TD calculations using the .tdi options file

Ther­mo­dy­nam­ic cal­cu­la­tions tak­ing into account the inter­nal rota­tions.
2. Man­u­al pro­ce­dure using the TD option file (.tdi)

Because auto­mat­ic pro­ce­dure has the restric­tions in the set­ting of the addi­tion­al cal­cu­la­tion para­me­ters, the man­u­al mode of the TD cal­cu­la­tions can be used. For this pur­pose a TD options file with exten­sion .tdi should be cre­at­ed. The tdi-file is a reg­u­lar ASCII file and can be cre­at­ed using any ASCII file edi­tor.

Using the pre­vi­ous exam­ple — SiF3OH mol­e­cule (file Moltran-Sam­ple1) — cre­ate the file Moltran-Sample1.tdi con­tain­ing two lines:

T=298.15 P=101325. ZeroModes=(1,2,3,4,5,6) RotNum=1 Vibr=3 Axes=(1,5) Group=(5,6) Gen­Co­ord V0=2.5 Rot=3

Here, the com­mand Vibr=3 means that the vibra­tion mode 3 will be con­sid­ered as an inter­nal rota­tion. Option Axes=(1,5) means that the rota­tion axis is the Si-O direc­tion (atoms 1 and 5), and the rotat­ing group is atoms 5 and 6 (Group=(5,6)). Note, that Group=(1,2,3,4) will give the same results. V0=2.5 means that the rota­tion bar­ri­er height is 2.5 kJ/mol. Rot=3 for the giv­en vibra­tion mode means that the rota­tion has the 3-fold bar­ri­er and the cor­re­spond­ing rota­tion sym­me­try num­ber (3) for this mode should be set. Com­mand Gen­Co­ord is not nec­es­sary and tells MOLTRAN gen­er­ate the input files (in GAMESS for­mat) for cal­cu­la­tion of the rota­tion poten­tial point-by-point. T= and P= options set the tem­per­a­ture and pres­sure, and Zero­Modes defines the nor­mal modes cor­re­spond­ing to trans­la­tions and rotati­tions of mol­e­cule as whole. Oth­er options which can be found in tdi-file are explained in the MOLTRAN man­u­al.

Please note that it is fre­quent­ly con­ve­nient to deter­mine val­ues of Axis, Group, and V0 options on the basis of ARIR results from the pre­vi­ous MOLTRAN run (see TD cal­cu­la­tions using ARIR).

After the .tdi-file is cre­at­ed, run the com­mand:

moltran Moltran-Sample1.txt /0

or just start MOLTRAN, set input and tdi-file names and run TD cal­cu­la­tions using menu items “Command”->“Thermodynamics”->“OK”. Close the pro­gram.

Inspect the out­put file (Moltran-Sample1.log). Skip­ping the begin­ning of file find the data marked with a head­er:

*** Con­tri­bu­tions of inter­nal rota­tions ***

The cal­cu­la­tion of inter­nal rota­tion con­tri­bu­tions starts here. At first, MOLTRAN  prints out the mol­e­c­u­lar para­me­ters used in the fur­ther analy­sis:

*** Internal rotation No.  1 (replacing the vibration mode  7)

Masses (amu) and moments of inertia (amu*bohr^2) of rotating groups:
Group 1:  M1=  17.00274   I1=    2.22532
Group 2:  M2=  84.97213   I2=  443.24832
Reduced I=I1*I2/(I1+I2)     =    2.21421
Pitzer's estimator I0       =    2.20962
Pitzer's estimator I        =    2.20962
Rotation axes:
Point 1:  Center of mass of Group1. Coords:  3.100751  0.160845  0.004723
Point 2:  Center of mass of Group2. Coords: -0.705404 -0.019023 -0.001077

The rota­tion bar­ri­er height is esti­mat­ed on the basis of max­i­mum val­ue of poten­tial curve. Because the obtained bar­ri­er height is low­er than 1.4RT at the giv­en tem­per­a­ture, the con­clu­sion is made that this rota­tion is free:

Rotation barrier height for n-fold potential V=V0/2*[1-Cos(n*x)] (n=1):
V0 =     2.4783   kJ/mol
0.5923 kcal/mol
0.9997 RT   (T=  298.15K) => Free rotation (V0<1.4RT)

Because of Gen­Co­ord option MOLTRAN gen­er­ates the coor­di­nates cor­re­spond­ing the point of rota­tion and print the coor­di­nates for all the probed points:

Unique point     : 1
Internal rotation: 1  Rotation angle:   0.0
------------------------------------------------------------
Si1          14           0.003045    0.007644    0.000019
F2            9          -0.586240    1.467400   -0.005417
F3            9          -0.546203   -0.757879    1.270605
F4            9          -0.541588   -0.765800   -1.267765
O5            8           1.608317    0.131687    0.002445
H6            1           2.157117   -0.654006    0.003357
------------------------------------------------------------

Please note that sev­er­al input files with these coor­di­nates will be cre­at­ed in the work­ing direc­to­ry ready for cal­cu­la­tion of ener­gy by quan­tum chem­i­cal method.

