We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.

We present a general formalism for polarizable electrostatics based on fluctuating bond-charge increments and polarizable dipoles and its application to a five-site model for water. The parametrization is based largely on quantum-chemical calculations and should be easily transferable to other molecules. To examine basis-set effects we parametrized two models from two sets of quantum calculations, using the aug-cc-pVTZ and aug-cc-pVQZ basis sets. We computed several gas-phase and condensed-phase properties and compared with experiment or ab initio calculations as available. The models are quite similar and give condensed-phase properties at ambient conditions that are in reasonable accord with experiment, but evince errors consistent with a liquid-state dipole moment that is slightly too large. The model fit to the aug-cc-pVTZ basis set has a smaller liquid-phase dipole moment and thus gives a somewhat better description of liquid water at ambient conditions. This model also performs well away from room temperature, deviating less than 2% from the experimental density from 0 to 100°C, and showing good agreement with experimental radial distribution functions, although the temperature of maximum density (ϳ20°C͒ is slightly too high and the model somewhat underpredicts the persistence of the hydrogen-bond network at elevated temperatures.

In the interests of making chemistry more environmentally friendly, room-temperature ionic liquids are currently being investigated as alternative solvents in industry and academia. In this paper, we present molecular dynamics simulations of 1-buthyl-3 methylimidazolium hexafluorophosphate ([bmim][PF 6 ]). We compute radial distribution functions, average density, and mean-square displacements for the individual ions. With this information, diffusion coefficients are calculated and conductivities are estimated using the Nernst-Einstein relation. The time history of the mean-square displacement of the ions appears to indicate that the system exhibits complex dynamics with at least two different time scales for diffusion. We model this behavior using a generalized Langevin approach. Results compare well with experimental data reported in the literature.

A reparameterization of the torsional parameters for the glycosidic dihedral angle, χ, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99χ. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99χ force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99χ force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) 1H, steady-state 1D 1H nuclear Overhauser effect (NOE), and transient 1D 1H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2′-endo sugar puckering of the pyrimidines, while the AMBER99χ force field’s predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310° for the base orientation of purines. The AMBER99χ force field prefers anti conformations around 185°, which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99χ force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

We have produced a polarizable force field for a series of small molecules, representative of functional groups found in organic and biochemical systems. We have used high-level ab initio results for fitting values of all the parameters except for the dispersion-term coefficient B in the -B/r 6 energy term, which, although obtained from comparison with experimental condensed-phase data, depended only on atomic number of the site in hand. Heats of vaporization and densities of the pure liquids, computed with molecular dynamics, agreed with experiment within ca. 0.5 kcal/mol and 5%, respectively.