ChemWiki - User contributions [en]

Mod:Hunt Research Group/calendar

2016-03-08T11:10:48Z

As1515:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Not Done)
| Jan Szopinski (Done)
| Aimee Darke (Not Done)
|-
| Vincent Chen (Not Done)
| Ken Watson (Not Done)
| Rebecca Rowe (Done)
|-
|Anil Bijoy (Done)
| Richard Fogarty (Not Done)
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun

|-
|7th March
|8th
|9th
|10th
|11th
| style="background: grey;" |12th
| style="background: grey;" |13th

|-
|14th
|15th
|16th
|17th
|18th
| style="background: grey;" |19th
| style="background: grey;" |20th

|-
|21st
|22nd
|style="background: yellow;" |23rd Last day of easter term
Jan away
| style="background: lime;" |24th College Closure Start

| style="background: lime;" |25th

| style="background: grey;" |26th
| style="background: grey;" |27th

|-
| style="background: lime;" |28th

| style="background: lime;" |29th

| style="background: lime;" |30th College Closure End

| style="background: lime;" |31st
Jan away

| style="background: blue; color: white;" |1st April
Jan away

| style="background: grey;" |2nd
| style="background: grey;" |3rd

|-
|4th
Jan away
|5th
Jan away
|6th
Jan away
|7th
|8th
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
|11th
Anil away
|12th
Anil away
|13th
Anil away
|14th
Becky away
|15th
Becky away
| style="background: grey;" |16th
| style="background: grey;" |17th

|-
|18th
Becky away
|19th
Becky away
|20th
Becky away
|21st
Becky away
|22nd
Becky away
| style="background: grey;" |23rd
| style="background: grey;" |24th

|-
|style="background: yellow;" |25th 1st day of summer term
|26th
|27th
|28th
|29th
| style="background: grey;" |30th
| style="background: grey;" |1st May

|}

Mod:Hunt Research Group/calendar

2015-11-30T08:12:33Z

As1515:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Done)
| Jan Szopinski (Done)
| Aimee Darke (Not Done)
|-
| Vincent Chen (Not Done)
| Ken Watson (Done)
| Rebecca Rowe (Done)
|-
|Anil Bijoy (Done)
| Richard Fogarty (Not Done)
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun

|-
|30th
| style="background: blue; color: white;" |1st December
Jan away
|2nd
|3rd
|4th
| style="background: grey;" |5th
| style="background: grey;" |6th

|-
|7th
|8th
|9th
|10th
|11th
| style="background: grey;" |12th
| style="background: grey;" |13th

|-
|14th
|15th
Jan away
|16th
Jan away
|17th
Jan away
| style="background: yellow;" |18th
End of term

Jan away
| style="background: grey;" |19th
| style="background: grey;" |20th

|-
|21st
Becky away

Ken away

Jan away

Anil away
|22nd
Tricia away

Becky away

Ken away

Jan away

Anil away
|23rd
Tricia away

Becky away

Ken away

Jan away

Anil Away
| style="background: lime;" |24th
College closure

| style="background: lime;" |25th

| style="background: grey;" |26th
| style="background: grey;" |27th

|-
| style="background: lime;" |28th

| style="background: lime;" |29th

| style="background: lime;" |30th

| style="background: lime;" |31st

| style="background: blue; color: white;" |1st January

| style="background: grey;" |2nd
| style="background: grey;" |3rd

|-
|4th College opens
Tricia maybe

Becky away

Ken away

Anil away
|5th
Tricia maybe

Becky away

Ken away

Anil Away
|6th
Tricia maybe

Becky away

Anil Away
|7th
Tricia maybe

Becky away
|8th
Tricia away

Becky away
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
| style="background: yellow;" |11th
Start of term
|12th
|13th
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th

|-
|18th
|19th
|20th
|21st
|22nd
| style="background: grey;" |23rd
| style="background: grey;" |24th

|-
|25th
|26th
|27th
|28th
|29th
| style="background: grey;" |30th
| style="background: grey;" |31st

