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Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations.


Type

Article

Change log

Authors

Wales, David J 
Carr, Joanne M 

Abstract

A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.

Description

Keywords

Chemistry, Computational Chemistry, Molecular Mechanics, Geometry optimization, Computer simulation, Protein, Peptide, Atomic Cluster

Journal Title

J Chem Theory Comput

Conference Name

Journal ISSN

1549-9618
1549-9626

Volume Title

Publisher

American Chemical Society (ACS)
Sponsorship
Engineering and Physical Sciences Research Council (EP/H042660/1)
This work was supported by the Engineering and Physical Sciences Research Council [grant number EP/H042660/1]