Rep:Mod:LIUXYLANA2
Program used: Gaussview 5.0.9
Week 1:Optimisation and Analysis of BH3, TlBr3, BBr3, NH3 and NH3BH3
Create and optimise Molecule: BH3 using basis set: 3-21G
Draw out the BH3 and change bond length to 1.5 angstrom.
Optimisation was done on the previously created BH3 molecule using OPT calculation with method: DFT; B3LYP and basis set: 3-21G.(Keywords: # opt b3lyp/3-21g geom=connectivity)
Results present as follow:
BH3 Optimisation Summary Table
| File Name | xlBH3_OPTIMISING_A_MOLECULE_RE |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 3-21G |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -26.46226338 a.u. |
| RMS Gradient Norm | 0.00020672 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3h |
| Job CPU Time | 0 days 0 hours 0 minutes 37.0 seconds |
Optimised Bond Length and Bond Angle for BH3
Optimised B-H bond distance 1.19349 angstrom.
Optimised H-B-H bond angle 120 degree.
Optimisation Log File of BH3
The optimisation file is linked to here.
Item Table for BH3 Optimisation
Item Value Threshold Converged?
Maximum Force 0.000413 0.000450 YES
RMS Force 0.000271 0.000300 YES
Maximum Displacement 0.001610 0.001800 YES
RMS Displacement 0.001054 0.001200 YES
Predicted change in Energy=-1.071764D-06
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1935 -DE/DX = 0.0004 !
! R2 R(1,3) 1.1935 -DE/DX = 0.0004 !
! R3 R(1,4) 1.1935 -DE/DX = 0.0004 !
! 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
Discussion
Converged forces and displacements for BH3.
Equal bond length(B-H) and bond angle(H-B-H), matched with the D3h point group(same chemical environment of bonds).
3-21G basis set was used to provide a quick but low accuracy calculation. Further optimisation see next step.
Further optimisation of BH3 using basis set: 6-31G(d,p)
Open the optimised log file from last step. Further optimisation was done using OPT calculation with method: DFT; B3LYP and a higher level basis set: 6-31G(d,p).(Keywords: # opt b3lyp/3-21g geom=connectivity)
Results present as follow:
BH3 Optimisation Summary Table
| File Name | xlBH3_OPTIMISING_A_MOLECULE_RE_BASISSET |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -26.61532252 a.u. |
| RMS Gradient Norm | 0.00021672 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3H |
| Job CPU Time | 0 days 0 hours 0 minutes 17.0 seconds |
Optimised Bond Length and Bond Angle for BH3
Optimised B-H bond distance 1.19143 angstrom.
Optimisd H-B-H bond angle 120 degree.
Optimisation Log File of BH3
The optimisation file is linked to here
Item Table for BH3 Optimisation
Item Value Threshold Converged?
Maximum Force 0.000433 0.000450 YES
RMS Force 0.000284 0.000300 YES
Maximum Displacement 0.001702 0.001800 YES
RMS Displacement 0.001114 0.001200 YES
Predicted change in Energy=-1.189019D-06
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1914 -DE/DX = 0.0004 !
! R2 R(1,3) 1.1914 -DE/DX = 0.0004 !
! R3 R(1,4) 1.1914 -DE/DX = 0.0004 !
! 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 !
--------------------------------------------------------------------------------
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Optimistion Total Energy and RMS Gradient of BBH3
Discussion
Converged forces and displacements for BH3.
Equal bond length(B-H) and bond angle(H-B-H), matched with the D3h point group(same chemical environment of bonds).
6-31G(d,p) basis set gave a better accuracy.
Comparison of Energies of BH3
Change in the energy was observed comparing two calculations using different basis set.
| Basis Set | Energy (a.u.) |
| 3-21G | -26.46226338 |
| 6-21G(d,p) | -26.61532252 |
| Difference in Energy | 0.15305914 |
By using 6-31G(d,p) basis set, the optimised system was 0.15305914 a.u.(401.85680268 kJ/mol) lower in energy. This is large compared to 'C-C' bond(348kJ/mol).
Create and optimise Molecule: TlBr3 using basis set: LanL2DZ
Draw out the TlBr3 trigonal planar and restrict its symmetry to point group: D3h and increase the tolerance to 'Very tight (0.0001)'.
Optimisation was done using OPT calculation with method: DFT; B3LYP and basis set: LanL2DZ (medium level basis set: D95V on first row atoms and Los Alamos ECP on heavier elements).(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Run calculation using HPC service.
Results present as follow:
TlBr3 Optimisation "D-space" File
The optimisation "D-space" file is linked to DOI:10042/21837
TlBr3 Optimisation Summary Table
| File Name | xlTlBr3_opt_output |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | LANL2DZ |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -91.21812851 a.u. |
| RMS Gradient Norm | 0.00000090 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3H |
| Job CPU Time | 0 days 0 hours 0 minutes 37.4 seconds |
Optimised Bond Length and Bond Angle for TlBr3
Optimised Tl-Br bond distance 2.65095 angstrom.
Optimisd Br-Tl-Br bond angle 120 degree.
Literature[1] bond length: 2.512 angstroms.(percentage difference 5.5%)
- ↑ [1] J. Glaser, G. Johansson. Acta Chemica Scandinavica, 1982, 36a, Pp. 125-135. .
Optimisation Log File of TlBr3
The optimisation file is linked to here
Item Table for TlBr3 Optimisation
Item Value Threshold Converged?
Maximum Force 0.000002 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000022 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-6.084030D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 2.651 -DE/DX = 0.0 !
! R2 R(1,3) 2.651 -DE/DX = 0.0 !
! R3 R(1,4) 2.651 -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 !
--------------------------------------------------------------------------------
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Discussion
Converged forces and displacements for TlBr3.
Equal bond length(B-H) and bond angle(H-B-H), matched with the D3h point group(same chemical environment of bonds).
Create and optimise Molecule: BBr3
Open 6-31G(d,p) optimised log file for BH3 and change 'H' to 'Br'.
Optimisation was done using OPT calculation with method: DFT; B3LYP, basis set: GEN and additional keywords 'pseudo=read gfinput'. ( Keywords: # opt b3lyp/gen nosymm geom=connectivity gfinput pseudo=cards)Save and open the saved copy. Go to the results tab and select view file, insert:
B 0 6-31G(d,p) **** Br 0 LanL2DZ **** Br 0 LanL2DZ
to the bottom section.
Run calculation using HPC service.
Results present as follow:
BBr3 Optimisation "D-space" File
The optimisation "D-space" file is linked toDOI:10042/21866 .
BBr3 Optimisation Summary Table
| File Name | log_66353 |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | Gen |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -64.436452961 a.u. |
| RMS Gradient Norm | 0.00000382 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3H |
| Job CPU Time | 0 days 0 hours 0 minutes 36.0 seconds |
Optimised Bond Length and Bond Angle for BBr3
Optimised B-Br bond distance 1.93396 angstrom.
Optimisd Br-B-Br bond angle 120 degree.
Optimisation Log File of BBr3
The optimisation file is linked to here
Item Table for BBr3 Optimisation
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026780D-10
Optimization completed.
-- Stationary point found.
----------------------------
! 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) 120.0 -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
Discussion
Converged forces and displacements for BBr3.
Equal bond length(B-Br) and bond angle(Br-B-Br), matched with the D3h point group(same chemical environment of bonds).
Analysis: BH3, BBr3, and TlBr3 Bond Distance and Bond Angle
| Molecule | Bond Distances | Bond Angle |
| BH3 | 1.19143 angstrom | 120 degree |
| BBr3 | 1.93396 angstrom | 120 degree |
| TlBr3 | 2.65095 angstrom | 120 degree |
For all BH3, BBr3, and TlBr3, trigonal planar structure were observed(with 120 degrees bond angles and D3h symmetry). Therefore, change in ligands and central atom will not affect the bond angle as long as the symmetry does not change.
Bond length increases down the table as both the size of ligand and central atom increases(more electrons).
In Gaussview, bonding with distance that is higher the the calculated value,hence, weaker them expected bonds, are not shown. At that point, the interaction is considered to be too low to be considered as a bond but this doesn't mean there is no interactions between atoms.
Frequency analysis for BH3
Open the file: 6-31G(d,p) BH3 optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p). (Keywords: # freq b3lyp/6-31g(d,p) nosymm geom=connectivity)
Run calculation using HPC service.
Results present as follow:
BH3 Frequency Summary Table
| File Name | XLBH3_FREQUENCY |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -26.61532252a.u. |
| RMS Gradient Norm | 0.00021669 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3H |
| Job CPU Time | 0 days 0 hours 0 minutes 12.0 seconds |
Frequency Analysis Log File of BH3
The frequency analysis file is linked to here
Item Table for BH3 Frequency Analysis
Low frequencies --- -70.3431 -69.5542 -69.5540 -0.0055 0.0695 0.1595
Low frequencies --- 1161.4019 1212.1084 1212.1111
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1161.4019 1212.1084 1212.1111
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9959 0.9584 0.9584
IR Inten -- 92.7103 13.9813 13.9849
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00
4 5 6
A1' E' E'
Frequencies -- 2587.8127 2721.5176 2721.5188
Red. masses -- 1.0078 1.1273 1.1273
Frc consts -- 3.9765 4.9196 4.9196
IR Inten -- 0.0000 126.1376 126.1280
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.00 0.11 0.00 0.00 0.00 0.11 0.00
2 1 0.00 0.58 0.00 0.02 0.00 0.00 0.00 -0.81 0.00
3 1 0.50 -0.29 0.00 -0.60 0.36 0.00 0.36 -0.19 0.00
4 1 -0.50 -0.29 0.00 -0.60 -0.36 0.00 -0.36 -0.19 0.00
Vibration Modes of BH3
| Number | Form of Vibration | Frequency | Intensity | Symmetry D3h Point Group |
| 1 |  Wagging Mode, 3 H atoms always in the same plane |
1161.40 | 92.7103 | a2 |
| 2 |  Symmetrical Stretching, 2 H atoms coming close |
1121.11 | 13.9813 | e' |
| 3 |  Rocking Mode, with 2 H atoms moving anticlockwise and the other moving clockwise. |
1121.11 | 13.9849 | e' |
| 4 |  Symmetric Stretching, along B-H bonds |
2587.81 | 0.0000 | a1' |
| 5 |  Asymmetrical Stretching, 2 H atoms. The other H atom remains unmoved. |
2721.52 | 126.1376 | e' |
| 6 |  Symmetrical Stretching, 2 H atoms. The other H atom stretch along B-H bond. |
2721.52 | 126.1280 | e' |
IR Spectrum of BH3
The IR spectrum was shown as follow:
Only three out of six calculated peaks were observed in the IR spectrum. There is a few reasons for that:
1. Degenerate energy level(or very close in energy) combine to produce single peak.(Mode 2&3/5&6)
2. Some vibration modes have very low intensity(no/very small overall dipole) hence cannot be observed. (Mode 4)
Frequency analysis for TlBr3
Open the file: 6-31G(d,p) TlBr3 optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: LanL2DZ.(Keywords: # freq b3lyp/LanL2DZ nosymm geom=connectivity)
Run calculation using HPC service .
Results present as follow:
TlBr3 Frequency Analysis "D-space" File
The frequency analysis "D-space" file is linked to DOI:10042/21839
TlBr3 Frequency Summary Table
| File Name | Xllog_66236 |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | LANL2DZ |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -91.21812851 a.u. |
| RMS Gradient Norm | 0.00000088 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3H |
| Job CPU Time | 0 days 0 hours 0 minutes 28.3 seconds |
Frequency Analysis Log File of TlBr3
The frequency analysis file is linked to here
Item Table for TlBr3 Frequency Analysis
Low frequencies --- -3.4213 -0.0026 -0.0004 0.0015 3.9367 3.9367
Low frequencies --- 46.4289 46.4292 52.1449
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
E' E' A2"
Frequencies -- 46.4289 46.4292 52.1449
Red. masses -- 88.4613 88.4613 117.7209
Frc consts -- 0.1124 0.1124 0.1886
IR Inten -- 3.6867 3.6867 5.8466
Atom AN X Y Z X Y Z X Y Z
1 81 0.00 0.28 0.00 -0.28 0.00 0.00 0.00 0.00 0.55
2 35 0.00 0.26 0.00 0.74 0.00 0.00 0.00 0.00 -0.48
3 35 0.43 -0.49 0.00 -0.01 -0.43 0.00 0.00 0.00 -0.48
4 35 -0.43 -0.49 0.00 -0.01 0.43 0.00 0.00 0.00 -0.48
4 5 6
A1' E' E'
Frequencies -- 165.2685 210.6948 210.6948
Red. masses -- 78.9183 101.4032 101.4032
Frc consts -- 1.2700 2.6522 2.6522
IR Inten -- 0.0000 25.4830 25.4797
Atom AN X Y Z X Y Z X Y Z
1 81 0.00 0.00 0.00 0.42 0.00 0.00 0.00 0.42 0.00
2 35 0.00 -0.58 0.00 0.01 0.00 0.00 0.00 -0.74 0.00
3 35 0.50 0.29 0.00 -0.55 -0.32 0.00 -0.32 -0.18 0.00
4 35 -0.50 0.29 0.00 -0.55 0.32 0.00 0.32 -0.18 0.00
Vibration Modes of TlBr3
| Number | Form of Vibration | Frequency | Intensity | Symmetry D3h Point Group |
| 1 |  Symmetrical Stretching, 2 Br atoms coming close. The other H atom stretch along Tl-Br bond |
46.43(lowest normal mode) | 3.6867 | e' |
| 2 |  Rocking Mode, with 2 Br atoms moving anticlockwise and the other moving clockwise. Tl moving in and out the plane. |
46.43 | 3.6867 | e' |
| 3 |  Wagging Mode, 3 Br atoms always in the same plane
|
52.41 | 5.8466 | a2 |
| 4 |  Symmetrical Stretching
|
165.27 | 0.0000 | a1' |
| 5 |  Asymmetrical Stretching, 2 Br atoms. The other remains stationary.
|
210.69 | 25.4830 | e' |
| 6 |  Symmetrical Stretching, 2 Br atoms. The other Br atom stretch along Tl-Br bond.
|
210.69 | 25.4797 | e' |
IR Spectrum of TlBr3
The IR spectrum was shown as follow:
Only two out of six calculated peaks were observed in the IR spectrum. There is a few reasons for that:
1. Degenerate energy level(or very close in energy) combine to produce single peak.(Mode 1,2&3:produce broad peak/5&6)
2. Some vibration modes have very low intensity(no overall dipole) hence cannot be observed. (Mode 4)
IR analysis: BH3 and TlBr3
Although the spectra of BH3 and TlBr3 have very different frequencies, both of them shows 6 peaks with similar vibrations. Similar IR pattern are also observed with two low intensity(the two peaks of TlBr3 overlap to give a broad peak ) at relative low frequency and high intensity peak at relative high frequency.
The reason for very different frequency values is that much less energy is used for BH3 excitation as compared to TlBr3 excitation due to light molecular weight. The degree of effect of molecular weight on different vibration modes are different. Hence, different order of arrangement vibrational modes observed.
Why must you use the same method and basis set for both the optimisation and frequency analysis calculations?
The methods controls the way of calculation i.e. different mathematical approximation used during calculation and basis set controls the orbital used i.e. orbital approximation. Different methods and basis sets would give very different result in energy as shown above in the section 'Comparison of Energies of BH3'. The error margin is too large for the actual comparision. Hence, same method and basis set are used.
