Julianto Pranata

Monte Carlo simulations yield absolute free energies of binding for guanine—cytosine and adenine—uracil base pairs in chloroform

Abstract 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. 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) in chloroform at 25 °C. A + U → A−U ΔG= −3.6 kcal/mol G + C → G−C ΔG= −7.9 kcal/mol