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3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling |
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| Authors: | Raevsky Oleg A Skvortsov Vladlen S |
| Affiliation: | (1) Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432 Chernogolovka, Moscow region, Russia;(2) Laboratory of Molecular Graphics and Drug Design, Institute of Biomedical Chemistry of the Russian Medicinal Academy, 119932, Pogodinskaya Str., 10, Moscow, Russia |
| Abstract: | A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system. |
| Keywords: | distance function enthalpy H-bonding molecular modelling optimum energy optimum distance |
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