What is the purpose of carrying out a frequency analysis?
Optimisation gives lowest energy state(ground state) of the molecule which is obtained by calculation of first derivative. Frequency analysis is a test of second derivative, if all second derivative are positive, the first derivative is guaranteed to be a minimum. Hence, successful optimisation.
Molecular Orbitals of BH3
Open the '.chk file' from optimised of BH3.
Calculation was done using energy calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), NBO: full NBO, and additional keywords:'pop=full'. (Keywords: # b3lyp/6-31g(d,p) pop=(nbo,full) geom=connectivity)
Run calculation using HPC service.
Results present as follow:
BH3 Population Analysis "D-space" File
The population analysis "D-space" file is linked to DOI:10042/21840
BH3 MO Analysis Summary Table
| File Name | log_66265 |
| File Type | .log |
| Calculation Type | SP |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -26.61532252 a.u. |
| RMS Gradient Norm | |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | D3H |
| Job CPU Time | 0 days 0 hours 0 minutes 31.3 seconds |
MO Analysis Log File of BH3
The MO analysis file is linked to here
MOs of BH3
Discussion
Low lying 1s orbital of 'B' do not participate in mixing due to mismatch in energy(E=-6.77112). The second MO diagram corresponded to total bonding(a') of 1s bonding orbital of H3 with 2s orbital of 'B' and have a energy of -0.51267. The next energy level(E=-0.35088) has two degenerate levels, hence, e' symmetry. They are also the HOMO orbitals. The LUMO was a non-bonding orbital(E=-0.06602), corresponded to pz orbital of 'B'. Hence, it has a symmetry and the orbital is perpendicular to the BH3 plane. The next orbital is antibonding. It was produced by antibonding interaction of 1s bonding orbital of H3 with 2s orbital of 'B' and has the same symmetry as its bonding orbital(a'). The next two orbitals are degenerate in energy(e').
The calculated MOs looks very similar to the ones we used while drawing the MO diagrams. Good approximation.
Create and optimise NH3
Draw NH3.
Optimisation was done using OPT calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), and keywords:'nosymm'.(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Run calculation.
Results present as follow:
NH3 Optimisation Summary Table
| File Name | XLNH3_OPT |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -56.55776856 a.u. |
| RMS Gradient Norm | 0.00000885 a.u. |
| Imaginary Freq | |
| Dipole Moment | 1.8464 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 0 minutes 15.0 seconds |
Optimised Bond Length and Bond Angle for NH3
Optimised N-H bond distance 1.01799 angstrom.
Optimisd H-B-H bond angle 105.749 degree.
Optimisation Log File of NH3
The optimisation file is linked to here
Item Table for NH3 Optimisation
Variable Old X -DE/DX Delta X Delta X Delta X New X
(DIIS) (GDIIS) (Total)
R1 1.92368 0.00000 0.00000 -0.00001 -0.00001 1.92367
R2 1.92369 0.00000 0.00000 -0.00001 -0.00001 1.92368
R3 1.92373 -0.00002 0.00000 -0.00005 -0.00005 1.92368
A1 1.84553 0.00001 -0.00001 0.00008 0.00007 1.84561
A2 1.84566 -0.00001 -0.00001 -0.00005 -0.00006 1.84560
A3 1.84565 -0.00001 -0.00001 -0.00005 -0.00006 1.84559
D1 -1.95238 0.00000 0.00002 -0.00006 -0.00003 -1.95241
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
Predicted change in Energy=-1.629730D-09
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7413 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7486 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7479 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8631 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Discussion
Converged forces and displacements
Frequency analysis for NH3
Open the file: 6-31G(d,p) NH3 optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p). Run calculation using HPC service.
Results present as follow:
NH3 Frequency Summary Table
| File Name | XLNH3_FRE |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -56.55776856 a.u. |
| RMS Gradient Norm | 0.00000881 a.u. |
| Imaginary Freq | |
| Dipole Moment | 1.8464 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 0 minutes 11.0 seconds |
Frequency Analysis Log File of NH3
The frequency analysis file is linked to here
Item Table for NH3 Frequency Analysis
Low frequencies --- -30.7295 -0.0018 -0.0012 -0.0011 20.1705 28.2664
Low frequencies --- 1089.5535 1694.1244 1694.1856
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- 1089.5535 1694.1244 1694.1856
Red. masses -- 1.1800 1.0644 1.0644
Frc consts -- 0.8253 1.8000 1.8001
IR Inten -- 145.4405 13.5558 13.5560
Atom AN X Y Z X Y Z X Y Z
1 7 0.12 0.00 0.00 0.00 -0.02 -0.06 0.00 0.06 -0.02
2 1 -0.53 -0.21 0.00 -0.07 -0.04 0.73 0.25 0.14 0.20
3 1 -0.53 0.11 0.18 0.25 -0.24 -0.03 -0.07 -0.62 0.40
4 1 -0.53 0.11 -0.18 -0.18 0.52 0.18 -0.18 -0.41 -0.36
4 5 6
A A A
Frequencies -- 3460.9818 3589.3998 3589.5230
Red. masses -- 1.0272 1.0883 1.0883
Frc consts -- 7.2496 8.2615 8.2621
IR Inten -- 1.0593 0.2700 0.2709
Atom AN X Y Z X Y Z X Y Z
1 7 -0.04 0.00 0.00 0.00 -0.04 0.07 0.00 0.07 0.04
2 1 0.18 -0.55 0.00 -0.15 0.35 0.02 0.27 -0.66 0.01
3 1 0.18 0.27 0.47 -0.16 -0.22 -0.34 -0.26 -0.31 -0.56
4 1 0.18 0.27 -0.48 0.31 0.38 -0.65 -0.01 0.01 0.03
Vibration Modes of NH3
| Number | Form of Vibration | Frequency | Intensity | Symmetry D3h Point Group |
| 1 |  Wagging Mode, 3 H atoms always in the same plane |
1089.55 | 145.4405 | a |
| 2 |  Rocking Mode, with 2 H atoms moving anticlockwise and the other moving clockwise |
1694.12 | 13.5558 | a |
| 3 |  Rocking Mode, with 2 H atoms moving clockwise and the other moving anticlockwise |
1694.19 | 13.5560 | a |
| 4 |  Symmetric Stretching, along N-H bonds |
3460.98 | 1.0593 | a |
| 5 |  Symmetrical Stretching, 2 H atoms. The other H atom stretch along N-H bond. |
3589.40 | 0.2700 | a |
| 6 |  symmetrical Stretching, 2 H atoms. The other H atom remains unmoved. |
3589.52 | 0.2709 | a |
IR Spectrum of NH3
The IR spectrum was shown as follow:
Molecular Orbitals of NH3
Open the '.chk file' from optimised of NH3.
Calculation was done using energy calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), NBO: full NBO, and additional keywords:'pop=full'. (Keywords: # b3lyp/6-31g(d,p) pop=(nbo,full) geom=connectivity)
Run calculation.
Results present as follow:
NH3 MO Analysis Summary Table
| File Name | log_66264 |
| File Type | .log |
| Calculation Type | SP |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -56.55776856 a.u. |
| RMS Gradient Norm | |
| Imaginary Freq | |
| Dipole Moment | 1.8464 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 0 minutes 31.6 seconds |
MO Analysis Log File of NH3
The MO analysis file is linked to [[Media:Xllog 66264.log | here]
MOs of NH3
MOs of NH3:
Discussion
The MO of NH3 was derived from correlation diagram of BH3.
The symmetry is C2v as found from the point group analysis rather than the calculated C1.
The 1e' and 3a1' of the former BH3 orbital has raise in energy and become 1e and 4a1 respectively, whereas 1a2 and 2e' have been stablised and become 3a1 and 2e.
NBO Analysis of NH3
select type: NBO
Charge Distribution by Colour(range between -1 and 1)
Charge Distribution by Numbers
Ammonia-Borane
Optimisation of NH3BH3
Draw out the NH3BH3.
Optimisation was done on the previously created NH3BH3 molecule using OPT calculation with method: DFT; B3LYP and basis set: 6-21G(d,p).(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Results present as follow:
NH3BH3 Optimisation Summary Table
| File Name | XLNH3BH3_OPT |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -83.22468958 a.u. |
| RMS Gradient Norm | 0.00005841 a.u. |
| Imaginary Freq | |
| Dipole Moment | 5.5651 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 1 minutes 29.0 seconds. |
Optimised Bond Length and Bond Angle for NH3BH3
Optimised B-H bond distance 1.21005 angstrom. Optimised N-H bond distance 1.01860 angstrom. Optimised H-B-H bond angle 113.874 degree. Optimised H-N-H bond angle 107.870 degree.
Optimisation Log File of NH3BH3
The optimisation file is linked to here
Item Table for NH3BH3 Optimisation
Item Value Threshold Converged?
Maximum Force 0.000124 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.000660 0.001800 YES
RMS Displacement 0.000304 0.001200 YES
Predicted change in Energy=-1.649776D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,8) 1.21 -DE/DX = -0.0001 !
! R2 R(2,8) 1.21 -DE/DX = -0.0001 !
! R3 R(3,8) 1.21 -DE/DX = -0.0001 !
! R4 R(4,7) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,7) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,7) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(4,7,5) 107.8698 -DE/DX = 0.0 !
! A2 A(4,7,6) 107.8683 -DE/DX = 0.0 !
! A3 A(4,7,8) 111.0271 -DE/DX = 0.0 !
! A4 A(5,7,6) 107.87 -DE/DX = 0.0 !
! A5 A(5,7,8) 111.0319 -DE/DX = 0.0 !
! A6 A(6,7,8) 111.0285 -DE/DX = 0.0 !
! A7 A(1,8,2) 113.8754 -DE/DX = 0.0 !
! A8 A(1,8,3) 113.8742 -DE/DX = 0.0 !
! A9 A(1,8,7) 104.5931 -DE/DX = 0.0 !
! A10 A(2,8,3) 113.8743 -DE/DX = 0.0 !
! A11 A(2,8,7) 104.5962 -DE/DX = 0.0 !
! A12 A(3,8,7) 104.6001 -DE/DX = 0.0 !
! D1 D(4,7,8,1) 179.998 -DE/DX = 0.0 !
! D2 D(4,7,8,2) -60.0028 -DE/DX = 0.0 !
! D3 D(4,7,8,3) 59.9984 -DE/DX = 0.0 !
! D4 D(5,7,8,1) -60.001 -DE/DX = 0.0 !
! D5 D(5,7,8,2) 59.9983 -DE/DX = 0.0 !
! D6 D(5,7,8,3) 179.9994 -DE/DX = 0.0 !
! D7 D(6,7,8,1) 60.0012 -DE/DX = 0.0 !
! D8 D(6,7,8,2) 180.0005 -DE/DX = 0.0 !
! D9 D(6,7,8,3) -59.9984 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Frequency Analysis of NH3BH3
Open the file: 6-31G(d,p) NH3BH3 optimisation and save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).
Run calculation.
Results present as follow:
NH3BH3 Frequency Analysis Summary Table
| File Name | XLNH3BH3_FRE |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -83.22468952 a.u. |
| RMS Gradient Norm | 0.00005894 a.u. |
| Imaginary Freq | |
| Dipole Moment | 5.5651 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 1 minutes 10.0 seconds |
Frequency Analysis Log File of NH3BH3
The Frequency Analysis file is linked to here
Item Table for NH3BH3 Optimisation
Low frequencies --- 0.0002 0.0005 0.0007 13.9034 20.3728 46.0643
Low frequencies --- 267.6343 632.2396 638.8438
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- 267.6314 632.2394 638.8438
Red. masses -- 1.0078 4.9984 1.0452
Frc consts -- 0.0425 1.1772 0.2513
IR Inten -- 0.0000 14.0306 3.5416
Atom AN X Y Z X Y Z X Y Z
1 1 -0.10 -0.35 -0.01 -0.03 0.02 -0.28 0.09 0.12 -0.23
2 1 0.35 0.09 0.00 0.01 -0.02 -0.30 0.12 0.09 -0.21
3 1 -0.26 0.26 0.01 0.02 0.04 -0.28 0.08 0.05 0.46
4 1 -0.12 -0.43 -0.02 0.00 -0.01 0.36 0.14 0.16 -0.30
5 1 -0.31 0.32 0.01 0.00 -0.01 0.37 0.13 0.09 0.59
6 1 0.43 0.11 0.00 0.00 -0.01 0.35 0.16 0.14 -0.28
7 7 0.00 0.00 0.00 0.00 -0.02 0.36 -0.03 -0.03 0.00
8 5 0.00 0.00 0.00 0.00 0.02 -0.48 -0.02 -0.02 0.00
4 5 6
A A A
Frequencies -- 639.9214 1069.1764 1069.7954
Red. masses -- 1.0452 1.3344 1.3344
Frc consts -- 0.2522 0.8988 0.8998
IR Inten -- 3.5231 40.4903 40.5310
Atom AN X Y Z X Y Z X Y Z
1 1 0.07 -0.09 -0.40 0.06 0.14 -0.34 0.01 -0.08 -0.53
2 1 0.10 -0.09 0.40 0.14 0.07 -0.28 0.08 -0.04 0.56
3 1 0.11 -0.11 -0.02 0.04 -0.01 0.63 0.12 -0.12 -0.04
4 1 0.11 -0.13 -0.50 -0.06 -0.10 0.24 -0.04 0.07 0.38
5 1 0.14 -0.15 -0.02 -0.05 -0.02 -0.45 -0.09 0.09 0.03
6 1 0.14 -0.14 0.51 -0.10 -0.07 0.20 -0.07 0.06 -0.40
7 7 -0.03 0.03 0.00 0.08 0.07 0.00 0.07 -0.08 0.00
8 5 -0.02 0.02 0.00 -0.10 -0.09 0.00 -0.09 0.10 0.00
7 8 9
A A A
Frequencies -- 1196.3509 1203.7904 1203.9079
Red. masses -- 1.1450 1.0609 1.0611
Frc consts -- 0.9656 0.9058 0.9061
IR Inten -- 109.1561 3.4905 3.6271
Atom AN X Y Z X Y Z X Y Z
1 1 -0.17 0.01 0.54 0.23 0.51 -0.17 0.04 0.51 0.24
2 1 0.02 -0.20 0.54 -0.13 -0.18 0.27 0.72 0.14 0.09
3 1 0.12 0.11 0.56 -0.53 0.49 -0.06 0.06 -0.23 -0.26
4 1 0.00 0.00 -0.02 0.00 -0.01 0.01 0.00 -0.01 -0.02
5 1 0.00 0.00 -0.02 0.01 -0.01 0.01 0.00 0.00 0.02
6 1 0.00 0.00 -0.02 0.00 0.00 -0.02 -0.02 0.00 -0.01
7 7 0.00 0.00 -0.02 0.00 -0.01 0.00 -0.01 0.00 0.00
8 5 0.00 0.01 -0.11 0.03 -0.06 0.00 -0.06 -0.03 0.00
10 11 12
A A A
Frequencies -- 1329.3064 1676.3194 1676.4809
Red. masses -- 1.1792 1.0555 1.0556
Frc consts -- 1.2277 1.7475 1.7480
IR Inten -- 113.3275 27.5448 27.5662
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.01
2 1 0.00 0.00 0.00 0.01 0.00 -0.01 -0.01 -0.01 -0.01
3 1 0.00 0.00 0.00 -0.01 0.00 0.01 -0.01 0.01 0.00
4 1 -0.20 0.03 0.53 0.19 0.72 0.05 0.16 0.02 -0.28
5 1 0.15 0.13 0.54 -0.33 0.15 -0.25 -0.42 0.52 0.15
6 1 0.05 -0.23 0.52 0.43 -0.03 0.24 -0.58 -0.24 0.15
7 7 0.00 0.00 -0.11 -0.02 -0.06 0.00 0.06 -0.02 0.00
8 5 0.00 0.00 0.00 0.00 -0.01 0.00 0.01 0.00 0.00
13 14 15
A A A
Frequencies -- 2470.3393 2530.2491 2530.4379
Red. masses -- 1.0218 1.1176 1.1176
Frc consts -- 3.6740 4.2157 4.2163
IR Inten -- 67.2211 231.3528 231.4100
Atom AN X Y Z X Y Z X Y Z
1 1 0.54 -0.16 0.14 0.62 -0.19 0.17 -0.43 0.11 -0.12
2 1 -0.14 0.53 0.17 -0.03 0.05 0.02 -0.19 0.75 0.25
3 1 -0.40 -0.40 0.13 0.50 0.51 -0.17 0.25 0.23 -0.08
4 1 0.00 0.00 -0.01 -0.01 0.00 0.00 0.00 0.00 0.00
5 1 0.00 0.00 -0.01 -0.01 0.00 0.00 0.00 -0.01 0.00
6 1 0.00 0.00 -0.01 0.00 0.00 0.00 0.00 -0.01 0.00
7 7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
8 5 0.00 0.00 -0.04 -0.10 -0.03 0.00 0.03 -0.10 0.00
16 17 18
A A A
Frequencies -- 3462.5296 3579.4421 3579.5459
Red. masses -- 1.0270 1.0921 1.0921
Frc consts -- 7.2545 8.2440 8.2446
IR Inten -- 2.5098 27.9258 27.9297
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00
2 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.01 0.00
3 1 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00
4 1 0.53 -0.15 0.17 0.55 -0.17 0.20 0.49 -0.13 0.18
5 1 -0.39 -0.39 0.16 0.51 0.52 -0.25 -0.18 -0.16 0.08
6 1 -0.14 0.52 0.20 -0.05 0.14 0.06 0.18 -0.71 -0.31
7 7 0.00 0.00 -0.04 -0.07 -0.04 0.00 -0.04 0.07 0.00
8 5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Association Energy Analysis
The association energy is calculate by subtracting the energy of starting materials from the product.
