I.2 Description of
KiSThelP
Input File for a ReactionPath:
In order to perform a rate constant calculation, the user
must prepare two (unimolecular) or three (bimolecular) files. For an unimolecular reaction one file need for the reactant and another one for the transition state.
For a bimolecular reaction, two files are expected for the two reactants and one for the transition state. For reactant(s), the expected file format
is exactly the same as the one used for Molecular System single calculations. For the transition state, a so-called
reactionpath .kinp input file must be supplied. This reactionpath .kinp file has a specific file format. It is important to note that in KiSThelP a transition
state is considered as a reaction path involving only one point. Thus, if you want to compute TST rate constant,
a reactionpath file must be supplied. Of course, for VTST calculations, this reactionpath file
will include several path points.
We focus here on the specific format of the reactionpath input file
that slightly differs from the "Molecular" input file format.
The first way to build a ReactionPath input file is by manually writing an ASCII input file. Alternatively, it is to be noted that KiSThelP provides a "build reaction path" tool in the "Data" menu. Then, a single ReactionPath.kinp file is built (see section II.2). This is the easiest way to build (automatically) a ReactionPath .kinp file from existing individual .kinp files or either quantum chemistry output files directly ! Using this possibility involves the following procedure:
a) perform an IRC calculation
b) perform a frequency calculation on each individual reaction path points, including the TS !
c) run the "build reaction path" facility ( see section II.2 ) to generate the reactionpath.kinp file, which will be used for VTST calculations next.
A ReactionPath input file describes one (transition state) or more points along the reaction path.
In the extrem case, this file reduces to the description of the transition state alone. For each point along
the reaction path, the 7 keywords (MASS, FREQUENCIES,
NUMBER OF SYMMETRY, LINEAR, MOMENT
OF INERTIA, POTENTIAL ENERGY,
ELECTRONIC DEGENERACY), the same as before for a molecular
system, are wrapped into a new section entitled : **POINT ... **END. But additionnaly, a 8th keyword
appears: *IRC, that tells KiSThelP the IRC coordinate of that point and that enables VTST calculations to be run.
DIFFERENT SECTIONS :
**POINT
*IRC
0.0 (signed reaction coordinate corresponding to the transition state point on
the reaction path)
*END
*MASS
mass of the system in amu
*END
*FREQUENCIES
list of vibrational frequencies in cm-1, including the imaginary
frequency
*END
*LINEAR
only "linear" or "not
linear" text values are allowed
here
*END
*NUMBER OF SYMMETRY
rotational symmetry number
*END
*MOMENT OF INERTIA
list of
moments of inertia in amu bohr**2
*END
*POTENTIAL ENERGY
electronic energy in hartree
*END
*ELECTRONIC DEGENERACY
degeneracy of the electronic state
*END
**END
****** Remark 1 ******
Though
the "NUMBER OF SYMMETRY" section must always be
given, the reaction path degeneracy (given through GUI) will be
used
instead to
perform rate constant calculations. In this case (rate constant
calculation),
the symetry number is unused in statistical calculations.
****** Remark 2 ******
To account for deviations from the harmonic oscillator, a hindered
rotor approach has been implemented in KiSThelP (HRDS treatment).
To perform such calculation on a selected vibrational mode, a second
parameter (rotational energy barrier in kJ/mol) is required in addition
to the vibrational frequency number (see section I.1).
*********************
EXAMPLE 1 for a Transition State :
**POINT
*IRC
0.0
*END
*MASS (in uma)
75.04460
*END
*FREQUENCIES (in cm-1)
3772.7857
3265.5143
3260.2959
3219.8950
3174.8060
3130.8936
1795.7441
1575.8614
1533.3768
1522.9003
1486.8323
1438.1602
1301.6499
1237.1175
1151.1885
1126.8853
990.9077
936.8436
895.1968
821.3156
725.8243
530.7972
489.6153
451.7419
338.7840
249.6141
182.3330
129.7635
41.1522
2272.1539i
*END
*LINEAR
not linear
*END
*NUMBER OF SYMMETRY
1
*END
*MOMENT OF INERTIA (in au)
189.08579
640.69700
799.95573
*END
*POTENTIAL ENERGY (in hartree)
-268.09618214
*END
*ELECTRONIC DEGENERACY
2
*END
**END
EXAMPLE 2 for a Reaction Path :
**POINT
*IRC
0.0
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
1770.0579i
570.0592
570.0614
1139.3232
1203.1477
1203.1480
1502.7396
1502.7400
1903.6500
3185.6870
3349.6264
3349.6268
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
11.92294961757795
30.48669371604351
30.48669371604351
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8323867
*END
**END
**POINT
*IRC
-0.1
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
2114.0966i
545.2454
545.2486
1192.0494
1289.5267
1289.5271
1509.8776
1509.8786
1551.5818
3179.1802
3338.7423
3338.7467
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
11.889417921927286
30.071718150999292
30.07172316173638
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8333658
*END
**END
**POINT
*IRC
-0.2
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
1969.125i
450.7630
450.7636
1246.8886
1352.5269
1352.5270
1394.3540
1521.8283
1521.8288
3173.3135
3328.0834
3328.0878
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
11.859106454739242
29.798236748052844
29.798246588080772
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8352914
*END
**END
**POINT
*IRC
-0.3
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
1329.825i
297.1806
297.1825
1321.2164
1387.2080
1392.9268
1392.9274
1540.1792
1540.1795
3168.2341
3317.8268
3317.8289
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
11.82726308294923
29.630046350884125
29.63005121551389
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8380552
*END
**END
**POINT
*IRC
-0.4
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
198.0781i
105.8839i
105.8749i
1330.1773
1410.4263
1410.4268
1561.5494
1561.5496
1767.1986
3164.4650
3308.5387
3308.5430
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
11.789673900467806
29.566461320842393
29.566466164615896
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8412647
*END
**END
**POINT
*IRC
0.1
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
1242.2258i
538.1267
538.1315
1086.7276
1093.4453
1093.4457
1498.5914
1498.5927
2458.3411
3192.4154
3360.0432
3360.0486
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
11.961791238427828
31.066591258301905
31.066601953834386
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8323049
*END
**END
**POINT
*IRC
0.2
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
843.9706i
487.1358
487.1406
977.2909
977.2911
1038.8413
1496.1562
1496.1574
2985.7624
3199.4437
3368.8246
3368.8293
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
12.004385481520156
31.77531951968226
31.775325114230053
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8328432
*END
**END
**POINT
*IRC
0.3
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
564.8542i
442.3524
442.3549
879.8362
879.8363
994.9133
1494.4878
1494.4883
3199.0251
3368.8540
3376.7781
3376.7800
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
12.047765887046097
32.59172289909308
32.59172289909308
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8337871
*END
**END
**POINT
*IRC
0.4
*END
*MASS (in amu)
17.03913
*END
*NUMBER OF SYMMETRY
1
*END
*FREQUENCIES (in cm-1)
320.1659i
405.5857
405.5921
800.3698
800.3702
953.9149
1493.3058
1493.3071
3204.8097
3383.4875
3383.4929
3635.4116
*END
*ELECTRONIC DEGENERACY
2
*END
*MOMENT OF INERTIA (in Amu.bohr**2)
12.090603115464381
33.465705324450965
33.465705324450965
*END
*LINEAR
not linear
*END
*POTENTIAL ENERGY (in hartree)
-40.8349497
*END
**END