Correlation-induced corrections to the band structure of boron nitride: a wave-function-based approach

We present a systematic study of the correlation-induced corrections to the electronic band structure of zinc-blende BN. Our investigation employs an ab initio wave-function-based local Hamiltonian formalism which offers a rigorous approach to the calculation of the polarization and local charge redistribution effects around an extra electron or hole placed into the conduction or valence bands of semiconducting and insulating materials. Moreover, electron correlations beyond relaxation and polarization can be readily incorporated. The electron correlation treatment is performed on finite clusters. In conducting our study, we make use of localized Wannier functions and embedding potentials derived explicitly from prior periodic Hartree-Fock calculations. The on-site and nearest-neighbor charge relaxation bring corrections of several eV to the Hartree-Fock band gap. Additional corrections are caused by long-range polarization effects. In contrast, the dispersion of the Hartree-Fock bands is marginally affected by electron correlations. Our final result for the fundamental gap of zinc-blende BN compares well with that derived from soft x-ray experiments at the B and N K-edges.Comment: 18 pages, 8 figures; the following article has been submitted to J. Chem. Phy

Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn Source Package for Research in Electronic Structure, Simulation, and Optimization". It is freely available to researchers around the world under the terms of the GNU General Public License. Quantum ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively-parallel architectures, and a great effort being devoted to user friendliness. Quantum ESPRESSO is evolving towards a distribution of independent and inter-operable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Fragment-based drug discovery using NMR and x-ray crystallographic methods has proven utility but also non-trivial time, materials, and labor costs. Current computational fragment-based approaches circumvent these issues but suffer from limited representations of protein flexibility and solvation effects, leading to difficulties with rigorous ranking of fragment affinities. To overcome these limitations we describe an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a protein for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment∶protein interactions. Applied to the two-fold symmetric oncoprotein BCL-6, the SILCS method yields two-fold symmetric FragMaps that recapitulate the crystallographic binding modes of the SMRT and BCOR peptides. These FragMaps account both for important sequence and structure differences in the C-terminal halves of the two peptides and also the high mobility of the BCL-6 His116 sidechain in the peptide-binding groove. Such SILCS FragMaps can be used to qualitatively inform the design of small-molecule inhibitors or as scoring grids for high-throughput in silico docking that incorporate both an atomic-level description of solvation and protein flexibility

A structural study of a C3H3 species coadsorbed with CO on Pd(1 1 1)

The combination of chemical-state-specific C 1s scanned-energy mode photoelectron diffraction (PhD) and O K-edge near-edge X-ray absorption fine structure (NEXAFS) has been used to determine the local adsorption geometry of the coadsorbed C3H3 and CO species formed on Pd(1 1 1) by dissociation of molecular furan. CO is found to adopt the same geometry as in the Pd(1 1 1)c(4 × 2)-CO phase, occupying the two inequivalent three-fold coordinated hollow sites with the C–O axis perpendicular to the surface. C3H3 is found to lie with its molecular plane almost parallel to the surface, most probably with the two ‘outer’ C atoms in equivalent off-atop sites, although the PhD analysis formally fails to distinguish between two distinct local adsorption sites