Tautomerization of N₆, N₆-dimethyl 2,6-diaminobenz[cd]indole in the gas phase and in aqueous solution : a combined quantum mechanical and free energy perturbation study

Agouron Pharmaceuticals, Inc 3565 General Atomics Court, San Diego, CA 92121, USA.

Abstract

A theoretical study of gas phase and solution tautomerization equilibria involving N6,N6-dimethyl 2,6-diamino benz[cd]indole (I) and its anti (IIA) and syn (IIB) imino tautomers has been carried out in order to examine the effect of solvent and to assess the suitability of this molecule as an inhibitor of thymidylate synthase (TS), an enzyme of known structure which plays a crucial role in DNA biosynthesis. Fully optimized geometries and energies of all three tautomers in isolation have been obtained at the MP2/6-31G**//3-21G level. Zero point and thermal energies and entropies were calculated from harmonic frequencies obtained with a 3-21G basis set and, for comparison, with the semiempirical AM1 method. Quantum mechanical free energy totals for the isolated molecules indicate that tautomer I is intrinsically more stable than the anti (IIA) and syn (IIB) tautomers. Relative solvation free energies were calculated by means of free energy perturbation molecular dynamics simulations in solvent and in the gas phase. Water is found to preferentially stabilize tautomer I while tautomer IIA is least strongly solvated. Insight into these results is provided by an analysis of molecular dynamics trajectories which shows differences in interaction energies with solvent, particularly differences in the strength of hydrogen bonds. The total free energy differences in solution (solvent stabilization plus the intrinsic stability of the isolated molecules) indicate that form I predominates over the two imino tautomers. Form IIB is favored over IIA in solution, a reversal of their gas phase ordering. Tautomer IIB, which is expected to interact most favorably with the enzyme, is predicted to constitute only 1 % of the solute in aqueous solution.