Vibrational Modes Format

Standard Vibrational Modes

The file format of the vibrational nodes has 4 columns corresponding to the four elements of the VibrationalStructures table:

• ElementName: The name of the structure representing the particular vibration
• StructureName: This is general structure that has to be matched within the molecule.
• Frequency: The frequency of the vibration
• Symmetry: The symmetry of the vibrational mode.

Symmetry

The symmetry number reflects to aspects of the structure.

The first is the structure bonding symmetry, that is to say that the structure can be matched to the same set of atoms in different ways. For example, two single bonded carbons, C1 and C2, bonded together with a single bond, C1-C2, can be matched as two carbons within a molecule, for example ethane as C1-C2 or C2-C1. The symmetry of 2 would reflect that the number of times that C1-C2 is matched in a molecule should be divided by 2.

The second is whether, when matched, the symmetry contribution should be added or subtracted from the total. This is a consequence of how the vibrational structures are used within JThermodynamics, namely for radical calculations. For example, for the calculation ethyl radical, c2h5, the difference in the vibrational modes are are found between c2h6 and c2h5.

For example, the radical loses one CCH bend because the loss of a hydrogen (according to the difference method).

However, in calculating the CCH bend using structures, the structure C-C-H is used. In c2h6, there are 6 matches for the c2h6, but actually no matches for the c2h5 because of the radical. For this reason, two more structures are needed to compensate for the radical, namely:

• C.-C-H: A radical on the non-hydrogen carbon
• C-C.-H A radical on the carbon with the hydrogen

Here, there are no matches for c2h6. C.-C-H matches 3 times for the three hydrogens away from the radical. C-C.H now matches two times for the hydrogens on the radical carbon. The sum total is 6-3-2=1, which reflects the loss of one CCH bend on the radical compared to the base calculation. This means that the symmetry factor is plus 1 for C-C-H structure and minus 1 for both C.-C-H and C-C.-H. The vibrational modes file would look something like:

CCH(tw)-Bend                          CCHStructure                  1150.0   1

CCH(tw)-Bend-RadicalComp              CC.HStructure                  1150.0  -1

CCH(tw)-Bend-RadicalComp              C.CHStructure                  1150.0  -1

The three structures are with no radical, with the carbon radical away from the hydrogens and the carbon radical with the hydrogen.

Unfortunately, this arrangement is a consequence of the substructure method.

Example input