Then, the rota­tion bar­ri­er and free-rota­tion par­ti­tion func­tions are print­ed:

Rotation barrier height for n-fold potential V=V0/2*[1-Cos(n*x)] (n=3):
V0 =     2.5000   kJ/mol
0.5975 kcal/mol
1.0085 RT   (T=  298.15K) => Free rotation (V0<1.4RT)

Free-rotation function: 1/Qf =     6.130750E-01   Qf =     1.631122E+00
Free-rotation (Pitzer): 1/Qf =     6.137101E-01   Qf =     1.629434E+00

Now, the ther­mo­dy­nam­ic con­tri­bu­tion is esti­mat­ed using three dif­fer­ent approx­i­ma­tions: har­mon­ic oscil­la­tor, free rota­tor, and Pitzer-Gwinn mod­el. The most com­pre­hen­sive is the last col­umn (obtained on the basis of Pitzer-Gwinn’s numer­ic tables for com­pre­hen­sive esti­ma­tor of iner­tia moments). The results are print­ed for sev­er­al sep­a­rate vibra­tions (if any) and for total con­tri­bu­tion of all the inter­nal rota­tions.

Thermodynamic functions for internal rotation  1 (vibration mode  7)

Harmonic   Free Rotator   Pitzer-Gwinn tables
Ocsillator  I(*)    I(**)     I(*)    I(**)
C,    J/K/mol=    8.110    4.157    4.157    4.672    4.672
U,    kJ/mol =    2.541    1.239    1.239    1.259    1.259
H,    kJ/mol =    2.541    1.239    1.239    1.259    1.259
S,    J/K/mol=   13.428    8.225    8.217    7.892    7.883
G,    kJ/mol =   -1.463   -1.213   -1.210   -1.094   -1.092
U+ZPE,kJ/mol =    3.219    1.918    1.918    1.938    1.937
H+ZPE,kJ/mol =    3.219    1.918    1.918    1.938    1.937
G+ZPE,kJ/mol =   -0.785   -0.534   -0.532   -0.415   -0.413
I(*)  - reduced moments of inertia are calculated by formula 1/I=1/Ia+1/Ib
I(**) - reduced moments of inertia are calculated by Pitzer-Gwinn formulas
Note: I(*)=I(**) for symmetric rotors.

Then, the total val­ues of ther­mo­dy­nam­ic func­tions of the mol­e­cule are print­ed togeth­er with total ener­gy val­ues cor­rect­ed for the total (electr+trans+rota+vibr+int.rot.) ther­mo­dy­nam­ic con­tri­bu­tions.

Total values of thermodynamic functions (T=  298.15 K,  P= 101325.00 Pa)
taking into account  1 internal rotations  (in different approximations)
----------------------------------------------------------------------------------------------------------------------
Harmonic   Free Rotator   Pitzer-Gwinn tables
Ocsillator  I(*)    I(**)     I(*)    I(**)
----------------------------------------------------------------------------------------------------------------------
Cv, J/K/mol=   77.176   73.223   73.223   73.738   73.737
Cp, J/K/mol=   85.490   81.537   81.537   82.053   82.052
U,  kJ/mol =   76.986   75.007   75.007   75.705   75.704
H,  kJ/mol =   79.465   77.486   77.486   78.184   78.183
S,  J/K/mol=  318.525  313.322  313.314  312.989  312.980
G,  kJ/mol =  -15.503  -15.931  -15.929  -15.134  -15.132
----------------------------------------------------------------------------------------------------------------------
I(*)  - reduced moments of inertia are calculated by formula 1/I=1/Ia+1/Ib
I(**) - reduced moments of inertia are calculated by Pitzer-Gwinn formulas
Note: Internal rotation contributions to U, H, G include U0=H0=ZPE
in HO and PG models (U0=H0=0 in FR model)

*** Total energy corrected by TD functions (including internal rotations) ****
Minimum electronic-nuclear energy was taken from the input file at step:   4
Minimum Etot:    -665.26660848  (Please check the program decision manually!)

Harmonic             Free Rotator               Pitzer-Gwinn tables
Ocsillator        I(*)           I(**)          I(*)           I(**)
E      -665.26660848  -665.26660848  -665.26660848  -665.26660848  -665.26660848
E+ZPE  -665.24329545  -665.24329545  -665.24329545  -665.24329545  -665.24329545
E+U    -665.23728531  -665.23803928  -665.23803928  -665.23777341  -665.23777352
E+H    -665.23634110  -665.23709507  -665.23709507  -665.23682920  -665.23682931
E+G    -665.27251350  -665.27267658  -665.27267561  -665.27237283  -665.27237201

The val­ues here are the results of total ener­gy cor­rect­ed by the con­tri­bu­tions of inter­nal rota­tion cal­cu­lat­ed at the cur­rent tem­per­a­ture and pres­sure ( pro­gram defaults: T=298.15K, P=101325Pa).

The file is fin­ished with the ther­mo­dy­nam­ic func­tions cal­cu­lat­ed at dif­fer­ent tem­per­a­tures. As before, the tem­per­a­ture range can be set man­u­al­ly (default 0–500 K). Now, the inter­nal rota­tion con­tri­bu­tions are includ­ed. The WARNING’s are just a result of numer­i­cal errors dur­ing the inter­po­la­tion of Pitzer-Gwinn tables for low tem­per­a­tures for the light mol­e­cules (the tables are giv­en for the val­ues of the rota­tion par­ti­tion func­tion Qf large enough and their extrap­o­la­tion to zero is fre­quent­ly unro­bust). In this case, just ignore the val­ues with warn­ings. These val­ues can be incor­rect and should not be used. How­ev­er, they have no effect on the remain­ing val­ues.