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Implementation and use of the method of prudent ascent in conformational analysis using molecular mechanics
Author(s) -
Hooft Rob W. W.,
Kanters Jan A.,
Kroon Jan
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120806
Subject(s) - dihedral angle , energy minimization , order (exchange) , cellobiose , basis (linear algebra) , minification , potential energy , point (geometry) , degrees of freedom (physics and chemistry) , computational chemistry , potential energy surface , chemistry , computer science , molecule , mathematics , mathematical optimization , thermodynamics , classical mechanics , physics , geometry , cellulose , hydrogen bond , organic chemistry , finance , economics , cellulase
In two‐dimensional conformational analysis the current practice is to perform an energy minimization for all possible combinations of two dihedral angles in the molecule, in a fixed order, and apply a certain dihedral angle step‐size. A newly developed method is presented in which the order of the evaluation points on the energy‐surface is not fixed, but is dependent on all previous results in a way which we call “the method of prudent ascent.” In this method the most promising calculation is carried out first, thus minimizing the risk of atomic collisions. In order to be able to take care of the many additional degrees of conformational freedom present in, e.g., carbohydrate molecules, all minimizations are performed using a set of different promising starting conformations on the basis of previous calculations, and only the lowest energy result for each point is saved. An application of the method to conformational analysis of methyl‐cellobiose and the artificial sweetener trichlorogalactosucrose is also presented.