Rep:Mod:Asaddat0987654321

Computational Chemistry Training

Molecule Summary Table
	BH₃ 3-21G	BH₃ 6-31G	GaBr₃	BBr₃	NH₃
r(1-2)	1.19467	1.19227	2.35018	1.93395	1.01798
r(1-3)	1.19445	1.19227	2.35018	1.93397	1.01798
r(1-4)	1.19480	1.19234	2.35018	1.93396	1.01798
r(2-1-3)	120.16	120.003	120.000	119.999	105.745
r(2-1-4)	119.986	119.994	120.000	120.000	105.745
r(3-1-4)	119.998	120.003	120.000	120.001	105.745

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 here

summary data

convergence

Jmol

File:09112105 AS BH3 321G OPT.LOG

 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.

optimised BH3 molecule

                          ----------------------------
                          !   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

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 here

summary data

convergence

Jmol

File:09112105 AS BH3 631G OPT.LOG

 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.

optimised BH3 molecule

                          ----------------------------
                          !   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                 !
--------------------------------------------------------------------------------
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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  here

summary data

convergence

Jmol

File:HPC DLOAD GABR3 09112015.log

 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.

optimised GaBr3 molecule

                          ----------------------------
                          !   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 here

summary data

convergence

Jmol

File:09112015 BBR3 HPC OPT.log

 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.

optimised BH3 molecule

                          ----------------------------
                          !   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                 !
--------------------------------------------------------------------------------
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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 here

summary data

convergence

Jmol

File:09112105 AS BH3 631G FREQUENCY.LOG

 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.

optimised BH3 molecule

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

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 here

summary data

convergence

Jmol

File:HPC DLOAD FAGABR3.log

 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.

optimised GaBr3 molecule

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

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

2nd molecular orbital

3rd molecular orbital

Highest occupied molecular orbital

Lowest unoccupied molecular orbital

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 here

summary data

convergence

Jmol

File:10112015 NH3 631G OPT.LOG

 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.

optimised NH3 molecule

Optimisation log file here

summary data

convergence

Jmol

File:10112015 NH3 631G FREQ Log.txt

 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.

optimised NH3 molecule

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 here

summary data

convergence

Jmol

File:10112015 NH3 631G POP LOG.txt

N/A

optimised NH3 molecule

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

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 here

summary data

convergence

Jmol

File:10112015 NH3BH3 631G LOG.txt

 
 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.

optimised NH3 molecule

Optimisation log file here

summary data

convergence

Jmol

File:10112015 NH3BH3 631G FREQ LOG.txt

 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.

optimised NH3 molecule

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.

Tetra-Butyl Ammonium Ion Analysis

Optimization summary

N(C4H9)4+ Optimization
File Name = QUATAMMONIUM_OPT
File Type = .log
Calculation Type = FOPT
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 1
Spin = Singlet
E(RB3LYP) = -685.98649942 a.u.
RMS Gradient Norm = 0.00000128 a.u.
Imaginary Freq = 
Dipole Moment = 1.2182 Debye
Point Group = C1
Job cpu time:       0 days  3 hours 39 minutes 48.3 seconds.

Optimisation log file here

summary data

convergence

Jmol

File:QUATAMMONIUM OPT Log.txt

 
 Item                     Value        Threshold  Converged?
 Maximum Force            0.000005     0.000450     YES
 RMS     Force            0.000001     0.000300     YES
 Maximum Displacement     0.001413     0.001800     YES
 RMS     Displacement     0.000197     0.001200     YES
 Predicted change in Energy=-2.152879D-09
 Optimization completed.
    -- Stationary point found.

optimised tetrabutyl ammonium ion molecule

Frequency Analysis summary

N(C4H9)4+ Frequency
File Name = QUATAMMONIUM_FREQ_LOG
File Type = .log
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
Charge = 1
Spin = Singlet
E(RB3LYP) = -685.98649942 a.u.
RMS Gradient Norm = 0.00000127 a.u.
Imaginary Freq = 0
Dipole Moment = 1.2182 Debye
Point Group = C1
Job cpu time:       0 days  4 hours 33 minutes 13.1 seconds.

Optimisation log file here

summary data

convergence

Jmol

File:QUATAMMONIUM FREQ LOG.log

 
Item               Value     Threshold  Converged?
 Maximum Force            0.000005     0.000450     YES
 RMS     Force            0.000001     0.000300     YES
 Maximum Displacement     0.002534     0.001800     NO 
 RMS     Displacement     0.000482     0.001200     YES
 Predicted change in Energy=-3.711258D-09

optimised tetrabutyl ammonium ion molecule

Low frequencies ---   -3.3879   -0.0010   -0.0007    0.0006    2.9807    4.1293
Low frequencies ---   35.3771   40.8237   46.9011

IR Spectrum Analysis

MO analysis

Optimisation log file here

summary data

convergence

Jmol

File:QUATAMMONIUM MO LOG.log

N/A

optimised tetrabutyl ammonium ion molecule

HOMO

LUMO

Charge according to color

Charge numeric representation

Week 1 Practice

Day 1 Calculations

BH3 3-21G Optimization

Day 2 Calculations

BH3 6-31G Optimization

GaBr3 LAN2DZ Optimization

BBr3 6-31G Optimization

BH3 6-31G Frequency analysis

GaBr3 LANL2DZ Frequency analysis

Molecular Orbitals of BH3

NH3 6-31G analysis

Ammonia-Borane Analysis

Tetra-Butyl Ammonium Ion Analysis

BH₃ 3-21G Optimization

BH₃ 6-31G Optimization

GaBr₃ LAN2DZ Optimization

BBr₃ 6-31G Optimization

BH₃ 6-31G Frequency analysis

GaBr₃ LANL2DZ Frequency analysis

Molecular Orbitals of BH₃

NH₃ 6-31G analysis