CONFORMATIONAL FLEXIBILITY OF PHOSPHATE, PHOSPHONATE, AND PHOSPHOROTHIOATE METHYL-ESTERS IN AQUEOUS-SOLUTION

The intrinsic rotational barriers of the alpha and zeta coordinates of the native and modified DNA linkages were examined using neutral and ionic methyl phosphates, phosphorothioates, and phosphonates as model systems. Free energy profiles of the pathways from the right- (g(-)g(- )) to the left-handed (gg) conformers of dimethyl phosphate anion (CH3 OP(O-2)OCH3-), dimethyl phosphorothioate anion (CH3OP(O)(S)OCH3-), dim ethyl methylphosphonate (CH3OP(O)(CH3)OCH3), and methyl ethylphosphona te anion (CH3CH2P(O-2)OCH3) were evaluated using ab initio MP2/6-31 GG*//HF/6-31G* quantum mechanical calculations coupled with the Langev in dipoles and polarized continuum solvation models. Differences in th e gas-phase conformational properties of the studied molecules were fo und to diminish in aqueous solution. In solution, the,og (g-g-) confor mations are the most stable for dimethyl phosphate anion and the neutr al phosphonate, whereas the gt conformation was predicted to prevail f or dimethyl phosphorothioate anion. For methyl ethylphosphonate anion, which was found to be the most flexible of all the studied molecules, three stable conformations involving the gg, gt(-), and t(-)g rotamer s were predicted. The calculated activation free energies for the g(-) g(-) <-> gg transition in aqueous solution amount to 2.7, 1.7, 2.1, an d 1.5 kcal/mol for the dimethyl phosphate anion, dimethyl phosphorothi oate anion, and the neutral and ionic phosphonate ester, respectively. For the S-p and R-p stereoisomers of the DNA linkage containing the n eutral phosphonate, the structures of the corresponding transition sta tes involve the cis conformation around the PO3' or PO5' bonds, respec tively. The calculated similarities in the conformational behavior of the phosphate, phosphorothioate, and phosphonate methyl esters are qui te informative. In particular, they provide formal justification for t he use of the substitution experiments to study the role of intermolec ular interactions involving ionic and ester phosphate oxygens in the s tabilization of the structure of nucleic acids and DNA-protein complex es.