Donald Ephraim Curtis

Bio: Donald Ephraim Curtis is an academic researcher from Coe College. The author has contributed to research in topics: Molecule editor & Visualization. The author has an hindex of 1, co-authored 1 publications receiving 3987 citations.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Abstract: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net .

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Abstract: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr_2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

RESEARCH ARTICLE Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Abstract: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Small-Molecule Library Screening by Docking with PyRx

Abstract: Virtual molecular screening is used to dock small-molecule libraries to a macromolecule in order to find lead compounds with desired biological function. This in silico method is well known for its application in computer-aided drug design. This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems (Linux, Windows, and Mac OS). Specific steps for using PyRx, as well as considerations for data preparation, docking, and data analysis, are also described.

The ORCA quantum chemistry program package

Abstract: In this contribution to the special software-centered issue, the ORCA program package is described. We start with a short historical perspective of how the project began and go on to discuss its current feature set. ORCA has grown into a rather comprehensive general-purpose package for theoretical research in all areas of chemistry and many neighboring disciplines such as materials sciences and biochemistry. ORCA features density functional theory, a range of wavefunction based correlation methods, semi-empirical methods, and even force-field methods. A range of solvation and embedding models is featured as well as a complete intrinsic to ORCA quantum mechanics/molecular mechanics engine. A specialty of ORCA always has been a focus on transition metals and spectroscopy as well as a focus on applicability of the implemented methods to "real-life" chemical applications involving systems with a few hundred atoms. In addition to being efficient, user friendly, and, to the largest extent possible, platform independent, ORCA features a number of methods that are either unique to ORCA or have been first implemented in the course of the ORCA development. Next to a range of spectroscopic and magnetic properties, the linear- or low-order single- and multi-reference local correlation methods based on pair natural orbitals (domain based local pair natural orbital methods) should be mentioned here. Consequently, ORCA is a widely used program in various areas of chemistry and spectroscopy with a current user base of over 22 000 registered users in academic research and in industry.

Structure of polydopamine: a never-ending story?

Abstract: Polydopamine (PDA) formed by the oxidation of dopamine is an important polymer, in particular, for coating various surfaces. It is composed of dihydroxyindole, indoledione, and dopamine units, which are assumed to be covalently linked. Although PDA has been applied in a manifold way, its structure is still under discussion. Similarities have been observed in melanins/eumelanins as naturally occurring, deeply colored polymer pigments derived from l-DOPA. Recently, an alternative structure was proposed for PDA wherein dihydroxyindoline, indolinedione, and eventually dopamine units are not covalently linked to each other but are held together by hydrogen bonding between oxygen atoms or π stacking. In this study, we show that this structural proposal is very unlikely to occur taking into account unambiguous results obtained by different analytical methods, among them 13C CPPI MAS NMR (cross-polarization polarization–inversion magic angle spinning NMR), 1H MAS NMR (magic angle spinning NMR), and ES-HRMS (elect...