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Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules.

Authors
Hnizdo-V; Darian-E; Fedorowicz-A; Demchuk-E; Li-S; Singh-H
Source
J Comput Chem 2007 Feb; 28(3):655-668
NIOSHTIC No.
20031402
Abstract
A method for estimating the configurational (i.e., non-kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest-neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi-harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information-theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters.
Keywords
Computer-models; Simulation-methods; Motion-studies; Molecular-structure; Molecular-biology; Sampling; Sampling-methods
CODEN
JCCHDD
Publication Date
20070201
Document Type
Journal Article
Email Address
vbh5@cdc.gov
Fiscal Year
2007
NTIS Accession No.
NTIS Price
Issue of Publication
3
ISSN
0192-8651
NIOSH Division
HELD
Source Name
Journal of Computational Chemistry
State
WV
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