Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused more by different parameterization and less by methods and indicates the need for further improvement of implicit solvent models parameterization. Within the same parameterization, various implicit methods give practically the same correlation with results obtained in explicit solvent model for ligands and proteins: e.g. correlation values of polar ligand solvation energies and the corresponding energies in the frame of explicit solvent were 0.953-0.966 for the APBS program, the GBNSR6 program and all models used in the DISOLV program. The DISOLV program proved to be on a par with the other used programs in the case of proteins and ligands solvation energy calculation. However, the solution of the Poisson-Boltzmann equation (APBS program) and Generalized Born method (implemented in the GBNSR6 program) proved to be the most accurate in calculating the desolvation energies of complexes

Quantum kinetic theory of shift current electron pumping in semiconductors

We develop a theory of laser beam generation of shift currents in non-centrosymmetric semiconductors. The currents originate when the excited electrons transfer between different bands or scatter inside these bands, and asymmetrically shift their centers of mass in elementary cells. Quantum kinetic equations for hot-carrier distributions and expressions for the induced currents are derived by nonequilibrium Green functions. In applications, we simplify the approach to the Boltzmann limit and use it to model laser-excited GaAs in the presence of LO phonon scattering. The shift currents are calculated in a steady-state regime.Comment: 23 pages, 5 figures (Latex

Structure and electrical levels of point defects in monoclinic zirconia

We performed plane wave density functional theory (DFT) calculations of formation energies, relaxed structures, and electrical levels of oxygen vacancies and interstitial oxygen atoms in monoclinic zirconia. The atomic structures of positively and negatively charged vacancies and interstitial oxygen atoms are also investigated. The ionization energies and electron affinities of interstitial oxygen atoms and oxygen vacancies in different charge states are calculated with respect to the bottom of the zirconia conduction band. Using the experimental band offset values at the interface of ZrO2 films grown on silicon, we have found the positions of defect levels with respect to the bottom of silicon conduction band. The results demonstrate that interstitial oxygen atoms and positively charged oxygen vacancies can trap electrons from the bottom of the zirconia conduction band and from silicon. Neutral oxygen vacancy serves as a shallow hole trap for electrons injected from the silicon valence band. The calculations predict negative U for the O− center and stability of V+ centers with respect to disproportionation into V2+ and V0 in monoclinic zirconia.Peer reviewe