FREE-ENERGY CALCULATIONS INVOLVING INTERNAL COORDINATE CONSTRAINTS TO DETERMINE PUCKERING OF A 6-MEMBERED RING MOLECULE

The free energy of boatlike puckering is examined for dihydropyridine (DHP) and dihydronicotinamide mononucleoside (NMSH) by thermodynamic simulations with an empirical force field. The interest in the conformation of the dihydropyridine ring stems from the question of a nonplanar ring conformation to facilitate hydride transfer between the cofactor NADH (reduced nicotinamide adenine dinucleotide) and the substrate in enzyme complexes. To investigate this question we secure a set of empirical force field parameters for the nonaromatic six-membered ring molecule dihydropyridine. A reaction coordinate comprising two dihedral angles is used to constrain the ring in a given boat conformation to calculate the free energy of ring puckering. In agreement with small molecule crystallographic structures, the free energy minimum lies close to a planar ring, but importantly, a broad minimum exists which would allow a range of boat conformations. In addition to the bonding interactions of the dihydropyridine ring, the NMSH free energy profile for puckering depends on nonbonded interactions between the ribose and base as determined by the anti or syn orientation of the glycosidic bonds and pyramidalization of the ring nitrogen. The parameters and computational approach reported here will be useful in calculations on any of the wealth of enzyme complexes involving the cofactor NADH.