Molecular Modeling


TYPO3 Templates

The 3D molecular models are created, energy optimized and the molecular conformational spaces are mapped by using a molecular modelling system based on a proprietary force field for which the parametrization was derived from MMFF94  through substantial development.

The conformational solvent effects are taken into account through dielectric constant, which is varied due to the distance between the atomic charges. The atomic partial charges are calculated by an algorithm based on the Lewis-Langmuir charges.

The conformational space mapping is performed by using Metropolis Monte Carlo for rotating bonds + Molecular Dynamics type procedure. For cyclic systems with no rotating substituents only MD is performed.

A typical total time for the MMC+MD calculation of 10 carbons molecule is 10 sec, and the time depends linearly on the number of atoms so that, for example, for cyclosporin A the mapping takes about 30 min.

The achieved conformational space is used in the NMR prediction.