Studies of Trans- and Cis-Xylomollin Molecular Structures Using Molecular Dynamics Simulations

Abstract

The present work describes the comparative study of the trans- and the cis-xylomollin structures. We have determined the two bridgehead H5 and H9 configurations using simulation calculations for both trans- and cis- distereoisomers. Molecular Dynamic (MD) simulations of the trans- and cis- xylomollin were performed with an efficient program. The geometries, interaction energies, bonds, angles, and the Van der Waals (VDW) interactions were carried out in solution and gas phases. This comparative study shows that the trans-xylomollin acquires the high configuration energy under the AMBER field using MD method. This molecule reaches its high stable configuration state in solution environment. Our MD simulation results are goods and in agreement with those of literature.

Dynamics Simulation Studies of Solvation Effect on the Trans-Xylomollin Conformation

“…Molecular dynamics (MD) is a useful technique to study the kinetics and thermodynamics properties of macroscopic systems involving a few molecules such as biomolecules, heterocyclic compounds, proteins and other macromolecules in order to provide diffusion [28,29], thermodynamic and structural [29,30], conformational properties [32,33] and structure-activity relationship [34]. The success of MD is the study process energy of organic compounds as protein, heterocyclic, and important conformational changes in a small time step size.…”