Robert Konečný

Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson–Boltzmann analytical and a semi‐analytical solver, an optimized boundary element solver, a geometry‐based geometric flow solvation model, a graph theory‐based algorithm for determining p K a values, and an improved web‐based visualization tool for viewing electrostatics.

Adsorption of water on the Si(100)-(2×1) surface has been investigated using density functional theory and cluster models of the surface. The reaction pathway and geometries of the product, the transition state and a molecular precursor state are described. There is no energy barrier to dissociative chemisorption. Adsorbed H and OH fragments are most stable when bonded to the same surface dimer with the hydroxyl oriented away from the surface dimer bond. The orbital and electrostatic interactions that determine the adsorbate and transition state geometries are analyzed. Surface distortion (dimer buckling) is a recurring theme in this analysis. Interactions of adsorbed molecular fragments with each other and with dangling bonds have significant effects, modifying the adsorbate geometry and leading to adsorbate islanding. Calculated vibrational frequencies of adsorbed H2O on Si(100)-(2×1) are discussed. The theoretical results are consistent with most available experimental results, and provide a microscopic description of the interactions that account for the observations.

First-principles electronic structure calculations have been used to study the structure, energetics and vibrational spectra of the chemisorption products of several unsaturated hydrocarbons on the Si(100)-(2×1) surface. The calculations use a hybrid non-local density functional theory and a cluster model of the surface. Ethylene and acetylene react by a [2s+2s] cycloaddition mechanism. Conjugated dienes (1,3-cyclohexadiene, 1,3-butadiene, 2,3-dimethyl-1,3-butadiene) and benzene can also react by a novel [4s+2s] cycloaddition, or Diels–Alder mechanism. For each diene, the Diels–Alder product is energetically favored over the more strained [2s+2s] product. The reaction mechanism for Diels–Alder addition, other competing reactions, and the effects of post-hydrogenation are all discussed. Comparisons to experimental observations are made throughout.

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTheoretical Prediction of a Facile Diels−Alder Reaction on the Si(100)-2×1 SurfaceR. Konecny and D. J. DorenView Author Information Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 Cite this: J. Am. Chem. Soc. 1997, 119, 45, 11098–11099Publication Date (Web):November 12, 1997Publication History Received7 July 1997Published online12 November 1997Published inissue 1 November 1997https://pubs.acs.org/doi/10.1021/ja972247ahttps://doi.org/10.1021/ja972247arapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views470Altmetric-Citations158LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Addition reactions,Adducts,Chemical reactions,Oligomers,Organic reactions Get e-Alerts

The structures, energetics, and orbital- and charge-dependent properties of copper zinc superoxide dismutase (CuZnSOD) have been studied using density functional and electrostatic methods. The CuZnSOD was represented with a model consisting of copper and zinc sites connected by a bridging histidine ligand. In addition to the bridge, three histidine ligands and one water molecule were bonded to the Cu ion in the copper site as first-shell ligands. Two histidine ligands and an aspartate were coordinated to the zinc ion in the zinc site. Full optimization of the model was performed using different functionals, both local and nonlocal. Geometrical parameters calculated with the nonlocal functionals agree well with the experimental X-ray data. In our calculated results, the His61 Nepsilon-Cu bond in the active site breaks during the reduction and protonation, consistent with a number of X-ray structures and with EXAFS and NMR evidence. The reduction potential and pK(a) of the coupled electron/proton reaction catalyzed by CuZnSOD were determined using different models for the extended environment-from an electrostatic representation of continuum solvent, to the full protein/solvent environment using a Poisson-Boltzmann method. The predicted redox potential and pK(a) values determined using the model with the full protein/solvent environment are in excellent agreement with experiment. Inclusion of the full protein environment is essential for an accurate description of the redox process. Although the zinc ion does not play a direct redox role in the dismutation, its electronic contribution is very important for the catalytic mechanism.