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Step 1
Computation of Vibrational Modes |
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Computational chemistry programs (use these to generate vibrational modes for
molecules)
Method
- Full geometry optimization to a
local minimum
- Vibrational analysis (Gaussian
keyword FREQ, Hyperchem requires level 9 output)
- Extract vibrational modes
using
VIBREAD98, 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.
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(updated 11 Aug 2000)