Step 1 Computation of Vibrational Modes

• Spartan versions 4.0 and higher for UNIX and 32-bit PC-Windows
• Gaussian 90, 94, 98, 03 (in progress) for UNIX
• GAMESS for UNIX
• Hyperchem 5.0 and higher (in progress) for PC-Windows

Method

• Full geometry optimization to a local minimum
• Vibrational analysis (Gaussian keyword FREQ, Hyperchem requires level 9 output)
• Extract vibrational modes using VIBREAD03, a program written by P. M. Lahti. Caveat emptor! No claims are made for bugfree nature of VIBREAD, but PML tries to implement fixes brought to his attention. Expansion of functionality is slow to nonexistent, due to lack of time (sorry).

User controlled options for creating a page that shows molecules and molecular spectra

• 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).
• You have control over linking computed modes to the actual spectra (note that most computational levels of theory overestimate the frequencies of the normal vibrational modes by 10-18% ).

Result

• A molecular geometry for the system (convert to PDB with hydrogen atoms, or any other format that can be read by Chime) is created by the computations.
• A set of XYZ files that encode (in ASCII) the vibrational normal modes is extracted from the output of the computational run. Each file is named as the computed frequency of the normal mode.
• The page designer will use his/her own digitized spectrum, in the international standard JCAMP-DX format.