibonding orbital. Vacant 
[[File:MS8017_PH5_HOMO.PNG]] 
HOMO orbital of PH5. Formed by combining a 3dz2 (P) with a 1s of H. Bonding orbital. Occupied 
[[File:MS8017_PH5_LUMO.PNG]] 
LUMO orbital of PH5. Contribution from 3d orbital of P and 1s orbital of H. Vacant 
[[File:MS8017_PH5_3PANTI.PNG]] 
Antibonding orbital formed by combining 3p orbital of P with 1s orbital of H. Vacant 
These orbitals can be found in the HOMO/LUMO energy region. We can see the orbitals 1-5 are in the core band. They are the non bonding 1s, 2s and 2p orbitals of the P.
====Optimisation of PH5====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000055 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-1.032823D-09
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.4332 -DE/DX = 0.0 !
! R2 R(1,3) 1.4869 -DE/DX = 0.0 !
! R3 R(1,4) 1.4869 -DE/DX = 0.0 !
! R4 R(1,5) 1.4332 -DE/DX = 0.0 !
! R5 R(1,6) 1.4332 -DE/DX = 0.0 !
! A1 A(2,1,3) 90.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 90.0 -DE/DX = 0.0 !
! A3 A(2,1,5) 120.0 -DE/DX = 0.0 !
! A4 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A5 A(3,1,5) 90.0 -DE/DX = 0.0 !
! A6 A(3,1,6) 90.0 -DE/DX = 0.0 !
! A7 A(4,1,5) 90.0 -DE/DX = 0.0 !
! A8 A(4,1,6) 90.0 -DE/DX = 0.0 !
! A9 A(5,1,6) 120.0 -DE/DX = 0.0 !
! A10 L(3,1,4,2,-1) 180.0 -DE/DX = 0.0 !
! A11 L(3,1,4,2,-2) 180.0 -DE/DX = 0.0 !
! D1 D(2,1,5,3) 90.0 -DE/DX = 0.0 !
! D2 D(2,1,6,3) -90.0 -DE/DX = 0.0 !
! D3 D(2,1,5,4) -90.0 -DE/DX = 0.0 !
! D4 D(2,1,6,4) 90.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 180.0 -DE/DX = 0.0 !
! D6 D(3,1,6,5) -90.0 -DE/DX = 0.0 !
! D7 D(4,1,6,5) 90.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>
<pre>
PH5 optimisation
File Name = MS8017_PH5_OPTFRQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -344.25491049 a.u.
RMS Gradient Norm = 0.00000471 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
</pre>