| Molecule | Energy (a.u.) |
| BH3 | -26.61532252 |
| NH3 | -56.55776856 |
| NH3BH3 | -83.22468958 |
Association Energy (A.E)= E(NH3BH3)-E(NH3)-E(BH3)
=-83.22468958-(-56.55776856)-(-26.61532252)
=-0.0515985 a.u. = 135.4718721 kJ/mol
Week2: Optimisation and Analysis of Aromatic Compounds
Benzene
Create and optimise Benzene
Draw out the benzene.
Optimisation was done using OPT calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Run calculation using HPC service.
Results present as follow:
Benzene Optimisation "D-space" File
The optimisation "D-space" file is linked to DOI:10042/21907
Benzene Optimisation Summary Table
[File:XLBZOPTSUM.PNG|right|thumb|300px|Benzene Optimisation Summary Table]]
| File Name | XLlog_66438 |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -232.25820551 a.u. |
| RMS Gradient Norm | 0.00009549 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0000 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 2 minutes 7.7 seconds. |
Optimised Bond Length and Bond Angle for Benzene
Optimised C-H bond distance 1.08606 angstrom.
Optimisd C-C-H bond angle 119.995 degree.
Optimisation Log File of Benzene
The optimisation file is linked to here
Item Table for Benzene Optimisation
Item Value Threshold Converged?
Maximum Force 0.000212 0.000450 YES
RMS Force 0.000085 0.000300 YES
Maximum Displacement 0.000991 0.001800 YES
RMS Displacement 0.000315 0.001200 YES
Predicted change in Energy=-5.157454D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3963 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3961 -DE/DX = 0.0002 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3961 -DE/DX = 0.0002 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3963 -DE/DX = 0.0001 !
! R7 R(3,9) 1.086 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3961 -DE/DX = 0.0002 !
! R9 R(4,10) 1.086 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3963 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 119.9972 -DE/DX = 0.0 !
! A2 A(2,1,7) 119.9949 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0079 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0079 -DE/DX = 0.0 !
! A5 A(1,2,8) 119.9881 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.004 -DE/DX = 0.0 !
! A7 A(2,3,4) 119.9948 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0086 -DE/DX = 0.0 !
! A9 A(4,3,9) 119.9966 -DE/DX = 0.0 !
! A10 A(3,4,5) 119.9972 -DE/DX = 0.0 !
! A11 A(3,4,10) 119.9934 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0094 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0083 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0014 -DE/DX = 0.0 !
! A15 A(6,5,11) 119.9904 -DE/DX = 0.0 !
! A16 A(1,6,5) 119.9946 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0106 -DE/DX = 0.0 !
! A18 A(5,6,12) 119.9948 -DE/DX = 0.0 !
! D1 D(6,1,2,3) -0.0059 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0023 -DE/DX = 0.0 !
! D3 D(7,1,2,3) -180.01 -DE/DX = 0.0 !
! D4 D(7,1,2,8) -0.0019 -DE/DX = 0.0 !
! D5 D(2,1,6,5) -0.0055 -DE/DX = 0.0 !
! D6 D(2,1,6,12) -179.9972 -DE/DX = 0.0 !
! D7 D(7,1,6,5) -180.0013 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.007 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0117 -DE/DX = 0.0 !
! D10 D(1,2,3,9) -179.9914 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0036 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0005 -DE/DX = 0.0 !
! D13 D(2,3,4,5) -0.0062 -DE/DX = 0.0 !
! D14 D(2,3,4,10) -180.0059 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 179.9969 -DE/DX = 0.0 !
! D16 D(9,3,4,10) -0.0028 -DE/DX = 0.0 !
! D17 D(3,4,5,6) -0.0051 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0058 -DE/DX = 0.0 !
! D19 D(10,4,5,6) -180.0055 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0054 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.011 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0027 -DE/DX = 0.0 !
! D23 D(11,5,6,1) -179.9999 -DE/DX = 0.0 !
! D24 D(11,5,6,12) -0.0082 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Discussion
Converged forces and displacements
Frequency analysis for Benzene
Open the file: 6-31G(d,p) benzene optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # freq b3lyp/6-31G(d,p) nosymm geom=connectivity)
Run calculation using HPC service.
Results present as follow:
Benzene Frequency Analysis "D-space" File
The frequency analysis "D-space" file is linked to DOI:10042/21908
Benzene Frequency Summary Table
| File Name | xllog_66441_fre |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -232.25820551 a.u. |
| RMS Gradient Norm | 0.00009549 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0001 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 5 minutes 34.9 seconds. |
Frequency Analysis Log File of Benzene
The frequency analysis file is linked to here
Item Table for Benzene Frequency Analysis
Low frequencies --- -17.2788 -14.5868 -9.6527 0.0003 0.0003 0.0006
Low frequencies --- 413.7971 414.4697 620.8545
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- 413.7971 414.4697 620.8540
Red. masses -- 2.9404 2.9434 6.0705
Frc consts -- 0.2966 0.2979 1.3786
IR Inten -- 0.0000 0.0000 0.0000
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.15 0.00 0.00 0.19 0.23 -0.26 0.00
2 6 0.00 0.00 0.24 0.00 0.00 0.03 0.16 0.05 0.00
3 6 0.00 0.00 -0.09 0.00 0.00 -0.22 0.22 0.19 0.00
4 6 0.00 0.00 -0.15 0.00 0.00 0.19 -0.23 0.26 0.00
5 6 0.00 0.00 0.24 0.00 0.00 0.03 -0.16 -0.05 0.00
6 6 0.00 0.00 -0.09 0.00 0.00 -0.22 -0.22 -0.19 0.00
7 1 0.00 0.00 -0.32 0.00 0.00 0.42 0.30 -0.17 0.00
8 1 0.00 0.00 0.52 0.00 0.00 0.07 -0.20 0.11 0.00
9 1 0.00 0.00 -0.20 0.00 0.00 -0.48 0.30 -0.05 0.00
10 1 0.00 0.00 -0.32 0.00 0.00 0.42 -0.30 0.17 0.00
11 1 0.00 0.00 0.52 0.00 0.00 0.07 0.20 -0.11 0.00
12 1 0.00 0.00 -0.20 0.00 0.00 -0.48 -0.30 0.05 0.00
4 5 6
A A A
Frequencies -- 620.9440 693.3688 718.2383
Red. masses -- 6.0707 1.0848 3.8753
Frc consts -- 1.3791 0.3073 1.1778
IR Inten -- 0.0000 74.2532 0.0000
Atom AN X Y Z X Y Z X Y Z
1 6 0.18 0.04 0.00 0.00 0.00 0.03 0.00 0.00 0.21
2 6 0.03 0.35 0.00 0.00 0.00 0.03 0.00 0.00 -0.21
3 6 -0.27 0.03 0.00 0.00 0.00 0.03 0.00 0.00 0.21
4 6 -0.18 -0.04 0.00 0.00 0.00 0.03 0.00 0.00 -0.21
5 6 -0.03 -0.35 0.00 0.00 0.00 0.03 0.00 0.00 0.21
6 6 0.27 -0.03 0.00 0.00 0.00 0.03 0.00 0.00 -0.21
7 1 -0.06 -0.23 0.00 0.00 0.00 -0.41 0.00 0.00 0.35
8 1 0.11 0.34 0.00 0.00 0.00 -0.41 0.00 0.00 -0.35
9 1 -0.17 -0.24 0.00 0.00 0.00 -0.41 0.00 0.00 0.35
10 1 0.06 0.23 0.00 0.00 0.00 -0.41 0.00 0.00 -0.35
11 1 -0.11 -0.34 0.00 0.00 0.00 -0.41 0.00 0.00 0.35
12 1 0.17 0.24 0.00 0.00 0.00 -0.41 0.00 0.00 -0.35
7 8 9
A A A
Frequencies -- 864.3426 864.5073 973.7668
Red. masses -- 1.2476 1.2475 1.3597
Frc consts -- 0.5491 0.5493 0.7596
IR Inten -- 0.0000 0.0000 0.0000
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.05 0.00 0.00 -0.07 0.00 0.00 0.06
2 6 0.00 0.00 -0.09 0.00 0.00 0.01 0.00 0.00 -0.10
3 6 0.00 0.00 -0.04 0.00 0.00 0.08 0.00 0.00 0.04
4 6 0.00 0.00 0.05 0.00 0.00 0.07 0.00 0.00 0.06
5 6 0.00 0.00 0.09 0.00 0.00 -0.01 0.00 0.00 -0.10
6 6 0.00 0.00 0.04 0.00 0.00 -0.08 0.00 0.00 0.04
7 1 0.00 0.00 0.32 0.00 0.00 0.47 0.00 0.00 -0.34
8 1 0.00 0.00 0.57 0.00 0.00 -0.04 0.00 0.00 0.56
9 1 0.00 0.00 0.25 0.00 0.00 -0.51 0.00 0.00 -0.22
10 1 0.00 0.00 -0.32 0.00 0.00 -0.47 0.00 0.00 -0.34
11 1 0.00 0.00 -0.57 0.00 0.00 0.04 0.00 0.00 0.56
12 1 0.00 0.00 -0.25 0.00 0.00 0.51 0.00 0.00 -0.22
10 11 12
A A A
Frequencies -- 974.1397 1012.6793 1017.9234
Red. masses -- 1.3590 1.2232 6.5554
Frc consts -- 0.7598 0.7391 4.0020
IR Inten -- 0.0000 0.0000 0.0000
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.08 0.00 0.00 -0.06 0.22 -0.19 0.00
2 6 0.00 0.00 -0.01 0.00 0.00 0.06 0.05 0.29 0.00
3 6 0.00 0.00 0.10 0.00 0.00 -0.06 -0.27 -0.10 0.00
4 6 0.00 0.00 -0.08 0.00 0.00 0.06 0.22 -0.19 0.00
5 6 0.00 0.00 -0.01 0.00 0.00 -0.06 0.05 0.29 0.00
6 6 0.00 0.00 0.10 0.00 0.00 0.06 -0.27 -0.10 0.00
7 1 0.00 0.00 0.45 0.00 0.00 0.40 0.22 -0.19 0.00
8 1 0.00 0.00 0.07 0.00 0.00 -0.40 0.05 0.28 0.00
9 1 0.00 0.00 -0.52 0.00 0.00 0.40 -0.27 -0.10 0.00
10 1 0.00 0.00 0.45 0.00 0.00 -0.40 0.22 -0.19 0.00
11 1 0.00 0.00 0.07 0.00 0.00 0.40 0.05 0.28 0.00
12 1 0.00 0.00 -0.52 0.00 0.00 -0.40 -0.27 -0.10 0.00
13 14 15
A A A
Frequencies -- 1019.9280 1066.1247 1066.4791
Red. masses -- 6.0153 1.6852 1.6855
Frc consts -- 3.6868 1.1285 1.1295
IR Inten -- 0.0000 3.3878 3.3887
Atom AN X Y Z X Y Z X Y Z
1 6 -0.21 0.18 0.00 -0.02 -0.09 0.00 -0.10 0.05 0.00
2 6 0.05 0.27 0.00 -0.05 0.08 0.00 0.07 0.08 0.00
3 6 0.26 0.09 0.00 0.11 0.03 0.00 0.01 -0.08 0.00
4 6 0.21 -0.18 0.00 -0.02 -0.09 0.00 -0.10 0.05 0.00
5 6 -0.05 -0.27 0.00 -0.05 0.08 0.00 0.07 0.08 0.00
6 6 -0.26 -0.09 0.00 0.11 0.03 0.00 0.01 -0.08 0.00
7 1 -0.23 0.20 0.00 -0.29 -0.41 0.00 -0.22 -0.08 0.00
8 1 0.06 0.30 0.00 -0.41 0.15 0.00 0.35 0.04 0.00
9 1 0.28 0.10 0.00 0.14 -0.03 0.00 0.16 -0.51 0.00
10 1 0.23 -0.20 0.00 -0.29 -0.41 0.00 -0.22 -0.08 0.00
11 1 -0.05 -0.30 0.00 -0.41 0.15 0.00 0.35 0.04 0.00
12 1 -0.28 -0.10 0.00 0.14 -0.03 0.00 0.16 -0.51 0.00
16 17 18
A A A
Frequencies -- 1179.2886 1202.1376 1202.3607
Red. masses -- 1.0793 1.1338 1.1344
Frc consts -- 0.8844 0.9654 0.9662
IR Inten -- 0.0000 0.0000 0.0000
Atom AN X Y Z X Y Z X Y Z
1 6 -0.02 -0.03 0.00 -0.02 -0.03 0.00 0.03 0.04 0.00
2 6 0.03 -0.01 0.00 0.06 -0.01 0.00 0.01 0.00 0.00
3 6 -0.01 0.03 0.00 -0.01 0.03 0.00 -0.02 0.05 0.00
4 6 -0.02 -0.03 0.00 0.02 0.03 0.00 -0.03 -0.04 0.00
5 6 0.03 -0.01 0.00 -0.06 0.01 0.00 -0.01 0.00 0.00
6 6 -0.01 0.03 0.00 0.01 -0.03 0.00 0.02 -0.05 0.00
7 1 -0.26 -0.31 0.00 -0.21 -0.25 0.00 0.31 0.36 0.00
