We performed plane wave density functional theory ͑DFT͒ 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 ZrO 2 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 Ϫ center and stability of V ϩ centers with respect to disproportionation into V 2ϩ and V 0 in monoclinic zirconia.

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We briefly review some of the approaches which have been used to study the distributions of defect properties in amorphous silica and focus mainly on the implementation of the embedded cluster method. We illustrate some of the results obtained using this method and discuss the remaining problems using the example of oxygen vacancy defects in amorphous SiO 2 . The neutral vacancies are characterized by a wide distribution of formation energies and structural parameters. Our modelling predicts the two major structural kinds of positively charged vacancies (E centres): dimers and dangling bond centres. The local structure for both kinds of centres depends on the medium range structure of the surrounding amorphous network. We found that the majority of the dangling bond centres are unpuckered. The optical spectra and electron paramagnetic resonance parameters calculated for all defects are in good agreement with experimental data. The structural criteria which favour the formation of different kinds of centres in the original amorphous structure are formulated in terms of the average Si-O distance of oxygen ion with its two neighbouring silicon ions.

ABSTRACT:A systematic semiempirical quantum mechanical study of the interactions between proteins and ligands has been performed to determine the ability of this approach for the accurate estimation of the enthalpic contribution to the binding free energy of the protein-ligand systems. This approach has been applied for eight test protein-ligand complexes with experimentally known binding enthalpies. The calculations were performed using the semiempirical PM3 approach incorporated in the MOPAC 97, ZAVA originally elaborated in Algodign, and MOPAC 2002 with MOZYME facility packages. Special attention was paid to take into account structural water molecules, which were located in the protein-ligand binding site. It was shown that the results of binding enthalpy calculations fit experimental data within ϳ2 kcal/ mol in the presented approach.

This paper is devoted to results obtained by the docking program SOL and the post-processing program DISCORE at the CSAR benchmark. SOL and DISCORE programs are described. SOL is the original docking program developed on the basis of the genetic algorithm, MMFF94 force field, rigid protein, precalculated energy grid including desolvation in the frame of simplified GB model, vdW, and electrostatic interactions and taking into account the ligand internal strain energy. An important SOL feature is the single- or multi-processor performance for up to hundreds of CPUs. DISCORE improves the binding energy scoring by the local energy optimization of the ligand docked pose and a simple linear regression on the base of available experimental data. The docking program SOL has demonstrated a good ability for correct ligand positioning in the active sites of the tested proteins in most cases of CSAR exercises. SOL and DISCORE have not demonstrated very exciting results on the protein-ligand binding free energy estimation. Nevertheless, for some target proteins, SOL and DISCORE were among the first in prediction of inhibition activity. Ways to improve SOL and DISCORE are discussed.

We present the surface generalized born (S-GB) method, based on expansion of energy in a surface integral series. The method can be parametrized for simultaneous reproduction of the reaction field energy for small molecules as well as macromolecules. For a set of 195 small molecules, our S-GB model gives a root mean square (rms) of 0.13 kcal/mol relative to the rigorous polarizable continuum model (PCM).

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.