Hi all,
Based on QM vibrational frequency calculations of a small molecule/fragment, I have derived force constants from the Hessian matrix. Bond force constants are based on the notion of an atom pair A-B, where atom A feels the displacement of atom B. I have performed significant testing on my code, for example with variation in bond order e.g, N///N, N=N, N-N, I see a drop in the force constant, the further in to an organic straight chain ...C-C-C-C-C... the force constant becomes more uniform between C-Cs, an almost no existent force constant for atoms which are not bonded, and finally a huge negative force constant when both A-B are actually the same atom.
However, I face a problem.
Unless the molecule is diatomic, or I am close to the centre of a long chained organic, the force constant for A-B is not the same as B-A. This in theory is understandable on the principle that hydrogen of NCH experiences greater displacement than the carbon. So using second order tensors, the force constant for C-H is much greater than the force constant for H-C (where C is seen is the displacing atom, and H experiences the force).
I know this technique has been performed several times to modify zinc binding domains in Amber (e.g., J. Chem Theory. Comput., Vol. 6, No 6., 2010 - Lin and Wang) but no description has been given why ZN-NB (ZN feels the displacement of atom NB) force constant was calculated rather than NB-ZN.
Apologies for the length description, I hope someone can help.
Many thanks for your help
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
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Received on Thu Oct 15 2015 - 05:30:04 PDT
