Difference between revisions of "KusabsOliv"

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===Optimised Molecule===
 
===Optimised Molecule===
  
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[[File:Kusabs_imida_B_optflabelled.png|350px]]
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[[File:Kusabs_imida_B_optf_labelled.png|450px]]
  
 
====Calculation Data====
 
====Calculation Data====
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====Jmol rotatable molecule====
 
 
logfile:[[Media:KUSABS_IMIDA_B_OPTF.LOG]]
 
logfile:[[Media:KUSABS_IMIDA_B_OPTF.LOG]]
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<jmol><jmolApplet>
 
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<title>optimisedHMim-Clmolecule</title>
 
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<color>#f2bbf2</color>
 
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<size>450</size>
 
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<uploadedFileContents>KUSABS_IMIDA_B_OPTF.LOG</uploadedFileContents>
 
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</jmolApplet></jmol>
 
  
  

Revision as of 05:21, 12 May 2026

Contents

Lab1 Marking

It's good that you have a working wiki. However, you have optimised N2F2 with a wrong symmetry, have reported wrong charges, and have missed to include the low frequencies, torsion angle, and NN distance. Don't forget to consider the accuracy to which you report your data the next time. If you have any queries, please contact Prof. Hunt.

BH3 Molecule

Optimized Molecule Image

OK BH3 optf.png"

calculation data

molecule BH3
method RB3LYP
basis set 6-31G(d,p)
final energy -26.615324
RMS gradient 0.000002
point group D3h

Low frequencies

Low frequencies -11.6940 -11.6861 -6.5543 0.0007 0.0280 0.4289
Low frequencies 1162.9745 1213.1390 1213.1392

Item Table

Item               Value     Threshold  Converged?
 Maximum Force            0.000004     0.000015     YES
 RMS     Force            0.000003     0.000010     YES
 Maximum Displacement     0.000017     0.000060     YES
 RMS     Displacement     0.000011     0.000040     YES

Jmol rotatable molecule

logfile:Media:KUSABSOLIV_BH3_OPTF_POP.LOG

optimised BHmolecule

Important geometric parameters

optimized bond distance and angle for BH3
r(B-H)=1.19232Â
θ(H-B-H)=130°

Vibrational data

mode 1 2 2 4 5 6
wavenumber(cm-1) 1163 1213.14 1213.14 2582.58 2715.72 2715.72
symmetry A2" E' E' A1' E' E'
intensity 93 14 14 0 126 126

IR Spectrum

Ok bh3 optf IR.PNG

NH3BH3 Molecule

Optimized Molecule Image

OK nh3bh3 optf pop.png"

calculation data

molecule NH3BH3
method RB3LYP
basis set 6-31G(d,p)
final energy -83.224689
RMS gradient 0.000001
point group C1

Item Table

Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000043     0.000060     YES
 RMS     Displacement     0.000019     0.000040     YES

Low frequencies

Low frequencies -5.0440 -2.8838 0.0010 0.0012 0.0014 0.6125
Low frequencies 263.3825 632.9842 638.4293

Jmol rotatable molecule

logfile:Media:OK_NH3BH3_OPTF_POP.LOG

optimised NHmolecule

Important geometric parameters

optimized bond distance and angle for NH3BH3br r(N-H)=1.01847Â
r(B-H)=1.20977Â
r=(B-N)=1.66770Â
θ(H-N-H)=108°
θ(H-B-H)=114°
θ(H-N-B)=105°
θ(H-B-N)=1118°

Vibrational data

mode 1 2 2 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
wavenumber(cm-1) 263 633 638 638 1069 1069 1196 1204 1204 1329 1676 1676 2472 2532 2532 3464 3581 3581
symmetry A A A A A A A A A A A A A A A A A A
intensity 0 14 4 4 41 41 109 3 3 114 28 28 67 231 231 3 28 28

IR spectrum

Ok nh3bh3 optf pop IR.png

Association Energy

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05168 Hartrees
= -135.68584 kJ/mol
= 135.68584 kJ/mol (5 d.p)

Me3NH-Cl Molecule

Optimised Molecule

Ok me3nhcl optf pop.png

Calculation data

molecule Me3NH-Cl
method RB3LYP
basis set 3-21G
final energy -632.16208
RMS gradient 5e-06
point group C1

Item Table

Item Value Threshold Converged? 