8 1 0.40 -0.07 0.00 0.56 -0.10 0.00 0.04 0.00 0.00
9 1 -0.14 0.38 0.00 -0.08 0.24 0.00 -0.17 0.49 0.00
10 1 -0.26 -0.31 0.00 0.21 0.25 0.00 -0.31 -0.36 0.00
11 1 0.40 -0.07 0.00 -0.56 0.10 0.00 -0.04 0.00 0.00
12 1 -0.14 0.38 0.00 0.08 -0.23 0.00 0.17 -0.49 0.00
19 20 21
A A A
Frequencies -- 1355.9619 1380.2686 1524.1003
Red. masses -- 6.7084 1.2476 2.0368
Frc consts -- 7.2672 1.4004 2.7876
IR Inten -- 0.0000 0.0000 6.6362
Atom AN X Y Z X Y Z X Y Z
1 6 -0.19 -0.22 0.00 -0.04 -0.05 0.00 0.06 0.13 0.00
2 6 0.29 -0.05 0.00 -0.06 0.01 0.00 0.11 -0.08 0.00
3 6 -0.10 0.28 0.00 -0.02 0.06 0.00 -0.09 -0.01 0.00
4 6 -0.19 -0.22 0.00 0.04 0.05 0.00 0.06 0.13 0.00
5 6 0.29 -0.05 0.00 0.06 -0.01 0.00 0.11 -0.08 0.00
6 6 -0.10 0.28 0.00 0.02 -0.06 0.00 -0.09 -0.01 0.00
7 1 0.19 0.22 0.00 0.26 0.31 0.00 -0.36 -0.35 0.00
8 1 -0.28 0.05 0.00 0.40 -0.07 0.00 -0.43 0.01 0.00
9 1 0.09 -0.27 0.00 0.14 -0.38 0.00 -0.09 -0.10 0.00
10 1 0.18 0.22 0.00 -0.26 -0.31 0.00 -0.36 -0.35 0.00
11 1 -0.28 0.05 0.00 -0.40 0.07 0.00 -0.44 0.01 0.00
12 1 0.09 -0.27 0.00 -0.14 0.38 0.00 -0.09 -0.10 0.00
22 23 24
A A A
Frequencies -- 1524.5138 1652.8850 1653.1307
Red. masses -- 2.0363 5.3941 5.4064
Frc consts -- 2.7883 8.6828 8.7050
IR Inten -- 6.6274 0.0000 0.0000
Atom AN X Y Z X Y Z X Y Z
1 6 0.10 -0.01 0.00 0.18 0.27 0.00 0.17 -0.03 0.00
2 6 -0.10 -0.06 0.00 -0.11 -0.13 0.00 -0.31 0.10 0.00
3 6 -0.04 0.14 0.00 0.02 0.26 0.00 0.18 -0.19 0.00
4 6 0.10 -0.01 0.00 -0.18 -0.27 0.00 -0.17 0.03 0.00
5 6 -0.10 -0.06 0.00 0.11 0.13 0.00 0.31 -0.10 0.00
6 6 -0.04 0.14 0.00 -0.02 -0.26 0.00 -0.18 0.19 0.00
7 1 -0.06 -0.23 0.00 -0.29 -0.28 0.00 0.05 -0.19 0.00
8 1 0.30 -0.15 0.00 0.07 -0.18 0.00 0.40 -0.03 0.00
9 1 0.19 -0.50 0.00 0.21 -0.24 0.00 0.02 0.32 0.00
10 1 -0.06 -0.23 0.00 0.29 0.28 0.00 -0.05 0.19 0.00
11 1 0.30 -0.15 0.00 -0.08 0.18 0.00 -0.40 0.03 0.00
12 1 0.19 -0.50 0.00 -0.21 0.24 0.00 -0.01 -0.31 0.00
25 26 27
A A A
Frequencies -- 3175.3330 3184.7437 3185.0386
Red. masses -- 1.0834 1.0876 1.0876
Frc consts -- 6.4360 6.4992 6.5004
IR Inten -- 0.0030 0.0001 0.0001
Atom AN X Y Z X Y Z X Y Z
1 6 0.03 -0.02 0.00 -0.02 0.02 0.00 -0.03 0.03 0.00
2 6 0.01 0.03 0.00 -0.01 -0.05 0.00 0.00 0.00 0.00
3 6 -0.03 -0.01 0.00 0.02 0.01 0.00 -0.04 -0.01 0.00
4 6 0.03 -0.02 0.00 0.02 -0.02 0.00 0.03 -0.03 0.00
5 6 0.01 0.03 0.00 0.01 0.05 0.00 0.00 0.00 0.00
6 6 -0.03 -0.01 0.00 -0.03 -0.01 0.00 0.04 0.01 0.00
7 1 -0.31 0.26 0.00 0.19 -0.17 0.00 0.39 -0.33 0.00
8 1 -0.08 -0.41 0.00 0.11 0.57 0.00 0.00 0.04 0.00
9 1 0.38 0.13 0.00 -0.30 -0.11 0.00 0.45 0.16 0.00
10 1 -0.31 0.26 0.00 -0.19 0.17 0.00 -0.39 0.33 0.00
11 1 -0.07 -0.40 0.00 -0.11 -0.57 0.00 -0.01 -0.04 0.00
12 1 0.38 0.14 0.00 0.30 0.11 0.00 -0.45 -0.16 0.00
28 29 30
A A A
Frequencies -- 3200.4346 3200.6717 3211.1365
Red. masses -- 1.0953 1.0953 1.0997
Frc consts -- 6.6099 6.6109 6.6811
IR Inten -- 46.6015 46.5711 0.0003
Atom AN X Y Z X Y Z X Y Z
1 6 -0.02 0.01 0.00 0.03 -0.03 0.00 0.03 -0.02 0.00
2 6 0.01 0.05 0.00 0.00 0.00 0.00 -0.01 -0.04 0.00
3 6 0.03 0.01 0.00 0.04 0.02 0.00 -0.04 -0.01 0.00
4 6 -0.02 0.01 0.00 0.03 -0.03 0.00 -0.03 0.02 0.00
5 6 0.01 0.05 0.00 0.00 0.00 0.00 0.01 0.04 0.00
6 6 0.03 0.01 0.00 0.04 0.02 0.00 0.04 0.01 0.00
7 1 0.20 -0.17 0.00 -0.39 0.34 0.00 -0.31 0.26 0.00
8 1 -0.10 -0.56 0.00 0.01 0.03 0.00 0.07 0.40 0.00
9 1 -0.30 -0.10 0.00 -0.45 -0.16 0.00 0.39 0.14 0.00
10 1 0.20 -0.17 0.00 -0.39 0.34 0.00 0.31 -0.27 0.00
11 1 -0.10 -0.56 0.00 0.01 0.03 0.00 -0.07 -0.40 0.00
12 1 -0.30 -0.10 0.00 -0.45 -0.16 0.00 -0.38 -0.14 0.00
MO Analysis of Benzene
Open the '.chk file' from optimised benzene.
Calculation was done using energy calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), NBO: full NBO, and additional keywords:'pop=full'.
Run calculation using HPC service.
Results present as follow:
Benzene Population Analysis "D-space" File
The Population Analysis "D-space" file is linked to DOI:10042/21911
MOs of Benzene
The core orbitals are not considered in this analysis as they are an order of magnitude different in energy(about 10 time more negative) as compared to the ones sigma and pi interactions. Those Low lying orbitals do not participate in mixing due to mismatch in energy.
The seventh level is the first orbital generated from the mixing, it has the lowest energy, hence, total bonding(E=-0.84677). It is the result of the total bonding interactions of six 2s orbitals. The MO produced has the snowflake shape rather than in LCAO approximation, 6 balls joined by sticks. This is because orbitals are essentially electron clouds. Bonds formed by paired electrons are not sticks holding atoms together, but spacial interactions.
All levels between level seven to level seventeen are caused by different combination of px and py orbitals.
Level seventeen(E=-0.35998) is the first molecular orbital caused by pz orbital mixing. The total bonding interaction between those six pz orbital produced two disks of charges with the negative charge located above the six carbon plane and the positive disk below, in other words, delocalisation. The calculated MO illustrates the idea of pi electrons interacting with each other in those two plane which is widely known as the origin of aromaticity. The LCAO is not good enough to demonstrate the delocalisation in this case, as it does not shown the pi disks.
Energy level 20 and 21 are degenerate levels. They are the HOMO orbitals(E=-0.24691. The HOMO are also caused by pz interactions forming MOs with shapes very similar to dxy. The LUMO were also degenerate(level 22 and 23). Causing by pz interactions, LUMO(E=-0.00268) has MOs with shapes very similar to fxyz.
NBO Analysis of Benzene
select type: NBO
Charge Distribution by Colour(range between -1 and 1)
Charge Distribution by Numbers
Boratabenzene
Create and optimise Boratabenzene
Draw out the boratabenzene.
Optimisation was done using OPT calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Run calculation using HPC service.
Results present as follow:
Boratabenzene Optimisation "D-space" File
The optimisation "D-space" file is linked to DOI:10042/21918
Boratabenzene Optimisation Summary Table
| File Name | XLlog_66484 |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | -1 |
| Spin | Singlet |
| E(RB3LYP) | -219.02052984 a.u. |
| RMS Gradient Norm | 0.00015840 a.u. |
| Imaginary Freq | |
| Dipole Moment | 2.8465 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 3 minutes 59.2 seconds. |
Optimised Bond Length and Bond Angle for Boratabenzene
Optimised B-H bond distance 1.21849 angstrom.
Optimised C-H bond distance 1.09698; 1.09677; 1.09165 angstrom.
Optimisd C-B-H bond angle 122.448 degree.
Optimisd B-C-H bond angle 123.965 degree.
Optimisd C-C-H bond angle 117.437;119.773 degree.
Optimisation Log File of Boratabenzene
The optimisation file is linked to here
Item Table for Boratabenzene Optimisation
Item Value Threshold Converged?
Maximum Force 0.000159 0.000450 YES
RMS Force 0.000069 0.000300 YES
Maximum Displacement 0.000878 0.001800 YES
RMS Displacement 0.000326 0.001200 YES
Predicted change in Energy=-6.589451D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.4053 -DE/DX = -0.0001 !
! R2 R(1,5) 1.3989 -DE/DX = 0.0 !
! R3 R(1,6) 1.0968 -DE/DX = 0.0001 !
! R4 R(2,3) 1.4053 -DE/DX = -0.0001 !
! R5 R(2,7) 1.0916 -DE/DX = -0.0001 !
! R6 R(3,4) 1.3989 -DE/DX = 0.0 !
! R7 R(3,8) 1.0968 -DE/DX = 0.0001 !
! R8 R(4,9) 1.097 -DE/DX = -0.0001 !
! R9 R(4,12) 1.5137 -DE/DX = 0.0001 !
! R10 R(5,11) 1.097 -DE/DX = -0.0001 !
! R11 R(5,12) 1.5138 -DE/DX = 0.0001 !
! R12 R(10,12) 1.2185 -DE/DX = 0.0 !
! A1 A(2,1,5) 122.138 -DE/DX = 0.0001 !
! A2 A(2,1,6) 117.4354 -DE/DX = 0.0 !
! A3 A(5,1,6) 120.4266 -DE/DX = -0.0002 !
! A4 A(1,2,3) 120.4508 -DE/DX = -0.0001 !
! A5 A(1,2,7) 119.7734 -DE/DX = 0.0001 !
! A6 A(3,2,7) 119.7758 -DE/DX = 0.0001 !
! A7 A(2,3,4) 122.1395 -DE/DX = 0.0001 !
! A8 A(2,3,8) 117.4371 -DE/DX = 0.0 !
! A9 A(4,3,8) 120.4234 -DE/DX = -0.0002 !
! A10 A(3,4,9) 115.9493 -DE/DX = 0.0001 !
! A11 A(3,4,12) 120.0806 -DE/DX = -0.0001 !
! A12 A(9,4,12) 123.9701 -DE/DX = -0.0001 !
! A13 A(1,5,11) 115.9535 -DE/DX = 0.0001 !
! A14 A(1,5,12) 120.0812 -DE/DX = -0.0001 !
! A15 A(11,5,12) 123.9654 -DE/DX = -0.0001 !
! A16 A(4,12,5) 115.1098 -DE/DX = 0.0 !
! A17 A(4,12,10) 122.4482 -DE/DX = 0.0 !
! A18 A(5,12,10) 122.4419 -DE/DX = 0.0 !
! D1 D(5,1,2,3) 0.0057 -DE/DX = 0.0 !
! D2 D(5,1,2,7) 180.0027 -DE/DX = 0.0 !
! D3 D(6,1,2,3) 180.0038 -DE/DX = 0.0 !
! D4 D(6,1,2,7) 0.0008 -DE/DX = 0.0 !
! D5 D(2,1,5,11) -180.0018 -DE/DX = 0.0 !
! D6 D(2,1,5,12) -0.001 -DE/DX = 0.0 !
! D7 D(6,1,5,11) 0.0002 -DE/DX = 0.0 !
! D8 D(6,1,5,12) 180.001 -DE/DX = 0.0 !
! D9 D(1,2,3,4) -0.0074 -DE/DX = 0.0 !
! D10 D(1,2,3,8) -180.0016 -DE/DX = 0.0 !
! D11 D(7,2,3,4) -180.0044 -DE/DX = 0.0 !
! D12 D(7,2,3,8) 0.0014 -DE/DX = 0.0 !
! D13 D(2,3,4,9) 180.0049 -DE/DX = 0.0 !
! D14 D(2,3,4,12) 0.0042 -DE/DX = 0.0 !
! D15 D(8,3,4,9) -0.0011 -DE/DX = 0.0 !
! D16 D(8,3,4,12) -180.0018 -DE/DX = 0.0 !
! D17 D(3,4,12,5) 0.0005 -DE/DX = 0.0 !
! D18 D(3,4,12,10) -180.0 -DE/DX = 0.0 !
! D19 D(9,4,12,5) -180.0003 -DE/DX = 0.0 !
! D20 D(9,4,12,10) -0.0008 -DE/DX = 0.0 !
! D21 D(1,5,12,4) -0.002 -DE/DX = 0.0 !
! D22 D(1,5,12,10) -180.0015 -DE/DX = 0.0 !
! D23 D(11,5,12,4) 179.9989 -DE/DX = 0.0 !
! D24 D(11,5,12,10) -0.0006 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Discussion
Converged forces and displacements
Frequency analysis for Boratabenzene
Open the file: 6-31G(d,p) boratabenzene optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # freq b3lyp/6-31G(d,p) nosymm geom=connectivity)
Run calculation using HPC service.
