[KSCI] Korea Science Citation Index Service

http://dx.doi.org/10.13160/ricns.2013.6.1.008

Temperature Dependency on Conformational Sampling of 12-Crown-4 by Simulated Annealing

Gadhe, Changdev G. (Department of Biochemistry, Centre for Bioinformatics, University of Madras, Guindy campus)
Cho, Seung Joo (Department of Bio-New Drug Development and Department of Cellular.Molecular Medicine and Research Center for Resistant Cells, College of Medicine, Chosun University)

Publication Information

Journal of Integrative Natural Science / v.6, no.1, 2013 , pp. 8-11 More about this Journal

Abstract

In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next $6-31+G^*$ level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.

Keywords

Molecular Dynamics; Simulated Annealing; Conformational Sampling; PM6; $6-31^*$ ;

Citations & Related Records

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