Maximum Force            0.000008     0.000450     YES
RMS     Force            0.000003     0.000300     YES
Maximum Displacement     0.000932     0.001800     YES
RMS     Displacement     0.000257     0.001200     YES

Low Frequencies

Low frequencies -13.6743 -1.8717 -0.0006 0.0026 0.0036 2.7014
Low frequencies 55.5069 56.3300 89.8235

Jmol Rotatable Image

logfile:Media:OK_ME3NHCL_OPTF_POP.LOG

optimised MeNHClmolecule

Important Geometric Parameters

r(N-H)= 1.16Â
r(H-Cl)= 1.74 Â
r(N-Cl)= 2.90 Â

Me3HNCl Rigid Scan

Rigid Scan Raw Data Plot

OK ME3NHCl scan totalenergy.png

PES Raw Data Table

Scan Coordinate  Total Energy (Hartrees) Relative Total Energy (kJmol-1)
0.8 -632.0662517 229.8615
0.9 -632.1224204 82.39055
1.0 -632.1460690 20.30115
1.1 -632.1535075 0.771372
1.2 -632.1538013 0
1.3 -632.1515761 5.842263
1.4 -632.1490193 12.55514
1.5 -632.1470175 17.81087
1.6 -632.1457412 21.16179
1.7 -632.1447843 23.67413
1.8 -632.1429341 28.53183
1.9 -632.1375920 42.55752
2.0 -632.1238548 78.62454
2.1 -632.0932227 159.0491

Me3NHCl Scan Formal Graph

Plot of Total Relative Energy (kJ/mol) vs. Scan Coordinate (Â)

Kusabs Me3NHCL scangraphformal.png
The scan coordinate, which corresponds to the N-H bond length, starts at 0.8 Â and increasing in 0.1 Âincrements to 2.1 Â. When the N-Cl bond distance is set to 3.2 Â,the scan data plot shows that a minima occurs at 1.2Â. This displays an ion-pair Me3NH+ --- Cl-, and the minima proves that this is the most stable state. The graph captures the gradual shift of the proton between as the proton is pushed over to the Cl, where it forms a neutral pair Me3N---HCl. The energy goes up, with no stable minima formed, rather a 'shelf' appears in the PES. The ion-pair, forms a doubly ionic H-bond between the Me3NH+ and Cl-, the neutral pair forms a normal bond between Me3N and HCl.

Ionic Liquid pair 1-methyl Imadizolium chloride (HMim-Cl)

Molecule a)

Optimised molecule

Kusabs imida optf.png

Calculation data

name of submitted log file KUSABS_IMIDA_A_OPTF.LOG
molecule HMim-Cl b)
method RB3LYP
basis set 3-21G
RMS gradient 3.88e-07
final energy -722.6879
point group C1

Item Table

Item               Value     Threshold  Converged?
Maximum Force            0.000008     0.000450     YES
RMS     Force            0.000003     0.000300     YES
Maximum Displacement     0.000932     0.001800     YES
RMS     Displacement     0.000257     0.001200     YES

Low Frequencies

Low frequencies -13.6743 -1.8717 -0.0006 0.0026 0.0036 2.7014
Low frequencies 55.5609 56.3300 189.8235

Jmol rotatable molecule

logfile:Media:OK_ME3NHCL_OPTF_POP.LOG

optimised HMim-Clmolecule


Important Geometric Parameters

(9-7)r(N-H) =1.17767 Â
(9-14)r(N-Cl) = 2.89146 Â
(7-14)r(H-Cl) = 1.71933 Â
(1-4)r(C-H) = 1.07478 Â
(8-10)r(N-C) = 1.47703 Â
(2-5)r(C-H)=1.07442 Â
(2-8)r(C-N)=1.39999 Â

HMim-Cl Molecule a) Scan

HMim-Cl Scan Plot

Kusabs imida A scandataplot.PNG

PES Raw Data Table

Scan Coordinate  Total Energy (Hartrees) Relative Total Energy (kJmol-1)
0.8000000000 -722.5958117770 219.390797
0.9000000000 -722.6503978670 76.07501772
1.0000000000 -722.6727650930 17.34986586
1.1000000000 -722.6793733070 0
1.2000000000 -722.6792906370 0.217050085
1.3000000000 -722.6772128790 5.672203714
1.4000000000 -722.6753243470 10.63054448
1.5000000000 -722.6744432030 12.94398805
1.6000000000 -722.6746286280 12.45715471
1.7000000000 -722.6753546570 10.55096558
1.8000000000 -722.6753493050 10.56501725
1.9000000000 -722.6721372910 18.99816001
2.0000000000 -722.6613012230 47.44825654
2.1000000000 -722.6354468750 115.3288472

Hmim-Cl Formal Graph

Plot of Total Relative Energy (kJ/mol) vs. Scan Coordinate (Â)

