3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling.
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.
Raevsky
Oleg A
OA
Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Chernogolovka, Moscow region. raevsky@ipac.ac.ru
Skvortsov
Vladlen S
VS
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry; D012984:Software; D013816:Thermodynamics; D014961:X-Ray Diffraction
D012313:RNA