In my bachelor thesis, I am trying to use the VEDA program to analyze the vibrational energy distribution to associate different vibrations to the calculated modes from gaussian. I am stuck now because the VEDA program seems to provide unrealistic output. I calculated methane as a simple way to show my problems.
The input file to gaussian:
%chk=methan.chk
#p opt freq=SaveNormalmodes B3LYP/6-311G(d,p) nosymm
methan
0 1
6 -2.69391 0.67007 0.00000
1 -1.62391 0.67007 0.00000
1 -3.05057 -0.15258 -0.58389
1 -3.05058 1.58706 -0.42049
1 -3.05058 0.57573 1.00438
I use the log and fchk file from this calculation as input for VEDA. VEDA creates the .fmv file from this input.
#p opt freq=SaveNormalmodes B3LYP/6-311G(d,p) nosymm
Atomic orientation and masses
1 6 -2.69391033 0.67006991 0.00000005 12.00000000
2 1 -1.60343431 0.67007262 0.00000174 1.00782504
3 1 -3.05739820 -0.16832644 -0.59506760 1.00782504
4 1 -3.05740398 1.60460983 -0.42853870 1.00782504
5 1 -3.05740406 0.57392428 1.02360451 1.00782504
Force constants in Cartesian coordinates
5.33572579E+00 3.66810060E-02 3.66778578E-02 3.66800417E-02 3.04938267E-02
4.78002374E-02 9.34030448E-02 -1.23337201E-02 -7.49599366E-02 -8.44033441E-02
5.90658770E-02 -4.86412743E-02 6.40541790E-02 1.12695453E-01 0.00000000E+00
3.66810060E-02 5.33567095E+00 3.66758568E-02 3.66792176E-02 3.05027864E-02
-1.23355319E-02 -7.49650905E-02 4.77820938E-02 9.34122780E-02 -8.43965515E-02
5.90646100E-02 -4.86546903E-02 -1.12696475E-01 -6.40417842E-02 0.00000000E+00
3.66778578E-02 3.66758568E-02 5.33575627E+00 3.66785235E-02 -1.91501878E-02
5.31942717E-02 -8.29810618E-02 5.32006592E-02 -8.29790123E-02 7.87153470E-02
4.16992065E-02 1.25083636E-01 6.25372507E-02 -6.25463857E-02 0.00000000E+00
3.66800417E-02 3.66792176E-02 3.66785235E-02 5.33573582E+00 -4.18424802E-02
-8.86563336E-02 6.45291179E-02 -8.86563832E-02 6.45448771E-02 9.00810935E-02
-1.59827744E-01 -2.77950854E-02 -1.39023999E-02 1.38926855E-02 0.00000000E+00
3.04938267E-02 3.05027864E-02 -1.91501878E-02 -4.18424802E-02 3.03668368E-01
-1.34786428E-01 -2.01270285E-01 -1.34786926E-01 -2.01266979E-01 3.68441953E-01
2.06837032E-01 -1.25413382E-01 -6.27074976E-02 6.27058841E-02 7.78459520E+01
4.78002374E-02 -1.23355319E-02 5.31942717E-02 -8.86563336E-02 -1.34786428E-01
5.72465784E-01 -3.47913849E-01 -3.19509681E-02 3.82124777E-01 -4.39938925E-01
1.65917376E-01 1.44129337E-01 2.18665399E-01 7.45360625E-02 -6.80511800E+00
9.34030448E-02 -7.49650905E-02 -8.29810618E-02 6.45291179E-02 -2.01270285E-01
-3.47913849E-01 1.11839029E+00 3.82124891E-01 -5.42349371E-01 -4.08981216E-01
-2.25554975E-01 -1.06247502E-01 8.31603827E-03 1.14563541E-01 1.70127922E+00
-1.23337201E-02 4.77820938E-02 5.32006592E-02 -8.86563832E-02 -1.34786926E-01
-3.19509681E-02 3.82124891E-01 5.72467245E-01 -3.47916055E-01 -4.39937727E-01
1.65917460E-01 1.44130988E-01 -7.45350363E-02 -2.18666024E-01 1.70128008E+00
-7.49599366E-02 9.34122780E-02 -8.29790123E-02 6.45448771E-02 -2.01266979E-01
3.82124777E-01 -5.42349371E-01 -3.47916055E-01 1.11839152E+00 -4.08983943E-01
-2.25552099E-01 -1.06251760E-01 -1.14564521E-01 -8.31276143E-03 1.70127939E+00
-8.44033441E-02 -8.43965515E-02 7.87153470E-02 9.00810935E-02 3.68441953E-01
-4.39938925E-01 -4.08981216E-01 -4.39937727E-01 -4.08983943E-01 1.32939890E+00
-8.75646378E-02 4.96524369E-02 2.48257890E-02 -2.48266478E-02 1.70127933E+00
5.90658770E-02 5.90646100E-02 4.16992065E-02 -1.59827744E-01 2.06837032E-01
1.65917376E-01 -2.25554975E-01 1.65917460E-01 -2.25552099E-01 -8.75646378E-02
4.56529024E-01 2.29232226E-02 1.14607952E-02 -1.14624275E-02 0.00000000E+00
-4.86412743E-02 -4.86546903E-02 1.25083636E-01 -2.77950854E-02 -1.25413382E-01
1.44129337E-01 -1.06247502E-01 1.44130988E-01 -1.06251760E-01 4.96524369E-02
