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Title of Journal: J Math Chem

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Abbravation: Journal of Mathematical Chemistry

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Springer Netherlands

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DOI

10.1016/0164-1212(91)90086-l

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ISSN

1572-8897

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Normal mode analysis of molecular motions in curvi

Authors: Janne Pesonen Krister O E Henriksson Jose Ramon LópezBlanco Pablo Chacón
Publish Date: 2012/03/11
Volume: 50, Issue: 6, Pages: 1521-1549
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Abstract

Normal mode analysis NMA was introduced in 1930s as a framework to understand the structure of the observed vibrationrotation spectrum of several small molecules During the past three decades NMA has also become a popular alternative to figuring out the largescale motion of proteins and other macromolecules However the “standard” NMA is based on approximations which sometimes are unphysical Especially problematic is the assumption that atoms move only “infinitesimally” which of course is an oxymoron when large amplitude motions are concerned The “infinitesimal” approximation has the further unfortunate side effect of masking the physical importance of the coupling between vibrational and rotational degrees of freedom Here we present a novel formulation of the NMA which is applied for finite motions in nonEckart bodyframe Contrary to standard normal mode theory our approach starts by assuming a harmonic potential in generalized coordinates and tries to avoid the linearization of the coordinates It also takes explicitly into account the Coriolis terms which couple vibrations and rotations and the terms involving Christoffel symbols which are ignored by default in the standard NMA We also computationally explore the effect of various terms to the solutions of the NMA equation of motions

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