MONTE-CARLO SIMULATIONS YIELD ABSOLUTE FREE-ENERGIES OF BINDING FOR GUANINE CYTOSINE AND ADENINE URACIL BASE-PAIRS IN CHLOROFORM

Monte Carlo simulations with statistical perturbation theory and the OPLS potential functions were employed to calculate the absolute free energies of binding between 9-methyladenine (A) and 1-methyluracil (U) and between 9-methylguanine (G) and 1-methylcytosine (C). The results for both A-U (ca. -3.6 kcal/mol) and G-C (ca. -7.9 kcal/mol) compare well with the values from experimentally determined association constants for these systems. Several thermodynamic cycles were also considered that demonstrated the high precision of the methodology.