|}

Mod:Hunt Research Group/calendar

2015-11-30T08:10:51Z

As1515:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Done)
| Jan Szopinski (Done)
| Aimee Darke (Not Done)
|-
| Vincent Chen (Not Done)
| Ken Watson (Done)
| Rebecca Rowe (Done)
|-
|Anil Bijoy (Not Done)
| Richard Fogarty (Not Done)
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun

|-
|30th
| style="background: blue; color: white;" |1st December
Jan away
|2nd
|3rd
|4th
| style="background: grey;" |5th
| style="background: grey;" |6th

|-
|7th
|8th
|9th
|10th
|11th
| style="background: grey;" |12th
| style="background: grey;" |13th

|-
|14th
|15th
Jan away
|16th
Jan away
|17th
Jan away
| style="background: yellow;" |18th
End of term

Jan away
| style="background: grey;" |19th
| style="background: grey;" |20th

|-
|21st
Becky away

Ken away

Jan away

Anil away
|22nd
Tricia away

Becky away

Ken away

Jan away

Anil away
|23rd
Tricia away

Becky away

Ken away

Jan away

Anil Away
| style="background: lime;" |24th
College closure

| style="background: lime;" |25th

| style="background: grey;" |26th
| style="background: grey;" |27th

|-
| style="background: lime;" |28th

| style="background: lime;" |29th

| style="background: lime;" |30th

| style="background: lime;" |31st

| style="background: blue; color: white;" |1st January

| style="background: grey;" |2nd
| style="background: grey;" |3rd

|-
|4th College opens
Tricia maybe

Becky away

Ken away

Anil away
|5th
Tricia maybe

Becky away

Ken away

Anil Away
|6th
Tricia maybe

Becky away

Anil Away
|7th
Tricia maybe

Becky away
|8th
Tricia away

Becky away
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
| style="background: yellow;" |11th
Start of term
|12th
|13th
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th

|-
|18th
|19th
|20th
|21st
|22nd
| style="background: grey;" |23rd
| style="background: grey;" |24th

|-
|25th
|26th
|27th
|28th
|29th
| style="background: grey;" |30th
| style="background: grey;" |31st

|}

Rep:Mod:Asaddat0987654321

2015-11-23T12:09:16Z

2015-11-12T19:54:14Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015 NH3BH3 631G MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015 NH3BH3 631G MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

E(NH3)= -56.55776873 au
E(BH3)= -26.61532361 au
E(NH3BH3)= -83.22468883 au

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
ΔE = -83.22468883 –(-26.61532361)-( -56.55776873)
ΔE = -0.05159649 au = 135.4666 Kj/mol

This is a relatively weak bond.

Rep:Mod:Asaddat0987654321

2015-11-12T19:51:52Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015 NH3BH3 631G MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015 NH3BH3 631G MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

E(NH3)= -56.55776873 au
E(BH3)= -26.61532361 au
E(NH3BH3)= -83.22468883 au

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
ΔE = -83.22468883 –(-26.61532361)-( -56.55776873)
ΔE = -0.05159649 au = 135.4666 Kj/mol

Rep:Mod:Asaddat0987654321

2015-11-12T19:47:52Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015 NH3BH3 631G MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015 NH3BH3 631G MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Rep:Mod:Asaddat0987654321

2015-11-12T19:45:27Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

Rep:Mod:Asaddat0987654321

2015-11-12T19:44:38Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015_NH3BH3_631G_MOL.mol</jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

File:10112015 NH3BH3 631G MOL.mol

2015-11-12T19:43:51Z

As1515: As1515 uploaded a new version of File:10112015 NH3BH3 631G MOL.mol

Rep:Mod:Asaddat0987654321

2015-11-12T19:43:30Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015_NH3BH3_631G_MOL.mol</jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015_NH3BH3_631G_MOL.mol</jmol>
|}

Rep:Mod:Asaddat0987654321

2015-11-12T19:42:11Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

Rep:Mod:Asaddat0987654321

2015-11-12T19:40:42Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:10112015_NH3BH3_631G_LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

Optimisation log file [[Media:10112015_NH3BH3_631G_FREQ_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3BH3_631G_FREQ_LOG.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet>10112015 NH3BH3 631G MOL.mol</jmol>
|}

