Conformational analysis of dimethylphosphate with quantum-mechanical and classical methods

In order to shed light on the conformational behavior of polynucleotide chains, and in particular to clarify the origins of the barriers to internal rotation in the phosphodiester linkage, we computed, with a quantum-mechanical ab initio procedure, the energies associated to 86 combinations of the two torsion angles in the dimethylphosphate anion (CH₃O)₂PO₂^–, and then we sought for an analytical expression apt to reproduce these energies with the highest possible accuracy. An excellent agreement (standard deviation of the fitted energies from the ab initio energies 0.28 kcal/mole) with the quantum-mechanical calculations was reached with a potential consisting of four terms: 1) a 6–12 Lennard-Jones contribution, in which different parameters are used to describe the interactions of methyls with the ester oxygens and with the anionic oxygens; 2) a contribution with twofold periodicity, accounting for the anomeric effects connected to the interactions between the lone pair electrons and the polar bonds of phosphorus with the anionic oxygens; 3) a contribution with threefold periodicity, representing the usual bond-staggering term; and 4) a Coulombic contribution, arising from electrostatic interactions between partially charged atoms.