Results present as follow:
Boratabenzene Frequency Analysis "D-space" File
The frequency analysis "D-space" file is linked to DOI:10042/22004
Boratabenzene Frequency Summary Table
| File Name | log_66533_XLFRE |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | -1 |
| Spin | Singlet |
| E(RB3LYP) | -219.02052984 a.u. |
| RMS Gradient Norm | 0.00015838 a.u. |
| Imaginary Freq | |
| Dipole Moment | 2.8465 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 5 minutes 33.6 seconds. |
Frequency Analysis Log File of Boratabenzene
The frequency analysis file is linked to here
Item Table for Boratabenzene Frequency Analysis
Low frequencies --- -13.1275 -0.0008 0.0008 0.0008 15.0447 18.1653
Low frequencies --- 371.3454 404.2334 565.2534
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- 371.3453 404.2327 565.2534
Red. masses -- 2.6885 3.2177 5.7648
Frc consts -- 0.2184 0.3098 1.0852
IR Inten -- 2.3000 0.0000 0.1576
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.08 0.00 0.00 0.22 0.23 -0.21 0.00
2 6 0.00 0.00 0.21 0.00 0.00 0.00 0.14 0.00 0.00
3 6 0.00 0.00 -0.08 0.00 0.00 -0.22 0.23 0.22 0.00
4 6 0.00 0.00 -0.14 0.00 0.00 0.23 -0.22 0.21 0.00
5 6 0.00 0.00 -0.14 0.00 0.00 -0.23 -0.22 -0.21 0.00
6 1 0.00 0.00 -0.20 0.00 0.00 0.52 0.31 -0.08 0.00
7 1 0.00 0.00 0.38 0.00 0.00 0.00 -0.21 0.00 0.00
8 1 0.00 0.00 -0.20 0.00 0.00 -0.52 0.31 0.08 0.00
9 1 0.00 0.00 -0.35 0.00 0.00 0.36 -0.34 -0.06 0.00
10 1 0.00 0.00 0.62 0.00 0.00 0.00 0.29 0.00 0.00
11 1 0.00 0.00 -0.35 0.00 0.00 -0.36 -0.34 0.06 0.00
12 5 0.00 0.00 0.25 0.00 0.00 0.00 -0.17 0.00 0.00
4 5 6
A A A
Frequencies -- 568.4826 607.7721 710.6176
Red. masses -- 6.2901 1.4155 2.2961
Frc consts -- 1.1977 0.3081 0.6832
IR Inten -- 0.0892 11.3880 3.2526
Atom AN X Y Z X Y Z X Y Z
1 6 0.20 0.03 0.00 0.00 0.00 -0.05 0.00 0.00 0.18
2 6 0.00 0.32 0.00 0.00 0.00 0.12 0.00 0.00 -0.14
3 6 -0.20 0.03 0.00 0.00 0.00 -0.05 0.00 0.00 0.18
4 6 -0.29 -0.01 0.00 0.00 0.00 0.10 0.00 0.00 -0.09
5 6 0.29 -0.01 0.00 0.00 0.00 0.10 0.00 0.00 -0.09
6 1 0.02 -0.24 0.00 0.00 0.00 -0.45 0.00 0.00 -0.08
7 1 0.00 0.32 0.00 0.00 0.00 -0.27 0.00 0.00 -0.58
8 1 -0.02 -0.24 0.00 0.00 0.00 -0.45 0.00 0.00 -0.08
9 1 -0.18 0.21 0.00 0.00 0.00 -0.31 0.00 0.00 -0.50
10 1 0.00 -0.37 0.00 0.00 0.00 -0.54 0.00 0.00 -0.19
11 1 0.18 0.21 0.00 0.00 0.00 -0.31 0.00 0.00 -0.50
12 5 0.00 -0.39 0.00 0.00 0.00 -0.01 0.00 0.00 0.13
7 8 9
A A A
Frequencies -- 757.2686 814.1622 873.3652
Red. masses -- 1.2409 1.2468 1.4374
Frc consts -- 0.4193 0.4869 0.6460
IR Inten -- 7.4062 0.0000 27.6659
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 0.01 0.00 0.00 0.08 0.00 0.00 0.05
2 6 0.00 0.00 0.12 0.00 0.00 0.00 0.00 0.00 -0.05
3 6 0.00 0.00 0.01 0.00 0.00 -0.08 0.00 0.00 0.05
4 6 0.00 0.00 -0.04 0.00 0.00 -0.07 0.00 0.00 0.06
5 6 0.00 0.00 -0.04 0.00 0.00 0.07 0.00 0.00 0.06
6 1 0.00 0.00 -0.09 0.00 0.00 -0.43 0.00 0.00 -0.28
7 1 0.00 0.00 -0.82 0.00 0.00 0.00 0.00 0.00 0.20
8 1 0.00 0.00 -0.09 0.00 0.00 0.43 0.00 0.00 -0.28
9 1 0.00 0.00 0.28 0.00 0.00 0.55 0.00 0.00 -0.29
10 1 0.00 0.00 0.36 0.00 0.00 0.00 0.00 0.00 0.77
11 1 0.00 0.00 0.28 0.00 0.00 -0.55 0.00 0.00 -0.29
12 5 0.00 0.00 -0.06 0.00 0.00 0.00 0.00 0.00 -0.17
10 11 12
A A A
Frequencies -- 906.3829 917.4211 950.6756
Red. masses -- 3.5398 1.2941 6.0005
Frc consts -- 1.7134 0.6417 3.1952
IR Inten -- 0.1166 0.8666 0.3382
Atom AN X Y Z X Y Z X Y Z
1 6 -0.02 0.06 0.00 -0.04 0.06 0.00 0.31 -0.18 0.00
2 6 0.00 0.13 0.00 0.03 0.00 0.00 0.00 0.22 0.00
3 6 0.02 0.06 0.00 -0.04 -0.06 0.00 -0.31 -0.18 0.00
4 6 0.25 -0.04 0.00 -0.06 0.00 0.00 0.13 -0.09 0.00
5 6 -0.26 -0.04 0.00 -0.06 0.00 0.00 -0.13 -0.09 0.00
6 1 0.04 0.17 0.00 0.00 0.12 0.00 0.25 -0.26 -0.01
7 1 0.00 0.14 0.00 0.19 0.00 0.00 0.00 0.20 0.00
8 1 -0.04 0.17 0.00 0.00 -0.12 0.00 -0.25 -0.26 0.01
9 1 0.43 0.33 0.00 -0.10 -0.08 0.00 0.21 0.15 -0.01
10 1 0.00 -0.30 0.00 0.94 0.00 0.00 0.00 0.32 0.00
11 1 -0.43 0.33 0.00 -0.10 0.08 0.00 -0.21 0.15 0.01
12 5 0.00 -0.28 0.00 0.10 0.00 0.00 0.00 0.32 0.00
13 14 15
A A A
Frequencies -- 950.9760 960.1455 1012.2229
Red. masses -- 1.3068 1.1660 2.3536
Frc consts -- 0.6963 0.6333 1.4208
IR Inten -- 0.0000 1.8320 3.9259
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.09 0.00 0.00 -0.06 -0.13 0.00 0.00
2 6 0.00 0.00 0.00 0.00 0.00 0.03 0.00 0.25 0.00
3 6 0.00 0.00 0.09 0.00 0.00 -0.06 0.13 0.00 0.00
4 6 0.00 0.00 -0.08 0.00 0.00 0.05 0.02 -0.10 0.00
5 6 0.00 0.00 0.08 0.00 0.00 0.05 -0.02 -0.10 0.00
6 1 0.00 0.00 0.53 0.00 0.00 0.53 -0.31 -0.25 0.00
7 1 0.00 0.00 0.00 0.00 0.00 -0.32 0.00 0.26 0.00
8 1 0.00 0.00 -0.53 0.00 0.00 0.53 0.31 -0.25 0.00
9 1 0.00 0.00 0.45 0.00 0.00 -0.38 -0.14 -0.48 0.00
10 1 0.00 0.00 0.00 0.00 0.00 0.15 0.00 0.05 0.00
11 1 0.00 0.00 -0.45 0.00 0.00 -0.38 0.14 -0.48 0.00
12 5 0.00 0.00 0.00 0.00 0.00 -0.02 0.00 0.05 0.00
16 17 18
A A A
Frequencies -- 1084.7880 1175.1269 1179.7025
Red. masses -- 1.3622 1.0800 1.1585
Frc consts -- 0.9444 0.8787 0.9499
IR Inten -- 3.3297 0.9541 1.0067
Atom AN X Y Z X Y Z X Y Z
1 6 0.04 -0.04 0.00 -0.03 -0.03 0.00 0.05 0.05 0.00
2 6 -0.09 0.00 0.00 0.05 0.00 0.00 0.00 0.01 0.00
3 6 0.04 0.04 0.00 -0.03 0.03 0.00 -0.05 0.05 0.00
4 6 0.04 -0.08 0.00 0.00 0.02 0.00 0.01 -0.04 0.00
5 6 0.04 0.08 0.00 0.00 -0.02 0.00 -0.01 -0.04 0.00
6 1 -0.08 -0.24 0.00 -0.24 -0.37 0.00 0.31 0.45 0.00
7 1 -0.43 0.00 0.00 0.72 0.00 0.00 0.00 0.01 0.00
8 1 -0.08 0.24 0.00 -0.24 0.37 0.00 -0.31 0.45 0.00
9 1 -0.15 -0.52 0.00 -0.08 -0.17 0.00 -0.15 -0.42 0.00
10 1 0.25 0.00 0.00 -0.09 0.00 0.00 0.00 -0.02 0.00
11 1 -0.15 0.52 0.00 -0.08 0.18 0.00 0.15 -0.42 0.00
12 5 -0.03 0.00 0.00 -0.01 0.00 0.00 0.00 -0.02 0.00
19 20 21
A A A
Frequencies -- 1227.8644 1333.1488 1448.9772
Red. masses -- 2.3666 2.2970 1.9936
Frc consts -- 2.1022 2.4053 2.4661
IR Inten -- 1.3842 30.7160 9.0768
Atom AN X Y Z X Y Z X Y Z
1 6 0.04 0.06 0.00 0.02 0.09 0.00 0.08 -0.01 0.00
2 6 -0.05 0.00 0.00 -0.16 0.00 0.00 0.00 -0.04 0.00
3 6 0.04 -0.06 0.00 0.02 -0.09 0.00 -0.08 -0.01 0.00
4 6 0.09 0.02 0.00 0.08 0.17 0.00 0.09 0.15 0.00
5 6 0.09 -0.02 0.00 0.08 -0.17 0.00 -0.09 0.15 0.00
6 1 -0.12 -0.21 0.00 0.18 0.35 0.00 -0.15 -0.38 0.00
7 1 0.07 0.00 0.00 0.31 0.00 0.00 0.00 -0.06 0.00
8 1 -0.12 0.21 0.00 0.18 -0.35 0.00 0.15 -0.38 0.00
9 1 0.24 0.35 0.00 -0.19 -0.43 0.00 -0.19 -0.49 0.00
10 1 0.62 0.00 0.00 -0.16 0.00 0.00 0.00 -0.13 0.00
11 1 0.24 -0.35 0.00 -0.19 0.43 0.00 0.19 -0.49 0.00
12 5 -0.32 0.00 0.00 -0.05 0.00 0.00 0.00 -0.10 0.00
22 23 24
A A A
Frequencies -- 1463.0382 1564.4889 1591.8704
Red. masses -- 2.0567 4.1829 4.2860
Frc consts -- 2.5938 6.0322 6.3991
IR Inten -- 13.8494 7.1640 40.1173
Atom AN X Y Z X Y Z X Y Z
1 6 -0.05 -0.17 0.00 -0.20 -0.04 0.00 0.13 0.29 0.00
2 6 -0.05 0.00 0.00 0.37 0.00 0.00 0.00 -0.17 0.00
3 6 -0.05 0.17 0.00 -0.20 0.04 0.00 -0.13 0.29 0.00
4 6 0.04 -0.09 0.00 0.12 0.09 0.00 0.01 -0.19 0.00
5 6 0.04 0.09 0.00 0.12 -0.09 0.00 -0.01 -0.19 0.00
6 1 0.33 0.40 0.00 -0.06 0.20 0.00 -0.34 -0.46 0.00
7 1 0.56 0.00 0.00 -0.63 0.00 0.00 0.00 -0.18 0.00
8 1 0.33 -0.40 0.00 -0.06 -0.20 0.00 0.34 -0.46 0.00
9 1 0.09 -0.03 0.00 -0.07 -0.32 0.00 0.09 -0.02 0.00
10 1 0.20 0.00 0.00 0.09 0.00 0.00 0.00 0.05 0.00
11 1 0.09 0.03 0.00 -0.07 0.32 0.00 -0.09 -0.02 0.00
12 5 -0.08 0.00 0.00 -0.15 0.00 0.00 0.00 0.06 0.00
25 26 27
A A A
Frequencies -- 2446.9483 3028.3379 3030.3914
Red. masses -- 1.0948 1.0790 1.0825
Frc consts -- 3.8622 5.8299 5.8571
IR Inten -- 368.1575 108.7215 1.6967
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 0.00 -0.04 0.02 0.00 -0.03 0.02 0.00
2 6 0.00 0.00 0.00 0.00 -0.01 0.00 0.00 0.00 0.00
3 6 0.00 0.00 0.00 0.04 0.02 0.00 -0.03 -0.02 0.00
4 6 0.00 0.00 0.00 -0.03 0.01 0.00 0.04 -0.02 0.00
5 6 0.00 0.00 0.00 0.03 0.01 0.00 0.04 0.02 0.00
6 1 -0.01 0.00 0.00 0.44 -0.27 0.00 0.41 -0.26 0.00
7 1 0.00 0.00 0.00 0.00 0.17 0.00 0.00 0.00 0.00
8 1 0.01 0.00 0.00 -0.44 -0.27 0.00 0.41 0.26 0.00
9 1 0.02 -0.02 0.00 0.43 -0.19 0.00 -0.47 0.21 0.00
10 1 0.00 0.99 0.00 0.00 -0.01 0.00 0.00 0.00 0.00
11 1 -0.02 -0.02 0.00 -0.43 -0.19 0.00 -0.47 -0.21 0.00
12 5 0.00 -0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00
28 29 30
A A A
Frequencies -- 3060.4945 3061.6307 3115.9891
Red. masses -- 1.0927 1.0884 1.0929
Frc consts -- 6.0305 6.0109 6.2518
IR Inten -- 378.0706 8.4810 113.3910
Atom AN X Y Z X Y Z X Y Z
1 6 -0.04 0.03 0.00 0.03 -0.02 0.00 0.02 -0.01 0.00
2 6 0.00 0.00 0.00 0.00 0.02 0.00 0.00 -0.08 0.00
3 6 -0.04 -0.03 0.00 -0.03 -0.02 0.00 -0.02 -0.01 0.00
4 6 -0.04 0.02 0.00 -0.04 0.02 0.00 -0.01 0.00 0.00
5 6 -0.04 -0.02 0.00 0.04 0.02 0.00 0.01 0.00 0.00
6 1 0.43 -0.28 0.00 -0.36 0.23 0.00 -0.20 0.12 0.00
7 1 -0.01 0.00 0.00 0.00 -0.31 0.00 0.00 0.93 0.00
8 1 0.43 0.28 0.00 0.35 0.23 0.00 0.20 0.12 0.00
9 1 0.44 -0.20 0.00 0.48 -0.21 0.00 0.08 -0.04 0.00
10 1 0.00 0.00 0.00 0.00 -0.02 0.00 0.00 -0.01 0.00
11 1 0.44 0.20 0.00 -0.48 -0.21 0.00 -0.08 -0.04 0.00
12 5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
MO Analysis of Boratabenzene
Open the '.chk file' from optimised boratabenzene.