File:10112015 NH3BH3 631G FREQ LOG.txt

2015-11-12T19:37:54Z

As1515:

File:10112015 NH3BH3 631G LOG.txt

2015-11-12T19:37:43Z

As1515:

File:10112015 NH3BH3 631G MOL.mol

2015-11-12T19:37:29Z

As1515:

Rep:Mod:Asaddat0987654321

2015-11-12T19:35:34Z

As1515: /* Ammonia-Borane Analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
Predicted change in Energy=-1.635696D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000116 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.000581 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
Predicted change in Energy=-1.740048D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents></uploadedFileContents>
</jmolApplet></jmol>
|}

Rep:Mod:Asaddat0987654321

2015-11-12T19:31:38Z

As1515:

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

===Ammonia-Borane Analysis===

Optimization Summary

NH3BH3 Optimization
File Name = 10112015 NH3BH3 631G OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468893 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq =
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 36.0 seconds.

Frequency Analysis Summary

NH3BH3 Frequency
File Name = 10112015 NH3BH3 631G FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -83.22468883 a.u.
RMS Gradient Norm = 0.00005974 a.u.
Imaginary Freq = 0
Dipole Moment = 5.5651 Debye
Point Group = C1
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Rep:Mod:Asaddat0987654321

2015-11-12T19:21:20Z

As1515: /* NH3 6-31G analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:NH3 Charge range.jpg|300px]]

[[File:NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:NH3 charge distribution numbers.jpg|300px]]

Rep:Mod:Asaddat0987654321

2015-11-12T19:20:38Z

As1515: /* NH3 6-31G analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -0.0138 -0.0026 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:.NH3 Charge range.jpg|300px]]

[[File:.NH3 charge distribution.jpg|300px]]

What are the specific NBO charges for the nitrogen and hydrogen atoms?

[[File:.NH3 charge distribution numbers.jpg|300px]]

File:NH3 Charge range.jpg

2015-11-12T19:12:07Z

As1515: As1515 uploaded a new version of File:NH3 Charge range.jpg

File:NH3 charge distribution.jpg

2015-11-12T19:11:32Z

As1515: As1515 uploaded a new version of File:NH3 charge distribution.jpg

File:NH3 charge distribution numbers.jpg

2015-11-12T19:11:02Z

As1515: As1515 uploaded a new version of File:NH3 charge distribution numbers.jpg

Rep:Mod:Asaddat0987654321

2015-11-12T19:10:07Z

As1515: /* NH3 6-31G analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_POP_LOG.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_POP_LOG.txt|300px]]
|
<pre>
N/A
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

File:10112015 NH3 631G POP LOG.txt

2015-11-12T19:07:45Z

As1515: As1515 uploaded a new version of File:10112015 NH3 631G POP LOG.txt

Rep:Mod:Asaddat0987654321

2015-11-12T19:06:48Z

As1515: /* GaBr3 LANL2DZ Frequency analysis */

''Computational Chemistry Training''

{| class="wikitable" border="1"
|+ Molecule Summary Table
! !!BH3 3-21G!!BH3 6-31G!!GaBr3 !! BBr3 !! NH3
|-
|r(1-2) || 1.19467 || 1.19227 ||2.35018 ||1.93395||
|-
|r(1-3) || 1.19445 || 1.19227 ||2.35018 ||1.93397 ||
|-
|r(1-4) || 1.19480 || 1.19234 ||2.35018 ||1.93396 ||
|-
|r(2-1-3) || 120.16 || 120.003 ||120.000 ||119.999||
|-
|r(2-1-4) || 119.986 || 119.994 ||120.000 ||120.000||
|-
|r(3-1-4) || 119.998 || 120.003 ||120.000 ||120.001||
|}

