Vibrational frequency calculations should always be carried out to verify that a geometry optimisation has found a true minimum, and not just a saddle point.
They are also useful in their own right to find and visualise the normal modes of vibration.
The vibrational frequencies are only valid at an optimised geometry so we need to use the geometry obtained in the previous calculation.
To open a GAMESS output file in Avogadro, we need to first rename it from .out to .gamout. Once this is done, use File/Open in Avogadro to open the file.
Next click Extensions/GAMESS/”Input Generator” and choose “Frequencies” under Calculate. Click on Generate and save the GAMESS input file.
Run GAMESS using drag-and-drop as before.
It is worth opening the GAMESS output file in Wordpad and taking a look at the NORMAL COORDINATE ANALYSIS section (see below). (Hint: In Wordpad, it is useful to “Select All” and change the font size to 8 pt.)
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NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION
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ATOMIC WEIGHTS (AMU)
1 O 15.99491
2 H 1.00782
3 H 1.00782
MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS.
ANALYZING SYMMETRY OF NORMAL MODES...
FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2,
REDUCED MASSES IN AMU.
1 2 3 4 5
FREQUENCY: 1.33 0.16 0.00 0.33 6.17
SYMMETRY: A A A A A
REDUCED MASS: 1.01401 6.22305 6.00353 12.81051 1.03666
IR INTENSITY: 8.39984 0.00224 0.00000 0.52570 3.14657
1 O X -0.00000000 -0.04742972 0.23101688 -0.00000000 0.03749320
Y -0.00000000 0.23166471 0.04641338 -0.00000000 -0.02121402
Z -0.02017373 0.00000000 0.00000000 0.24794115 -0.00000000
2 H X -0.00000000 -0.04712588 0.23101681 -0.00000000 0.02610283
Y 0.00000000 0.21251345 0.04641346 -0.00000000 0.69693540
Z 0.87470814 0.00000000 0.00000000 0.02267176 -0.00000000
3 H X -0.00000000 -0.02927595 0.23101629 -0.00000000 -0.64326004
Y -0.00000000 0.23777094 0.04641325 -0.00000000 -0.25019888
Z 0.46974713 0.00000000 0.00000000 0.12677581 -0.00000000
TRANS. SAYVETZ X -0.00000000 -0.83563375 4.16074267 -0.00000000 -0.02228604
Y -0.00000000 4.15926402 0.83593088 -0.00000000 0.11091595
Z 1.03229856 0.00000000 0.00000000 4.11641335 -0.00000000
TOTAL 1.03229856 4.24237681 4.24388501 4.11641335 0.11313273
ROT. SAYVETZ X 0.74353714 -0.00000000 -0.00000000 -0.18361186 -0.00000000
Y -1.26256812 0.00000000 0.00000000 0.31924861 0.00000000
Z 0.00000000 -0.06777613 0.00000119 0.00000000 2.54154460
TOTAL 1.46523914 0.06777613 0.00000119 0.36828385 2.54154460
6 7 8 9
FREQUENCY: 8.88 1799.28 3812.34 3945.80
SYMMETRY: A A A A
REDUCED MASS: 1.01756 1.08983 1.03858 1.08500
IR INTENSITY: 0.86226 1.89217 0.00115 0.21702
1 O X 0.00000000 -0.04089486 -0.02564877 -0.05626299
Y -0.00000000 -0.05786491 -0.03630837 0.03975514
Z -0.02526058 0.00000000 -0.00000000 -0.00000000
2 H X 0.00000000 0.01882370 0.69075509 0.67710255
Y 0.00000000 0.67521698 -0.05628041 0.01073177
Z -0.47603300 0.00000000 -0.00000000 0.00000000
3 H X -0.00000000 0.63020849 -0.28369066 0.21583219
Y -0.00000000 0.24314193 0.63252054 -0.64167502
Z 0.86919577 -0.00000000 -0.00000000 0.00000000
TRANS. SAYVETZ X -0.00000000 0.00000129 -0.00000014 0.00000052
Y 0.00000000 0.00000111 0.00000004 -0.00000057
Z -0.00780139 0.00000000 -0.00000000 0.00000000
TOTAL 0.00780139 0.00000170 0.00000015 0.00000077
ROT. SAYVETZ X 1.50357589 -0.00000000 0.00000000 0.00000000
Y 1.38590886 -0.00000000 0.00000000 -0.00000000
Z 0.00000000 -0.00001496 -0.00000000 0.00000153
TOTAL 2.04486768 0.00001496 0.00000000 0.00000153
REFERENCE ON SAYVETZ CONDITIONS - A. SAYVETZ, J.CHEM.PHYS., 7, 383-389(1939).
NOTE - THE MODES J,K ARE ORTHONORMALIZED ACCORDING TO
SUM ON I M(I) * (X(I,J)*X(I,K) + Y(I,J)*Y(I,K) + Z(I,J)*Z(I,K)) = DELTA(J,K)
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THERMOCHEMISTRY AT T= 298.15 K
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USING IDEAL GAS, RIGID ROTOR, HARMONIC NORMAL MODE APPROXIMATIONS.
P= 1.01325E+05 PASCAL.
ALL FREQUENCIES ARE SCALED BY 1.00000
THE MOMENTS OF INERTIA ARE (IN AMU*BOHR**2)
2.07948 4.38456 6.46404
THE ROTATIONAL SYMMETRY NUMBER IS 1.0
THE ROTATIONAL CONSTANTS ARE (IN GHZ)
867.08597 411.23564 278.94127
THE HARMONIC ZERO POINT ENERGY IS (SCALED BY 1.000)
0.021773 HARTREE/MOLECULE 4778.712676 CM**-1/MOLECULE
13.663039 KCAL/MOL 57.166155 KJ/MOL
Q LN Q
ELEC. 1.00000E+00 0.000000
TRANS. 3.00431E+06 14.915558
ROT. 8.69029E+01 4.464791
VIB. 1.00017E+00 0.000170
TOT. 2.61127E+08 19.380518
E H G CV CP S
KJ/MOL KJ/MOL KJ/MOL J/MOL-K J/MOL-K J/MOL-K
ELEC. 0.000 0.000 0.000 0.000 0.000 0.000
TRANS. 3.718 6.197 -36.975 12.472 20.786 144.800
ROT. 3.718 3.718 -11.068 12.472 12.472 49.594
VIB. 57.170 57.170 57.166 0.106 0.106 0.014
TOTAL 64.607 67.086 9.123 25.050 33.364 194.407
VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 3.649 J/MOL
E H G CV CP S
KCAL/MOL KCAL/MOL KCAL/MOL CAL/MOL-K CAL/MOL-K CAL/MOL-K
ELEC. 0.000 0.000 0.000 0.000 0.000 0.000
TRANS. 0.889 1.481 -8.837 2.981 4.968 34.608
ROT. 0.889 0.889 -2.645 2.981 2.981 11.853
VIB. 13.664 13.664 13.663 0.025 0.025 0.003
TOTAL 15.441 16.034 2.180 5.987 7.974 46.464
VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 0.872 CAL/MOL
......END OF NORMAL COORDINATE ANALYSIS......
Open the output file in wxMacMolPlt. List the normal modes with Subwindow/Frequencies.
If you click on any mode, the main window will update to show you the displacement vectors associated with it. You can animate the vibration with View/Animate Mode.