| Abstract
| - Molecular dynamics simulations were carried out in the presence of 2380 water molecules (TIP3P) to explorethe conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) and 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C) and the H-bond network around them, using the empirical general AMBERforce field (GAFF). Specific angle and torsional parameters have been improved in order to match thegeometries of the minimum energy structures obtained from an earlier DFT/ab initio study in vacuo, takinginto account a few configurations [Alagona, G.; Ghio, C.; Monti, S. Phys. Chem. Chem. Phys. 2004, 6, 2849−2857]. RESP partial charges were assigned to reproduce the electrostatic potential determined at the HF/6-31G* level of theory. The analysis of trajectories allowed the conformations of bitucarpin and erybraedin aswell as the distribution of water molecules around them to be elucidated. During one of the simulations only,the scaffold of erybraedin undergoes interconversion from its most stable Ht conformation to the Ot one andvice versa. Radial distribution functions, coordination numbers, and angular distributions put forward theextent of solvent structure and the hydrogen bonding behavior of their various (methoxy, hydroxyl, or ethereal)oxygen atoms. The distribution of solvent molecules in the first and second solvation shells as well as theresidence times for the different solute−solvent interacting sites have been considered.
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