== Week 1 Practice ==

== Day 1 Calculations ==

09/11/2015

===BH3 3-21G Optimization===

09112015 BH3 OPT
File Name = 09112105_AS_BH3_321G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 3-21G
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.46226429 a.u.
RMS Gradient Norm = 0.00008851 a.u.
Imaginary Freq =
Dipole Moment = 0.0003 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 24.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_321G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_321G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_321G_OPT.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1948 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1947 -DE/DX = -0.0002 !
! R3 R(1,4) 1.1944 -DE/DX = -0.0001 !
! A1 A(2,1,3) 120.0157 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.986 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9983 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_OPT_GRADENERG.jpg|500px]]

== Day 2 Calculations ==

09/11/2015

===BH3 6-31G Optimization===

09112015 BH3 OPT 631G
File Name = 09112105_AS_BH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532361 a.u.
RMS Gradient Norm = 0.00000713 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 10.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000063 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-1.106101D-09
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1923 -DE/DX = 0.0 !
! R2 R(1,3) 1.1923 -DE/DX = 0.0 !
! R3 R(1,4) 1.1923 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0058 -DE/DX = 0.0 !
! A2 A(2,1,4) 119.9937 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0005 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

[[File:09112015_BH3_631G_ENERGGRAD.jpg|500px]]

===GaBr3 LAN2DZ Optimization===

09112015 GABR3 OPT HPC FIRST TRIAL
File Name = HPC_DLOAD_GABR3_09112015
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000016 a.u.
Imaginary Freq =
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 13.8 seconds.

Optimisation log file [[Media:HPC_DLOAD_GABR3_09112015.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:HPC_DLOAD_GABR3_09112015.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
Predicted change in Energy=-1.307738D-12
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.3502 -DE/DX = 0.0 !
! R2 R(1,3) 2.3502 -DE/DX = 0.0 !
! R3 R(1,4) 2.3502 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

===BBr3 6-31G Optimization===

09112015 BBR3 OPT GEN
File Name = 09112015_BBR3_HPC_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = Gen
Charge = 0
Spin = Singlet
E(RB3LYP) = -64.43644997 a.u.
RMS Gradient Norm = 0.00000392 a.u.
Imaginary Freq =
Dipole Moment = 0.0001 Debye
Point Group = CS
Job cpu time: 0 days 0 hours 0 minutes 23.7 seconds.

Optimisation log file [[Media:09112015_BBR3_HPC_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112015_BBR3_HPC_OPT.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000024 0.001200 YES
Predicted change in Energy=-4.123635D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112015_BBR3_HPC_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0009 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0001 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9991 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Provide DSPACE Link

===BH3 6-31G Frequency analysis===

09112015 BH3 OPT 631G Frequency
File Name = 09112105_AS_BH3_631G_Frequency
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -26.61532364 a.u.
RMS Gradient Norm = 0.00000530 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = D3H
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Optimisation log file [[Media:09112105_AS_BH3_631G_FREQUENCY.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:09112105_AS_BH3_631G_FREQUENCY.LOG|300px]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>09112105_AS_BH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -14.5183 -14.5142 -10.8197 0.0003 0.0169 0.3454
Low frequencies --- 1162.9508 1213.1230 1213.1232

[[File:09112015 BH3 IR SPECTRUM.jpg]]

Wavenumber Intensity Infrared Type
1162.95 92.5706 Yes Bend
1213.12 14.0539 Yes Bend
1213.12 14.0533 No Bend
2582.66 0.0000 No Strech
2715.81 126.3291 No Strech
2715.81 126.3231 Yes Strech

why are there 6 vibrations but only 3 peaks on the IR spectrum??

We know that for a given molecule the number of Vibration modes should be 3N - 6, where N is the number of atoms. In the case of BH3 since there are 4 atoms we get 6 vibration modes. As expected according to our Frequency analysis we find 6 vibrations modes which can be visualized. But, in the IR spectrum produced there are only 3 band peaks that we can observe. There are two reasons for this which have been detailed below.

1) According to the data there are two Vibrational modes at wavenumber 1213.12 cm-1 and 2715.81 cm-1. These have the same intensities and vibration frequency. Degenerate vibrations produce a single peak in the spectra because they have the same energy. Hence we see one peak for the two vibration frequency combined.

