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

Abstract

AbstractIn this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble ofconformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Moleculardynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. Atparticular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only uniqueconformations were retained for the next 6-31+G* level minimization. It was observed that upto certain increment intemperature the number of unique conformations were increased, but afterword it decreased.Keywords: Molecular Dynamics, Simulated Annealing, Conformational Sampling, PM6, 6-31* 1. Introduction In the drug discovery process, getting a low energyconformation of the drug or protein molecule is alwaysa big task. However, there are number of methods to geta lowest energy or global minimum conformation. Itincludes simulated annealing, replica exchange molec-ular dynamics and locally enhanced sampling