Calculation was done using energy calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), NBO: full NBO, and additional keywords:'pop=full'.
Run calculation using HPC service.
Results present as follow:
Boratabenzene Population Analysis "D-space" File
The Population Analysis "D-space" file is linked to DOI:10042/22005
Boratabenzne MO Analysis Summary Table
| File Name | log_66534_mo xl |
| File Type | .log |
| Calculation Type | SP |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | -1 |
| Spin | Singlet |
| E(RB3LYP) | -219.02052984 a.u. |
| RMS Gradient Norm | |
| Imaginary Freq | |
| Dipole Moment | 2.8465 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 1 minutes 9.1 seconds |
MO Analysis Log File of Boratabenzene
The MO analysis file is linked to here
NBO Analysis of Boratabenzene
select type: NBO
Charge Distribution by Colour(range between -1 and 1)
Charge Distribution by Numbers
Pyridinium
Create and optimise Pyridinium
Draw out the Pyridinium.
Optimisation was done using OPT calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Run calculation using HPC service.
Results present as follow:
Pyridinium Optimisation "D-space" File
The optimisation "D-space" file is linked to DOI:10042/21919
Pyridinium Optimisation Summary Table
| File Name | log_66494_opt_PBz |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 1 |
| Spin | Singlet |
| E(RB3LYP) | -248.66807396 a.u. |
| RMS Gradient Norm | 0.00003894 a.u. |
| Imaginary Freq | |
| Dipole Moment | 1.8727 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 3 minutes 59.9 seconds. |
Optimised Bond Length and Bond Angle for Pyridinium
Optimised N-H bond distance 1.01692 angstrom.
Optimised C-H bond distance 1.08324; 1.08352; 1.08520 angstrom.
Optimisd C-N-H bond angle 118.345 degree.
Optimisd N-C-H bond angle 116.834 degree.
Optimisd C-C-H bond angle 119.419;119.974 degree.
Optimisation Log File of Pyridinium
The optimisation file is linked to here
Item Table for Pyridinium Optimisation
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000826 0.001800 YES
RMS Displacement 0.000176 0.001200 YES
Predicted change in Energy=-6.972574D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3988 -DE/DX = 0.0 !
! R2 R(1,5) 1.3838 -DE/DX = 0.0 !
! R3 R(1,6) 1.0835 -DE/DX = 0.0 !
! R4 R(2,3) 1.3988 -DE/DX = 0.0 !
! R5 R(2,7) 1.0852 -DE/DX = 0.0 !
! R6 R(3,4) 1.3839 -DE/DX = 0.0 !
! R7 R(3,8) 1.0835 -DE/DX = 0.0 !
! R8 R(4,9) 1.0832 -DE/DX = 0.0 !
! R9 R(4,12) 1.3523 -DE/DX = 0.0001 !
! R10 R(5,11) 1.0832 -DE/DX = 0.0 !
! R11 R(5,12) 1.3524 -DE/DX = 0.0 !
! R12 R(10,12) 1.0169 -DE/DX = 0.0 !
! A1 A(2,1,5) 119.0827 -DE/DX = 0.0 !
! A2 A(2,1,6) 121.496 -DE/DX = -0.0001 !
! A3 A(5,1,6) 119.4213 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0549 -DE/DX = 0.0 !
! A5 A(1,2,7) 119.9711 -DE/DX = 0.0 !
! A6 A(3,2,7) 119.974 -DE/DX = 0.0 !
! A7 A(2,3,4) 119.082 -DE/DX = 0.0 !
! A8 A(2,3,8) 121.4988 -DE/DX = -0.0001 !
! A9 A(4,3,8) 119.4192 -DE/DX = 0.0001 !
! A10 A(3,4,9) 123.9297 -DE/DX = 0.0 !
! A11 A(3,4,12) 119.2363 -DE/DX = 0.0 !
! A12 A(9,4,12) 116.834 -DE/DX = 0.0 !
! A13 A(1,5,11) 123.9327 -DE/DX = 0.0 !
! A14 A(1,5,12) 119.2354 -DE/DX = 0.0 !
! A15 A(11,5,12) 116.8319 -DE/DX = 0.0 !
! A16 A(4,12,5) 123.3088 -DE/DX = 0.0 !
! A17 A(4,12,10) 118.3463 -DE/DX = 0.0 !
! A18 A(5,12,10) 118.345 -DE/DX = 0.0 !
! D1 D(5,1,2,3) 0.0006 -DE/DX = 0.0 !
! D2 D(5,1,2,7) -180.0023 -DE/DX = 0.0 !
! D3 D(6,1,2,3) 180.0015 -DE/DX = 0.0 !
! D4 D(6,1,2,7) -0.0014 -DE/DX = 0.0 !
! D5 D(2,1,5,11) -180.0005 -DE/DX = 0.0 !
! D6 D(2,1,5,12) 0.0021 -DE/DX = 0.0 !
! D7 D(6,1,5,11) -0.0014 -DE/DX = 0.0 !
! D8 D(6,1,5,12) 180.0012 -DE/DX = 0.0 !
! D9 D(1,2,3,4) -0.0024 -DE/DX = 0.0 !
! D10 D(1,2,3,8) -180.0018 -DE/DX = 0.0 !
! D11 D(7,2,3,4) 180.0005 -DE/DX = 0.0 !
! D12 D(7,2,3,8) 0.0012 -DE/DX = 0.0 !
! D13 D(2,3,4,9) 180.0002 -DE/DX = 0.0 !
! D14 D(2,3,4,12) 0.0015 -DE/DX = 0.0 !
! D15 D(8,3,4,9) -0.0004 -DE/DX = 0.0 !
! D16 D(8,3,4,12) 180.0008 -DE/DX = 0.0 !
! D17 D(3,4,12,5) 0.0014 -DE/DX = 0.0 !
! D18 D(3,4,12,10) -180.001 -DE/DX = 0.0 !
! D19 D(9,4,12,5) 180.0025 -DE/DX = 0.0 !
! D20 D(9,4,12,10) 0.0001 -DE/DX = 0.0 !
! D21 D(1,5,12,4) -0.0032 -DE/DX = 0.0 !
! D22 D(1,5,12,10) -180.0008 -DE/DX = 0.0 !
! D23 D(11,5,12,4) -180.0007 -DE/DX = 0.0 !
! D24 D(11,5,12,10) 0.0016 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Discussion
Converged forces and displacements
Frequency analysis for Pyridinium
Open the file: 6-31G(d,p)pyridinium optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # freq b3lyp/6-31G(d,p) nosymm geom=connectivity)
Run calculation using HPC service.
Results present as follow:
Pyridinium Frequency Analysis "D-space" File
The frequency analysis "D-space" file is linked to DOI:10042/22008
Pyridinium Frequency Summary Table
| File Name | log_66537_xlfre |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 1 |
| Spin | Singlet |
| E(RB3LYP) | -248.66807396 a.u. |
| RMS Gradient Norm | 0.00003897a.u. |
| Imaginary Freq | |
| Dipole Moment | 1.8727 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 5 minutes 39.6 seconds. |
Frequency Analysis Log File of Pyridinium
The frequency analysis file is linked to here
Item Table for Pyridinium Frequency Analysis
Low frequencies --- -7.2115 -0.0006 0.0009 0.0010 17.3444 18.5499
Low frequencies --- 392.4572 404.0614 620.4717
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- 392.4571 404.0614 620.4717
Red. masses -- 2.9474 2.7453 6.2544
Frc consts -- 0.2675 0.2641 1.4187
IR Inten -- 0.9649 0.0000 0.0144
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.14 0.00 0.00 0.20 0.03 0.23 0.00
2 6 0.00 0.00 0.25 0.00 0.00 0.00 0.39 0.00 0.00
3 6 0.00 0.00 -0.14 0.00 0.00 -0.20 0.03 -0.23 0.00
4 6 0.00 0.00 -0.11 0.00 0.00 0.19 -0.03 -0.20 0.00
5 6 0.00 0.00 -0.11 0.00 0.00 -0.19 -0.03 0.20 0.00
6 1 0.00 0.00 -0.29 0.00 0.00 0.40 -0.25 0.08 0.00
7 1 0.00 0.00 0.61 0.00 0.00 0.00 0.39 0.00 0.00
8 1 0.00 0.00 -0.29 0.00 0.00 -0.40 -0.25 -0.08 0.00
9 1 0.00 0.00 -0.20 0.00 0.00 0.51 0.25 -0.01 0.00
10 1 0.00 0.00 0.46 0.00 0.00 0.00 -0.35 0.00 0.00
11 1 0.00 0.00 -0.20 0.00 0.00 -0.51 0.25 0.01 0.00
12 7 0.00 0.00 0.21 0.00 0.00 0.00 -0.34 0.00 0.00
4 5 6
A A A
Frequencies -- 645.2547 676.9178 747.7767
Red. masses -- 6.2039 1.7605 1.5795
Frc consts -- 1.5219 0.4753 0.5204
IR Inten -- 0.2819 89.0887 82.2704
Atom AN X Y Z X Y Z X Y Z
1 6 -0.23 0.23 0.00 0.00 0.00 -0.11 0.00 0.00 -0.06
2 6 0.00 0.17 0.00 0.00 0.00 0.05 0.00 0.00 0.11
3 6 0.23 0.23 0.00 0.00 0.00 -0.11 0.00 0.00 -0.06
4 6 0.22 -0.23 0.00 0.00 0.00 0.08 0.00 0.00 0.12
5 6 -0.22 -0.23 0.00 0.00 0.00 0.08 0.00 0.00 0.12
6 1 -0.05 0.34 0.00 0.00 0.00 0.16 0.00 0.00 -0.51
7 1 0.00 -0.22 0.00 0.00 0.00 0.49 0.00 0.00 -0.17
8 1 0.05 0.34 0.00 0.00 0.00 0.16 0.00 0.00 -0.51
9 1 0.13 -0.30 0.00 0.00 0.00 0.54 0.00 0.00 -0.16
10 1 0.00 0.19 0.00 0.00 0.00 0.26 0.00 0.00 -0.59
11 1 -0.13 -0.30 0.00 0.00 0.00 0.54 0.00 0.00 -0.16
12 7 0.00 -0.15 0.00 0.00 0.00 -0.15 0.00 0.00 -0.06
7 8 9
A A A
Frequencies -- 855.0836 882.3273 991.9249
Red. masses -- 1.2250 1.2600 1.2774
Frc consts -- 0.5277 0.5780 0.7405
IR Inten -- 11.4070 0.0000 1.5937
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 0.05 0.00 0.00 0.05 0.00 0.00 0.03
2 6 0.00 0.00 0.05 0.00 0.00 0.00 0.00 0.00 0.06
3 6 0.00 0.00 0.05 0.00 0.00 -0.05 0.00 0.00 0.03
4 6 0.00 0.00 0.00 0.00 0.00 -0.09 0.00 0.00 -0.09
5 6 0.00 0.00 0.00 0.00 0.00 0.09 0.00 0.00 -0.09
6 1 0.00 0.00 -0.33 0.00 0.00 -0.46 0.00 0.00 -0.19
7 1 0.00 0.00 -0.39 0.00 0.00 0.00 0.00 0.00 -0.34
8 1 0.00 0.00 -0.33 0.00 0.00 0.46 0.00 0.00 -0.19
9 1 0.00 0.00 0.00 0.00 0.00 0.53 0.00 0.00 0.58
10 1 0.00 0.00 0.78 0.00 0.00 0.00 0.00 0.00 -0.33
11 1 0.00 0.00 0.00 0.00 0.00 -0.53 0.00 0.00 0.58
12 7 0.00 0.00 -0.10 0.00 0.00 0.00 0.00 0.00 0.05
10 11 12
A A A
Frequencies -- 1005.3166 1022.5083 1047.8931
Red. masses -- 1.3867 6.1927 4.2484
Frc consts -- 0.8257 3.8148 2.7486
IR Inten -- 0.0000 3.6242 0.4353
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.10 -0.18 0.32 0.00 -0.06 0.01 0.00
2 6 0.00 0.00 0.00 -0.11 0.00 0.00 0.35 0.00 0.00
3 6 0.00 0.00 0.10 -0.18 -0.32 0.00 -0.06 -0.01 0.00
4 6 0.00 0.00 -0.08 0.03 -0.13 0.00 -0.17 0.19 0.00
5 6 0.00 0.00 0.08 0.03 0.13 0.00 -0.17 -0.19 0.00
6 1 0.00 0.00 0.55 -0.24 0.32 0.00 -0.25 -0.10 0.00
7 1 0.00 0.00 0.00 -0.13 0.00 0.00 0.37 0.00 0.00
8 1 0.00 0.00 -0.55 -0.24 -0.32 0.00 -0.25 0.10 0.00
9 1 0.00 0.00 0.43 -0.01 -0.19 0.00 -0.45 0.02 0.00
10 1 0.00 0.00 0.00 0.39 0.00 0.00 0.17 0.00 0.00
11 1 0.00 0.00 -0.43 -0.01 0.19 0.00 -0.45 -0.02 0.00
12 7 0.00 0.00 0.00 0.36 0.00 0.00 0.16 0.00 0.00
13 14 15
A A A
Frequencies -- 1052.1824 1082.4673 1087.2372
Red. masses -- 1.3591 1.9461 1.7361
Frc consts -- 0.8865 1.3435 1.2091
IR Inten -- 0.3982 2.7481 4.2368
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 -0.08 0.02 0.12 0.00 -0.07 0.08 0.00
2 6 0.00 0.00 0.14 -0.04 0.00 0.00 0.00 -0.10 0.00
3 6 0.00 0.00 -0.08 0.02 -0.12 0.00 0.07 0.08 0.00
4 6 0.00 0.00 0.01 -0.02 0.15 0.00 -0.08 0.08 0.00
5 6 0.00 0.00 0.01 -0.02 -0.15 0.00 0.08 0.08 0.00
6 1 0.00 0.00 0.44 0.45 0.37 0.00 -0.31 -0.04 0.00
7 1 0.00 0.00 -0.75 -0.05 0.00 0.00 0.00 -0.57 0.00
8 1 0.00 0.00 0.44 0.45 -0.37 0.00 0.31 -0.04 0.00
9 1 0.00 0.00 -0.10 0.17 0.30 0.00 -0.35 -0.10 0.00