2) The intensity at the vibration frequency at 2582.66 cm-1 is a symmetrical stretch of BH3. And this frequency is inactive in the IR because this vibration produces no change in the dipole moment of the molecule. In order to be IR active, a vibration must cause a change in the dipole moment of the molecule.

===GaBr3 LANL2DZ Frequency analysis===

09112015 GABR3 Frequency analysis
File Name = HPC_DLOAD_FAGABR3
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = LANL2DZ
Charge = 0
Spin = Singlet
E(RB3LYP) = -41.70082770 a.u.
RMS Gradient Norm = 0.00000025 a.u.
Imaginary Freq = 0
Dipole Moment = 0.0000 Debye
Point Group = C3H
Job cpu time: 0 days 0 hours 0 minutes 12.4 seconds.

Optimisation log file [[Media:HPC_DLOAD_FAGABR3.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:HPC_DLOAD_FAGABR3.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000021 0.001200 YES
Predicted change in Energy=-6.630030D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>HPC_DLOAD_GABR3_09112015_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767

Wavenumber Intensity Infrared Type
76.39 3.3451 Yes Bend
76.39 3.3450 no Bend
99.68 9.2166 Yes Bend
197.33 0.0000 no Stretch
316.18 57.0655 no Stretch
316.18 57.0669 Yes Stretch

[[File:IR spectrum GaBr3.jpg]]

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?

The large difference in the frequencies indicate the difference in energy required to vibrate the BH3 molecule.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed?

The GaBr3 molecule vibrates more along its displacement axis in the A2" symmetry compared to the GaBr3 molecule

Why?

Longer bond length.

Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?

Basis sets determines the number of functions required to approximate the electronic structure of a certain molecule. An approximation made for a specific molecule needs to be compared to another molecule approximated using the exactly same method/basis set to keep the integrity of the values obtained. More importantly, when determining values like disassociation energy which needs to be calculated from values obtained from two different molecules but also the combined molecules, using different basis sets would lead to wrong values due to comparison of vastly different approximations.

What is the purpose of carrying out a frequency analysis?

The purpose of carrying out a frequency analysis is to figure out the minimum of our molecules potential energy surface. It helps figure out the vibration frequency which in turn helps predict Infrared spectroscopy peaks we might expect to see if the experiment was physically carried out.

What do the "Low frequencies" represent?

The low frequencies represent the motion of the center of mass of the molecule.

===Molecular Orbitals of BH3===

1st molecular orbital

[[File:1 shell energy.jpg|200px]]

2nd molecular orbital

[[File:2 shell energy.jpg|200px]]

3rd molecular orbital

[[File:3 shell energy.jpg|200px]]

Highest occupied molecular orbital

[[File:HOMO energy.jpg|200px]]

Lowest unoccupied molecular orbital

[[File:LUMO energy.jpg|200px]]

===NH3 6-31G analysis===

Summary :

NH3 molecule optimization
File Name = 10112015_NH3_631G_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000323 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group = C3V
Job cpu time: 0 days 0 hours 0 minutes 11.0 seconds.

Frequency Analysis Summary:

NH3 molecule frequency
File Name = 10112015_NH3_631G_FREQ
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 0
Spin = Singlet
E(RB3LYP) = -56.55776872 a.u.
RMS Gradient Norm = 0.00000322 a.u.
Imaginary Freq = 0
Dipole Moment = 1.8465 Debye
Point Group = C3
Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds.

Population Analysis Summary:

NH3 molecule Population
File Name = 10112015_NH3_631G_OPT
File Type = .chk
Calculation Type = SP
Calculation Method = RB3LYP
Basis Set = 6-31G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -56.55776873 a.u.
RMS Gradient Norm = 0.00000000 a.u.
Imaginary Freq =
Dipole Moment = 1.8465 Debye
Point Group =

Optimisation log file [[Media:10112015_NH3_631G_OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_OPT.LOG|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
Predicted change in Energy=-9.844602D-11
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Optimisation log file [[Media:10112015_NH3_631G_FREQ_Log.txt| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:10112015_NH3_631G_FREQ_Log.txt|300px]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-1.131567D-10
Optimization completed.
-- Stationary point found.
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>10112015_NH3_631G_OPT_MOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}