2.29232226E-02 2.83728369E-01 1.41864449E-01 -1.41863920E-01 0.00000000E+00
6.40541790E-02 -1.12696475E-01 6.25372507E-02 -1.39023999E-02 -6.27074976E-02
2.18665399E-01 8.31603827E-03 -7.45350363E-02 -1.14564521E-01 2.48257890E-02
1.14607952E-02 1.41864449E-01 2.88104389E-01 1.46239939E-01 0.00000000E+00
1.12695453E-01 -6.40417842E-02 -6.25463857E-02 1.38926855E-02 6.27058841E-02
7.45360625E-02 1.14563541E-01 -2.18666024E-01 -8.31276143E-03 -2.48266478E-02
-1.14624275E-02 -1.41863920E-01 1.46239939E-01 2.88103859E-01 3.11383808E+01
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 7.78459520E+01
-6.80511800E+00 1.70127922E+00 1.70128008E+00 1.70127939E+00 1.70127933E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 3.11383808E+01 0.00000000E+00
Harmonic frequencies
F =3134.24 IR = 27.91 S = A
3 -7 5 -31 -1 1 4 6 7 -28 72 -32 15 2 -40
F =3134.23 IR = 27.91 S = A
-7 1 5 69 0 1 -5 -8 -4 1 -7 5 22 6 -66
F =3134.22 IR = 27.91 S = A
-4 -6 -5 41 -1 -1 28 66 46 -7 15 -9 -10 -4 24
F =3028.36 IR = 0.00 S = A
0 0 0 50 0 0 -17 -38 -27 -17 43 -20 -17 -4 47
F =1560.38 IR = 0.00 S = A
0 0 0 0 -33 -38 46 -20 0 -14 16 46 -32 37 -8
F =1560.38 IR = 0.00 S = A
0 0 0 0 38 -33 -11 -25 42 45 21 6 -34 -33 -15
F =1341.02 IR = 16.94 S = A
0 -12 -4 0 57 19 -22 9 -15 15 16 38 4 59 5
F =1341.02 IR = 16.94 S = A
-7 3 -10 -5 -15 47 24 -38 31 18 27 28 47 -12 10
F =1341.02 IR = 16.94 S = A
-10 -3 7 -8 12 -32 47 5 -37 52 6 -29 31 7 20
To receive the potential energy distribution I create the .dd2 file with VEDA and use the standard optimization options in Veda. I optimize the file until there is no more improvement in the Emp value calculated by VEDA.
methan.vdf
abbreviation of: e:\bachelorarbeit\veda\methan\methan.ved
IR spectrum from file: e:\bachelorarbeit\veda\methan\methan.log
diagonality factor = 51.86 <EPm> = 53.85
IR CM-1
27.91 3134.24 *8201.25 s2 48 s5 10 s9 29
27.91 3134.23 *2652.43 s3 92
27.91 3134.22 *1441.36 s2 -10 s5 -16 s9 57
0.00 3028.36 *1434.71 s1 27 s7 -27 s8 37
0.00 1560.38 *1382.52 s4 -15 s5 14 s7 31 s8 22
0.00 1560.38 *1081.74 s4 55 s7 17 s8 16
16.94 1341.02 * 885.94 s1 51 s5 22
16.94 1341.02 * 447.29 s4 17 s6 76
16.94 1341.02 *-8129.88 s2 -40 s5 39 s8 12
with (*) frequencies calculated by Veda
methan.dd2
Average max. Potential Energy <EPm> = 53.852
TED Above 100 Factor TAF=0.000
Average coordinate population 1.333
Most complex coordinate No. 4 , population = 2
s 1 1.00 STRE 1 4 CH 1.090476 f1435 27 f886 51
s 2 1.00 STRE 1 5 CH 1.090476 f8201 48 f1441 10 f8130 40
s 3 1.00 STRE 1 2 CH 1.090476 f2652 92
s 4 1.00 STRE 1 4 CH 1.090476 f1383 15 f1082 55 f447 17
1.00 1 3 CH 1.090476
s 5 1.00 BEND 2 1 3 HCH 109.47 f8201 10 f1441 16 f1383 14 f886 22 f8130 39
1.00 3 1 4 HCH 109.47
s 6 1.00 BEND 3 1 4 HCH 109.47 f447 76
s 7 1.00 BEND 4 1 5 HCH 109.47 f1435 27 f1383 31 f1082 17
1.00 3 1 4 HCH 109.47
s 8 1.00 OUT 1 4 2 5 CHHH 19.47 f1435 37 f1383 22 f1082 16 f8130 12
s 9 1.00 OUT 1 3 2 4 CHHH 19.47 f8201 29 f1441 57
Why differ the calculated modes from methan.vdf file to this extent in comparison to the calculated modes from gaussian? Is there an error in my input, which results in that difference? The calculations of methane should result in CH-stretching vibrations at 3000 1/cm. The assignment by VEDA for the mode at 3134.23 1/cm from the gaussian log file or 2652.43 1/cm calculated by VEDA seems right. The other modes over 3000 1/cm are partly assigned to the bending-vibrations s5 and out-of-plane-vibrations s9 which are described in the dd2 file. I do not understand why the VEDA program assigns these vibrations to a mode at 3000 1/cm. In a vibration visualization by VEDA and other programs, the modes calculated over 3000 1/cm are clearly identified as CH-stretching vibrations.