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Intermolecular potential functions have been developed for urea. Ab initio 6-31G(d) calculations were performed on urea-water complexes to obtain interaction energies and hydrogen-bond lengths that were used in developing the partial charges for the OPLS model. An important test was made by computing through Monte Carlo simulations the difference in chloroform/water partition coefficients for urea and acetamide,~log P. The accord between the computed result from statistical perturbation theory for TIP4P water and OPLS chloroform (2.0 ± 0.1) and the experimental value (1.9) is excellent. The computed absolute free energy of hydration of acetamide (-9.5 ± 0.4 kcallmol) also matches the experimental data at 25°C (-9.68 kcallmol). These facts provide confidence in the computed value of -13.6 ± 0.4 kcallmol for the absolute free energy of hydration of urea, an experimentally unavailable result. The water structure around urea and acetamide was also characterized; the average numbers of solute-water hydrogen bonds are 5 for urea and 3-4 for acetamide.difference in chloroform/water log P values for urea and acetamide. Furthermore, it is demonstrated that the OPLS

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The formation and stability of self-assembled monolayers (SAMs) of aryl sulfmates and, for the first time, aryl sulfonates are described. The ways in which the molecules interact with the surface and the stability of the resulting SAMs were characterized by surface enhanced Raman (SER) spectroscopy. Aryl sulfinate monolayers can be reversibly oxidized to sulfonate monolayers, but the sulfonate is readily displaced by sulfinate in solution.The relative adsorptivities of aryl sulfur species were found to be ArSC>3_ < < ArSC>2-< ArS-. Through a novel application of perturbation theory, in which the adsorbate-surface Coulombic and charge transfer interactions and the change in the solvation free energy of the adsorbate are taken into account, we have been able to explain this trend. The differences in the adsorptivities of the anions studied here are primarily attributable to differences in the adsorbate-surface charge transfer interactions. These were evaluated by calculating the adsorbate HOMO energies at the ab initio HF/3-21G(d) level. Higher adsorbate HOMO energies are correlated with higher adsorptivities, consistent with established trends in the adsorptivities of soft, basic anions on metal electrodes. Statistical perturbation theory was used to calculate the relative free energies of hydration of the three anions. The sulfonate is most strongly solvated, followed by the sulfinate and thiolate. Thus, the trend in solvation energies is consistent with and probably reinforces the trend in the adsorbate-surface charge transfer interactions. The combination of computational methods used here may prove generally useful for predicting the relative adsorptivities of molecules and ions on metal surfaces.

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Monte Carlo computer simulations have been performed in conjunction with free-energy perturbation calculations to determine the relative binding constants of four benzamidine inhibitors with trypsin. The protein backbone was constrained in the simulations, but sampling of the side chains was allowed. The calculated free energies are very precise and are shown to yield closed thermodynamic cycles. The calculations correctly predict p-aminobenzamidine to be the strongest inhibitor and give relative free energies of binding for p-methyl-and p-chlorobenzamidine in excellent agreement with experiment. The predicted overly weak binding of the parent benzamidine is most likely due to a deficiency in the partial charges. The relative binding affinities are justified in terms of bulk-solvation arguments whereby the more polar inhibitors are preferentially stabilized in water. The calculations demonstrate that Monte Carlo computer simulations can be used to determine accurate and precise relative binding constants for protein systems.