Step 1 Computation of Vibrational Modes

Computational Engines

• Spartan versions 4.0 and higher for UNIX
• Gaussian 90, 92, 94, 98 for UNIX
• Hyperchem 5.0 for PC-Windows

Method

1. (1) Full geometry optimization to a local minimum
2. (2) Vibrational analysis (Gaussian keyword FREQ, Hyperchem requires level 9 output)
3. Extract vibrational modes using VIBREAD98, a program written by P. M. Lahti.

User controlled options

• Method of analysis (semiempirical is minimum level, but Gaussian allows computation up to the MP2 and DFT levels of theory).
• Size of vibrational mode distortion (in VIBREAD, the default is 0.3 of the standard normal mode deformation, to avoid anomalously long bond lengths).
• Alternative naming of any modes that have degenerate frequencies (note that most levels of theory overestimate by 10-18% the frequencies of the normal modes.

Result

• A molecular geometry for the system (convert to PDB with hydrogen atoms, or any other format that can be read by Chime.
• A set of XYZ files that encode (in ASCII) the vibrational normal modes. Each file is named as the computed frequency of the normal mode.

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