Kusabs imida A scangraphformal.png

Kusabs imida A scan process.png

1-methyl Imidazoliumm chloride B

Optimised Molecule

Kusabs imida B optf labelled.png

Calculation Data

name of submitted log file KUSABS_IMIDA_B_OPTF.LOG
molecule 1-methyl Imidazoliumm chloride B
method RB3LYP
basis set 3-21G
Final energy -722.666
RMS gradient 2.0678e-05
Point group C1

Item Table

Low Frequencies

Low frequencies -5.7142 -3.2659 -1.6460 -0.0033 -0.0016 0.0018
Low frequencies 45.3690 162.0925 198.8365

logfile:Media:KUSABS_IMIDA_B_OPTF.LOG


Important Geometric Parameters

(5-14) r(H-Cl)=2.13401 Â
(13-14)r(H-Cl)=2.27688 Â
(8-14) r(N-Cl)=3.64967 Â
(8-2) r(N-C)= 1.40258 Â

2-methyl Imidazolium chloride C

Jmol rotatable molecule

logfile:[[Media:KUSABS_IMIDA_C_OPTF2.LOG]

optimised HMim-Clmolecule

NH3 Molecule

calculation data

molecule NH3
method RB3LYP
basis set 6-31G(d,p)
final energy -56.557769
RMS gradient 1.53e-07
point group C3v

Item Table

 Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000015     YES
 RMS     Force            0.000000     0.000010     YES
 Maximum Displacement     0.000003     0.000060     YES
 RMS     Displacement     0.000001     0.000040     YES

Optimized Molecule Image

Kusabsoliv nh3 optf.png

Jmol rotatable molecule

logfile:Media:KUSABSOLIV_NH3_OPTF_POP.LOG

optimised NHmolecule

Important geometric parameters

optimized bond distance and angle for NH3
r(N-H)=1.018Â
θ(H-N-H)=106°

Kusabsoliv nh3 optf vibrations.png

Vibrational data

mode 1 2 2 4 5 6
wavenumber(cm-1) 1089 1694 1694 3461 3590 3590
symmetry A1 E E A1 E E
intensity 145 14 14 1 0 0

IR Spectrum

KUSABSOLIV NH3 OPTF IR POP ir.png

Charge Distribution Model

Kusabsoliv nh3 optf chargedistribution.png

Atom Charge
Nitrogen -1.13
Hydrogen 0.375

Kusabsoliv nh3 colourrange.PNG

N2F2 Molecule

calculation data

molecule N2F2
method RB3LYP
basis set 6-31G(d,p)
final energy -309.01241
RMS gradient 3.685e-06
point group C2v

Item Table

Item               Value     Threshold  Converged?
Maximum Force            0.000006     0.000015     YES
RMS     Force            0.000005     0.000010     YES
Maximum Displacement     0.000024     0.000060     YES
RMS     Displacement     0.000017     0.000040     YES


Low frequencies

Low frequencies -0.0012 -0.0012 0.0013 2.4177 4.2047 4.8781
Low frequencies 347.8622 561.2409 771.6170

Optimised Model Image

Kusabsoliv n2f2 optf pop image.png

Jmol Rotatable Molecule

logfile:Media:KUSABSOLIV_N2F2_OPTF_POP.LOG

optimised NFmolecule

Important geometric parameters

optimized bond distance and angle for N2F2 r(N-F)=1.39Â
θ(F-N-N)=114°

Kusabsoliv n2f2 optf vibrations.png

Vibrational data

mode 1 2 2 4 5 6
wavenumber(cm-1) 348 561 772 949 987 1637
symmetry A A B A B A
intensity 1 0 75 75 81 21

IR spectrum

Kuabsoliv n2f2 optf image IR.png

Charge Distribution Model

Kusabsoliv n2f2 optf chargedistribution.png

Atom Charge
Nitrogen -0.22
Fluorine 0.22

Kusabsoliv n2f2 optf displaychargedistribution.png


the molecule from the log file does not have bonds between the F and N atoms, what is going on here?

IR analysis

As there are 4 atoms in N2F2, 6 vibrations are expected from the 3N-6 rule. This matches to the 6 vibrations seen. There are four strong IR peaks shown at 772, 949, 989 and 1637. However, the peak at 348 does not show up as it is likely too low to detected, and the peak at 561 (A2, out of plane bending) is likely IR inactive as it does not change the molecules dipole. The vibration at 772cm-1, mode 3, is the asymmetric N-F stretch. The highest energy vibration at 1637cm-1 is the N=N double bond stretch.

Molecular Orbital Analysis

In N2F2, the core molecular orbitals are 1,2,3 and 4

MO9 for N2F2

Kusabsoliv n2f2 optf MO9 transparent png.PNG Kusabsoliv n2f2 optf LCAO.png

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