10 1 0.00 0.00 0.04 -0.06 0.00 0.00 0.00 -0.38 0.00
11 1 0.00 0.00 -0.10 0.17 -0.30 0.00 0.35 -0.10 0.00
12 7 0.00 0.00 0.01 -0.06 0.00 0.00 0.00 -0.09 0.00
16 17 18
A A A
Frequencies -- 1199.6094 1228.8861 1299.9150
Red. masses -- 1.0923 1.1871 1.3896
Frc consts -- 0.9261 1.0563 1.3835
IR Inten -- 2.7144 1.7901 3.1493
Atom AN X Y Z X Y Z X Y Z
1 6 -0.04 -0.02 0.00 -0.05 0.00 0.00 -0.02 -0.02 0.00
2 6 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.01 0.00
3 6 0.04 -0.02 0.00 -0.05 0.00 0.00 0.02 -0.02 0.00
4 6 -0.01 -0.01 0.00 0.05 0.06 0.00 -0.05 -0.06 0.00
5 6 0.01 -0.01 0.00 0.05 -0.06 0.00 0.05 -0.06 0.00
6 1 -0.45 -0.25 0.00 -0.40 -0.19 0.00 0.04 0.01 0.00
7 1 0.00 0.65 0.00 0.00 0.00 0.00 0.00 -0.19 0.00
8 1 0.45 -0.25 0.00 -0.40 0.19 0.00 -0.04 0.01 0.00
9 1 -0.12 -0.08 0.00 0.43 0.33 0.00 -0.40 -0.30 0.00
10 1 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.65 0.00
11 1 0.12 -0.08 0.00 0.43 -0.33 0.00 0.40 -0.30 0.00
12 7 0.00 -0.01 0.00 0.00 0.00 0.00 0.00 0.13 0.00
19 20 21
A A A
Frequencies -- 1374.1923 1415.9761 1523.8662
Red. masses -- 2.6541 1.4786 1.9719
Frc consts -- 2.9530 1.7467 2.6979
IR Inten -- 10.6772 3.0940 21.1838
Atom AN X Y Z X Y Z X Y Z
1 6 0.10 0.05 0.00 0.13 0.05 0.00 0.11 0.10 0.00
2 6 0.00 -0.19 0.00 0.00 0.02 0.00 -0.10 0.00 0.00
3 6 -0.10 0.05 0.00 -0.13 0.05 0.00 0.11 -0.10 0.00
4 6 0.17 0.10 0.00 0.02 -0.02 0.00 0.07 0.10 0.00
5 6 -0.17 0.10 0.00 -0.02 -0.02 0.00 0.07 -0.10 0.00
6 1 0.15 0.07 0.00 -0.39 -0.23 0.00 -0.44 -0.19 0.00
7 1 0.00 0.44 0.00 0.00 -0.45 0.00 -0.12 0.00 0.00
8 1 -0.15 0.07 0.00 0.39 -0.23 0.00 -0.44 0.19 0.00
9 1 -0.40 -0.31 0.00 0.21 0.10 0.00 -0.41 -0.22 0.00
10 1 0.00 0.31 0.00 0.00 0.50 0.00 -0.08 0.00 0.00
11 1 0.40 -0.31 0.00 -0.21 0.10 0.00 -0.41 0.22 0.00
12 7 0.00 -0.11 0.00 0.00 -0.05 0.00 -0.07 0.00 0.00
22 23 24
A A A
Frequencies -- 1580.2640 1656.6725 1676.8308
Red. masses -- 2.0693 3.4739 4.7964
Frc consts -- 3.0446 5.6175 7.9460
IR Inten -- 48.0004 31.7813 33.7083
Atom AN X Y Z X Y Z X Y Z
1 6 0.06 -0.08 0.00 -0.10 -0.13 0.00 0.26 0.05 0.00
2 6 0.00 0.20 0.00 0.00 0.22 0.00 -0.12 0.00 0.00
3 6 -0.06 -0.08 0.00 0.10 -0.13 0.00 0.26 -0.05 0.00
4 6 0.13 0.02 0.00 -0.01 0.14 0.00 -0.28 -0.09 0.00
5 6 -0.13 0.02 0.00 0.01 0.14 0.00 -0.28 0.09 0.00
6 1 -0.04 -0.16 0.00 0.20 0.02 0.00 -0.19 -0.22 0.00
7 1 0.00 -0.48 0.00 0.00 -0.23 0.00 -0.15 0.00 0.00
8 1 0.04 -0.16 0.00 -0.20 0.02 0.00 -0.19 0.22 0.00
9 1 -0.25 -0.26 0.00 -0.07 0.13 0.00 0.32 0.35 0.00
10 1 0.00 -0.60 0.00 0.00 0.78 0.00 0.14 0.00 0.00
11 1 0.25 -0.26 0.00 0.07 0.13 0.00 0.32 -0.35 0.00
12 7 0.00 0.06 0.00 0.00 -0.26 0.00 0.13 0.00 0.00
25 26 27
A A A
Frequencies -- 3224.5869 3241.0760 3242.5830
Red. masses -- 1.0920 1.0918 1.0949
Frc consts -- 6.6897 6.7573 6.7830
IR Inten -- 0.2809 0.7464 10.9674
Atom AN X Y Z X Y Z X Y Z
1 6 0.01 -0.02 0.00 0.03 -0.05 0.00 0.02 -0.04 0.00
2 6 -0.08 0.00 0.00 0.00 0.00 0.00 0.03 0.00 0.00
3 6 0.01 0.02 0.00 -0.03 -0.05 0.00 0.02 0.04 0.00
4 6 0.00 0.00 0.00 -0.02 0.02 0.00 0.02 -0.03 0.00
5 6 0.00 0.00 0.00 0.02 0.02 0.00 0.02 0.03 0.00
6 1 -0.12 0.21 0.00 -0.30 0.55 0.00 -0.26 0.49 0.00
7 1 0.93 0.00 0.00 0.00 0.00 0.00 -0.33 0.00 0.00
8 1 -0.12 -0.21 0.00 0.30 0.55 0.00 -0.26 -0.49 0.00
9 1 -0.03 0.05 0.00 0.19 -0.27 0.00 -0.21 0.30 0.00
10 1 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00
11 1 -0.03 -0.05 0.00 -0.19 -0.27 0.00 -0.21 -0.30 0.00
12 7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
28 29 30
A A A
Frequencies -- 3252.8316 3254.2318 3568.7462
Red. masses -- 1.0983 1.1007 1.0806
Frc consts -- 6.8470 6.8677 8.1086
IR Inten -- 20.5062 0.2741 158.4258
Atom AN X Y Z X Y Z X Y Z
1 6 0.02 -0.02 0.00 -0.02 0.03 0.00 0.00 0.00 0.00
2 6 0.00 0.00 0.00 -0.01 0.00 0.00 0.00 0.00 0.00
3 6 -0.02 -0.03 0.00 -0.02 -0.03 0.00 0.00 0.00 0.00
4 6 0.03 -0.04 0.00 0.03 -0.04 0.00 0.00 0.00 0.00
5 6 -0.03 -0.04 0.00 0.03 0.04 0.00 0.00 0.00 0.00
6 1 -0.16 0.29 0.00 0.17 -0.32 0.00 0.00 0.00 0.00
7 1 0.00 0.00 0.00 0.11 0.00 0.00 0.00 0.00 0.00
8 1 0.16 0.29 0.00 0.17 0.31 0.00 0.00 0.00 0.00
9 1 -0.36 0.51 0.00 -0.34 0.49 0.00 0.01 -0.01 0.00
10 1 0.00 -0.01 0.00 0.02 0.00 0.00 1.00 0.00 0.00
11 1 0.36 0.51 0.00 -0.35 -0.49 0.00 0.01 0.01 0.00
12 7 0.00 0.00 0.00 0.00 0.00 0.00 -0.07 0.00 0.00
MO Analysis of Pyridinium
Open the '.chk file' from optimised pyridinium.
Calculation was done using energy calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), NBO: full NBO, and additional keywords:'pop=full'.
Run calculation using HPC service.
Results present as follow:
Pyridinium Population Analysis "D-space" File
The Population Analysis "D-space" file is linked to DOI:10042/22006
Pyridinium MO Analysis Summary Table
| File Name | log_66537_xlpbzmo |
| File Type | .log |
| Calculation Type | SP |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 1 |
| Spin | Singlet |
| E(RB3LYP) | -248.66807396 a.u. |
| RMS Gradient Norm | |
| Imaginary Freq | |
| Dipole Moment | 1.8727 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 1 minutes 12.2 seconds |
MO Analysis Log File of Pyridinium
The MO analysis file is linked to here
NBO Analysis of Pyridinium
select type: NBO
Charge Distribution by Colour(range between -1 and 1)
Charge Distribution by Numbers
Borazine
Create and optimise Borazine
Draw out the Borazine.
Optimisation was done using OPT calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # opt b3lyp/6-31g(d,p) geom=connectivity nosymm)
Run calculation using HPC service.
Results present as follow:
Borazine Optimisation "D-space" File
The optimisation "D-space" file is linked to DOI:10042/22009
Borazine Optimisation Summary Table
| File Name | log_66728xlopt |
| File Type | .log |
| Calculation Type | FOPT |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -242.68458726 a.u. |
| RMS Gradient Norm | 0.00006608 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0002 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 5 minutes 8.8 seconds. |
Optimised Bond Length and Bond Angle for Borazine
Optimised N-H bond distance 1.00973 angstrom.
Optimised B-H bond distance 1.19493 angstrom.
Optimisd B-N-H bond angle 118.564 degree.
Optimisd N-B-H bond angle 121.434 degree.
Optimisation Log File of Borazine
The optimisation file is linked to here
Item Table for Borazine Optimisation
Item Value Threshold Converged?
Maximum Force 0.000093 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000341 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.028625D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,10) 1.1949 -DE/DX = 0.0001 !
! R2 R(2,7) 1.0097 -DE/DX = 0.0 !
! R3 R(3,12) 1.1949 -DE/DX = 0.0001 !
! R4 R(4,9) 1.0097 -DE/DX = 0.0 !
! R5 R(5,11) 1.1949 -DE/DX = 0.0001 !
! R6 R(6,8) 1.0097 -DE/DX = 0.0 !
! R7 R(7,10) 1.4307 -DE/DX = 0.0 !
! R8 R(7,12) 1.4307 -DE/DX = 0.0 !
! R9 R(8,10) 1.4306 -DE/DX = 0.0 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4306 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(2,7,10) 118.5622 -DE/DX = 0.0 !
! A2 A(2,7,12) 118.5639 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8739 -DE/DX = 0.0 !
! A4 A(6,8,10) 118.5584 -DE/DX = 0.0 !
! A5 A(6,8,11) 118.5563 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8853 -DE/DX = 0.0 !
! A7 A(4,9,11) 118.567 -DE/DX = 0.0 !
! A8 A(4,9,12) 118.5613 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8717 -DE/DX = 0.0 !
! A10 A(1,10,7) 121.4399 -DE/DX = 0.0 !
! A11 A(1,10,8) 121.4414 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1187 -DE/DX = 0.0 !
! A13 A(5,11,8) 121.4373 -DE/DX = 0.0 !
! A14 A(5,11,9) 121.4436 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.119 -DE/DX = 0.0001 !
! A16 A(3,12,7) 121.4348 -DE/DX = 0.0 !
! A17 A(3,12,9) 121.4337 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1314 -DE/DX = 0.0 !
! D1 D(2,7,10,1) -0.0061 -DE/DX = 0.0 !
! D2 D(2,7,10,8) 179.9942 -DE/DX = 0.0 !
! D3 D(12,7,10,1) -179.9955 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0048 -DE/DX = 0.0 !
! D5 D(2,7,12,3) 0.0034 -DE/DX = 0.0 !
! D6 D(2,7,12,9) -179.997 -DE/DX = 0.0 !
! D7 D(10,7,12,3) 179.9928 -DE/DX = 0.0 !
! D8 D(10,7,12,9) -0.0075 -DE/DX = 0.0 !
! D9 D(6,8,10,1) -0.0025 -DE/DX = 0.0 !
! D10 D(6,8,10,7) 179.9973 -DE/DX = 0.0 !
! D11 D(11,8,10,1) -179.9989 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0009 -DE/DX = 0.0 !
! D13 D(6,8,11,5) 0.0003 -DE/DX = 0.0 !
! D14 D(6,8,11,9) -179.9996 -DE/DX = 0.0 !
! D15 D(10,8,11,5) 179.9967 -DE/DX = 0.0 !
! D16 D(10,8,11,9) -0.0033 -DE/DX = 0.0 !
! D17 D(4,9,11,5) 0.0043 -DE/DX = 0.0 !
! D18 D(4,9,11,8) -179.9957 -DE/DX = 0.0 !
! D19 D(12,9,11,5) -179.9997 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0002 -DE/DX = 0.0 !
! D21 D(4,9,12,3) 0.0005 -DE/DX = 0.0 !
! D22 D(4,9,12,7) -179.9991 -DE/DX = 0.0 !
! D23 D(11,9,12,3) -179.9954 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.005 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Discussion
Converged forces and displacements
Frequency analysis for Borazine
Open the file: 6-31G(d,p)borazine optimisation and to save. Open the saved copy.
Calculation was done using frequency calculation with method: DFT; B3LYP and basis set: 6-31G(d,p).(Keywords: # freq b3lyp/6-31G(d,p) nosymm geom=connectivity)
Run calculation using HPC service.
Results present as follow:
Borazine Frequency Analysis "D-space" File
The frequency analysis "D-space" file is linked to DOI:10042/22055
Borazine Frequency Summary Table
| File Name | log_66804_FREXLCORRECTED |
| File Type | .log |
| Calculation Type | FREQ |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -242.68458724 a.u. |
| RMS Gradient Norm | 0.00006603 a.u. |
| Imaginary Freq | |
| Dipole Moment | 0.0002 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 5 minutes 32.8 seconds. |
Frequency Analysis Log File of Borazine
The frequency analysis file is linked to here
Item Table for Borazine Frequency Analysis
Low frequencies --- -17.2200 -10.7657 -6.6660 0.0007 0.0007 0.0007
Low frequencies --- 288.8527 289.6687 404.1667
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- 288.8524 289.6685 404.1664
Red. masses -- 2.9273 2.9246 1.9257
Frc consts -- 0.1439 0.1446 0.1853
IR Inten -- 0.0000 0.0000 23.5573
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.68 0.00 0.00 -0.13 0.00 0.00 -0.53
2 1 0.00 0.00 -0.18 0.00 0.00 -0.20 0.00 0.00 -0.16
3 1 0.00 0.00 -0.23 0.00 0.00 0.66 0.00 0.00 -0.53
4 1 0.00 0.00 0.26 0.00 0.00 -0.05 0.00 0.00 -0.16
5 1 0.00 0.00 -0.45 0.00 0.00 -0.53 0.00 0.00 -0.53
6 1 0.00 0.00 -0.09 0.00 0.00 0.25 0.00 0.00 -0.16
7 7 0.00 0.00 -0.16 0.00 0.00 -0.18 0.00 0.00 0.13
8 7 0.00 0.00 -0.08 0.00 0.00 0.23 0.00 0.00 0.13
9 7 0.00 0.00 0.24 0.00 0.00 -0.05 0.00 0.00 0.13
10 5 0.00 0.00 0.22 0.00 0.00 -0.04 0.00 0.00 -0.10
11 5 0.00 0.00 -0.15 0.00 0.00 -0.17 0.00 0.00 -0.10
12 5 0.00 0.00 -0.07 0.00 0.00 0.21 0.00 0.00 -0.10
4 5 6
A A A
Frequencies -- 525.0284 525.1387 710.1140
Red. masses -- 6.4513 6.4512 1.1571
Frc consts -- 1.0478 1.0482 0.3438
IR Inten -- 0.6317 0.6353 0.0239
Atom AN X Y Z X Y Z X Y Z
1 1 -0.21 -0.17 0.00 -0.27 0.21 0.00 0.00 0.00 0.08
2 1 0.27 0.24 0.00 0.16 -0.10 0.00 0.00 0.00 0.81
3 1 -0.17 -0.25 0.00 -0.19 0.25 0.00 0.00 0.00 0.05
4 1 0.18 0.11 0.00 0.29 -0.19 0.00 0.00 0.00 -0.46
5 1 -0.26 -0.25 0.00 -0.20 0.16 0.00 0.00 0.00 -0.13
6 1 0.11 0.25 0.00 0.15 -0.26 0.00 0.00 0.00 -0.31
7 7 0.31 0.19 0.00 -0.05 0.18 0.00 0.00 0.00 -0.07
8 7 -0.16 0.22 0.00 -0.08 -0.29 0.00 0.00 0.00 0.03
9 7 0.05 -0.20 0.00 0.34 -0.08 0.00 0.00 0.00 0.04
10 5 -0.06 0.16 0.00 -0.33 0.10 0.00 0.00 0.00 -0.03
11 5 -0.30 -0.19 0.00 0.02 -0.14 0.00 0.00 0.00 0.05
12 5 0.13 -0.22 0.00 0.05 0.28 0.00 0.00 0.00 -0.02
7 8 9
A A A
Frequencies -- 710.7247 732.5926 864.4186
Red. masses -- 1.1572 1.2622 7.4064
Frc consts -- 0.3444 0.3991 3.2606
IR Inten -- 0.0006 59.8104 0.0000
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.11 0.00 0.00 0.08 -0.02 0.01 0.00
2 1 0.00 0.00 -0.09 0.00 0.00 0.55 -0.33 -0.24 0.00
3 1 0.00 0.00 -0.12 0.00 0.00 0.08 0.00 -0.02 0.00
4 1 0.00 0.00 -0.65 0.00 0.00 0.57 0.38 -0.16 0.00
5 1 0.00 0.00 0.01 0.00 0.00 0.08 0.02 0.01 0.00
6 1 0.00 0.00 0.73 0.00 0.00 0.57 -0.05 0.41 0.00
7 7 0.00 0.00 0.01 0.00 0.00 0.02 -0.33 -0.24 0.00
8 7 0.00 0.00 -0.07 0.00 0.00 0.02 -0.05 0.40 0.00
9 7 0.00 0.00 0.06 0.00 0.00 0.02 0.37 -0.16 0.00
10 5 0.00 0.00 -0.04 0.00 0.00 -0.09 -0.01 0.00 0.00
11 5 0.00 0.00 -0.01 0.00 0.00 -0.09 0.01 0.00 0.00
12 5 0.00 0.00 0.05 0.00 0.00 -0.09 0.00 -0.01 0.00
10 11 12
A A A
Frequencies -- 927.3428 927.6238 936.8611
Red. masses -- 1.4796 1.4800 1.4552
Frc consts -- 0.7497 0.7503 0.7525
IR Inten -- 0.0428 0.0567 236.1530
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.78 0.00 0.00 -0.11 0.00 0.00 0.48
2 1 0.00 0.00 -0.07 0.00 0.00 0.17 0.00 0.00 -0.27
3 1 0.00 0.00 -0.46 0.00 0.00 -0.63 0.00 0.00 0.49
4 1 0.00 0.00 0.18 0.00 0.00 -0.02 0.00 0.00 -0.28
5 1 0.00 0.00 -0.29 0.00 0.00 0.71 0.00 0.00 0.51
6 1 0.00 0.00 -0.11 0.00 0.00 -0.14 0.00 0.00 -0.28
7 7 0.00 0.00 0.02 0.00 0.00 -0.05 0.00 0.00 0.06
8 7 0.00 0.00 0.03 0.00 0.00 0.04 0.00 0.00 0.06
9 7 0.00 0.00 -0.05 0.00 0.00 0.01 0.00 0.00 0.06
10 5 0.00 0.00 -0.17 0.00 0.00 0.02 0.00 0.00 -0.10
11 5 0.00 0.00 0.06 0.00 0.00 -0.15 0.00 0.00 -0.10
12 5 0.00 0.00 0.10 0.00 0.00 0.13 0.00 0.00 -0.10
13 14 15
A A A
Frequencies -- 944.2607 944.5018 944.9104
Red. masses -- 1.6673 1.6484 5.4625
Frc consts -- 0.8759 0.8664 2.8736
IR Inten -- 0.0035 0.0043 0.0001
Atom AN X Y Z X Y Z X Y Z
1 1 0.28 0.29 0.00 0.16 0.58 0.00 -0.33 0.18 0.00
2 1 -0.19 0.26 0.00 -0.07 -0.07 0.00 -0.05 0.06 0.00
3 1 -0.31 -0.13 0.00 0.63 0.00 0.00 -0.08 -0.44 0.00
4 1 0.14 0.13 0.00 0.06 0.27 0.00 0.04 0.00 0.00
5 1 -0.44 0.54 0.00 -0.09 -0.10 0.00 0.23 0.38 0.00
6 1 -0.14 -0.10 0.00 0.29 -0.01 0.00 -0.06 -0.01 0.00
7 7 -0.03 0.04 0.00 -0.07 -0.05 0.00 0.01 0.02 0.00
8 7 -0.01 -0.08 0.00 0.05 -0.04 0.00 -0.01 -0.02 0.00
9 7 0.08 -0.01 0.00 -0.03 0.06 0.00 0.01 0.00 0.00
10 5 0.15 0.00 0.00 -0.04 0.12 0.00 -0.32 0.15 0.00
11 5 -0.09 0.07 0.00 -0.09 -0.08 0.00 0.30 0.26 0.00
12 5 -0.04 -0.09 0.00 0.10 -0.06 0.00 0.03 -0.41 0.00
16 17 18
A A A
Frequencies -- 1051.8288 1080.6345 1080.6855
Red. masses -- 1.0306 1.2600 1.2604
Frc consts -- 0.6718 0.8669 0.8673
IR Inten -- 0.0000 0.1942 0.2000
Atom AN X Y Z X Y Z X Y Z
1 1 -0.20 -0.45 0.00 0.00 -0.12 0.00 -0.21 -0.46 0.00
2 1 -0.18 0.24 0.00 -0.34 0.48 0.00 -0.14 0.13 0.00
3 1 0.49 0.06 0.00 0.38 0.01 0.00 -0.34 -0.08 0.00
4 1 -0.12 -0.27 0.00 0.09 0.11 0.00 0.23 0.56 0.00
5 1 -0.29 0.39 0.00 0.31 -0.39 0.00 0.05 -0.16 0.00
6 1 0.30 0.03 0.00 -0.45 -0.08 0.00 0.42 0.02 0.00
7 7 -0.01 0.02 0.00 -0.05 0.08 0.00 -0.04 0.00 0.00
8 7 0.02 0.00 0.00 -0.07 -0.03 0.00 0.07 -0.02 0.00
9 7 -0.01 -0.02 0.00 0.04 0.00 0.00 0.03 0.09 0.00
10 5 0.00 0.01 0.00 0.04 -0.03 0.00 -0.02 -0.02 0.00
11 5 0.00 -0.01 0.00 0.03 -0.01 0.00 -0.04 -0.04 0.00
12 5 -0.01 0.00 0.00 0.02 -0.03 0.00 -0.01 -0.04 0.00
19 20 21
A A A
Frequencies -- 1245.1261 1314.1752 1399.9173
Red. masses -- 4.3302 1.4695 1.9480
Frc consts -- 3.9553 1.4953 2.2493
IR Inten -- 0.0001 0.0001 11.0687
Atom AN X Y Z X Y Z X Y Z
1 1 -0.11 -0.26 0.00 0.10 0.22 0.00 -0.04 -0.30 0.00
2 1 0.23 -0.31 0.00 -0.30 0.41 0.00 0.35 -0.49 0.00
3 1 0.28 0.03 0.00 -0.24 -0.03 0.00 0.18 -0.08 0.00
4 1 0.15 0.35 0.00 -0.20 -0.47 0.00 -0.09 -0.37 0.00
5 1 -0.17 0.23 0.00 0.14 -0.20 0.00 0.26 -0.38 0.00
6 1 -0.38 -0.04 0.00 0.51 0.06 0.00 0.24 -0.06 0.00
7 7 0.09 -0.12 0.00 0.06 -0.09 0.00 -0.05 0.05 0.00
8 7 -0.15 -0.02 0.00 -0.11 -0.01 0.00 -0.02 -0.08 0.00
9 7 0.06 0.13 0.00 0.04 0.10 0.00 0.08 0.02 0.00
10 5 0.12 0.26 0.00 0.01 0.01 0.00 0.10 0.09 0.00
11 5 0.17 -0.23 0.00 0.01 -0.01 0.00 -0.13 0.16 0.00
12 5 -0.29 -0.03 0.00 -0.01 0.00 0.00 -0.07 -0.08 0.00
22 23 24
A A A
Frequencies -- 1400.2306 1491.9990 1492.2754
Red. masses -- 1.9487 4.2204 4.2250
Frc consts -- 2.2511 5.5353 5.5434
IR Inten -- 11.1449 493.7928 493.7214
Atom AN X Y Z X Y Z X Y Z
1 1 -0.20 -0.31 0.00 -0.18 0.08 0.00 0.10 0.23 0.00
2 1 -0.12 0.02 0.00 -0.28 0.45 0.00 0.24 -0.20 0.00
3 1 -0.43 -0.09 0.00 0.20 0.12 0.00 0.14 -0.16 0.00
4 1 -0.24 -0.42 0.00 0.08 -0.04 0.00 -0.24 -0.56 0.00
5 1 -0.12 -0.01 0.00 0.05 -0.23 0.00 -0.21 0.00 0.00
6 1 -0.56 -0.10 0.00 -0.52 -0.10 0.00 -0.31 0.04 0.00
7 7 -0.06 -0.06 0.00 0.18 -0.17 0.00 -0.02 0.16 0.00
8 7 0.07 -0.02 0.00 0.25 -0.02 0.00 0.13 0.10 0.00
9 7 -0.02 0.07 0.00 0.09 -0.04 0.00 0.11 0.26 0.00
10 5 0.02 0.17 0.00 -0.16 0.07 0.00 -0.11 -0.24 0.00
11 5 -0.04 -0.07 0.00 -0.20 0.13 0.00 -0.04 -0.19 0.00
12 5 0.19 -0.01 0.00 -0.24 0.06 0.00 -0.11 -0.16 0.00
25 26 27
A A A
Frequencies -- 2640.8788 2641.1467 2650.9336
Red. masses -- 1.0987 1.0987 1.1009
Frc consts -- 4.5147 4.5156 4.5583
IR Inten -- 283.4834 283.5505 0.0937
Atom AN X Y Z X Y Z X Y Z
1 1 0.32 -0.14 0.00 -0.67 0.29 0.00 0.54 -0.23 0.00
2 1 0.00 0.00 0.00 0.01 -0.01 0.00 -0.01 0.00 0.00
3 1 -0.05 0.44 0.00 -0.07 0.67 0.00 -0.07 0.58 0.00
4 1 -0.01 -0.01 0.00 0.00 -0.01 0.00 0.01 0.00 0.00
5 1 0.66 0.49 0.00 -0.04 -0.03 0.00 -0.45 -0.33 0.00
6 1 -0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.00
7 7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
8 7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
9 7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
10 5 -0.03 0.01 0.00 0.06 -0.03 0.00 -0.05 0.02 0.00
11 5 -0.06 -0.05 0.00 0.00 0.00 0.00 0.04 0.03 0.00
12 5 0.01 -0.04 0.00 0.01 -0.06 0.00 0.01 -0.06 0.00
28 29 30
A A A
Frequencies -- 3641.5325 3643.2216 3643.5857
Red. masses -- 1.0768 1.0761 1.0761
Frc consts -- 8.4131 8.4156 8.4174
IR Inten -- 0.5688 39.6985 39.1803
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
2 1 -0.38 -0.28 0.00 0.04 0.03 0.00 0.70 0.52 0.00
3 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
4 1 0.56 -0.24 0.00 -0.64 0.28 0.00 0.34 -0.15 0.00
5 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
6 1 -0.07 0.63 0.00 -0.08 0.70 0.00 -0.03 0.30 0.00
7 7 0.03 0.02 0.00 0.00 0.00 0.00 -0.05 -0.04 0.00
8 7 0.01 -0.05 0.00 0.01 -0.05 0.00 0.00 -0.02 0.00
9 7 -0.04 0.02 0.00 0.05 -0.02 0.00 -0.02 0.01 0.00
10 5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
11 5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
12 5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
MO Analysis of Borazine
Open the '.chk file' from optimised borazine.
Calculation was done using energy calculation with method: DFT; B3LYP, basis set: 6-31G(d,p), NBO: full NBO, and additional keywords:'pop=full'.
Run calculation using HPC service.
Results present as follow:
Borazine Population Analysis "D-space" File
The Population Analysis "D-space" file is linked to DOI:10042/22011
Borazine MO Analysis Summary Table
| File Name | log_66730_xlmo |
| File Type | .log |
| Calculation Type | SP |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| Charge | 0 |
| Spin | Singlet |
| E(RB3LYP) | -242.68458727 a.u. |
| RMS Gradient Norm | |
| Imaginary Freq | |
| Dipole Moment | 0.0002 Debye |
| Point Group | C1 |
| Job CPU Time | 0 days 0 hours 1 minutes 7.1 seconds |
MO Analysis Log File of Borazine
The MO analysis file is linked to here
NBO Analysis of Borazine
select type: NBO
Charge Distribution by Colour(range between -1 and 1)
Charge Distribution by Numbers
Discussion
MO Analysis
| MOs | Benzene | Boratabenzene | Pyridinium | Borazine |
| Level 7 (sigma bonding) |  E=-0.84677 symmetrical |
 E=-0.60434 distorted, less on B |
 E=-1.21401 distorted, more near N |
 E=-0.27590 triangular, less on B more near N
|
| Level 17 (pi bonding) p orbital analog |  E=-0.35998 symmetrical |
 E=-0.13208 distorted, less on B |
 E=-0.64064 distorted, more near N |
 E=-0.36129 symmetrical, less on B more near N
|
| level 21 (HOMO) d orbital analog |  E=-0.24691 symmetrical |
 E=0.01094 distorted |
 E=-0.47885 symmetrical |
 E=-0.88852 distorted
|
analysis see next section.
NBO Analysis
| Type | Benzene | Boratabenzene | Pyridinium | Borazine |
| Charge Distribution: Colours select type: NBO(range between -1 and 1) | |
|
|
|
| Charge Distribution: Numbers | |
|
|
|
For benzene, charges are evenly distributed. ALL C atom in the benzene ring have a charge of -0.239 and H atom have a charge of 0.239
For boratabenzene, charge distribution changes due to change in structure(one of the C atoms replaced by B anion). B is more electropositive than C, hence, less electron density(0.202), positively charged in this case. Negative charge can be better delocalised at ortho(-0.588)/para(-0.340) position due to more available resonance structure. Hence, the meta position adopts the lowest electron density(-0.250) and more charge is delocalised to the ortho position as it is closer to B in location. The H linked to B has -0.096 charge and other H has similar charge(approx. 0.180).
For pyridinium, on the other hand, charge distribution changes due to change in structure(one of the C atoms replaced by N cation). N is more electronegativethan C, hence, more electron density(-0.476). Positive charge can be better delocalised at ortho(0.071)/para(-0.122) position due to more available resonance structure. Hence, the meta position adopts the highest electron density(-0.241) and more charge is delocalised to the ortho position as it is closer to B in location. The H linked to N has 0.483 charge and other H has similar charge(approx. 0.290).
For borazine, all of the B atoms have postive change(0.747) while all of N atoms have negative charge(-1.102). Compared to benzene, it has more bond polarity, hence, more reactive.