A consistent model for the key complex in chronic beryllium disease

Abstract A hypothesis on the structure of the key complex in chronic beryllium disease (CBD) is discussed with respect to the current knowledge on CBD, and with respect to the constraints implied by the coordination chemistry of beryllium and experimental data on the engaged protein complexes. The structure hypothesis is based on the [Be4O]6+ moiety as a coordination center, which is also found in the so called “basic beryllium carboxylates”. The structure of a small molecular model, optimized at the DFT level of theory, is used to compare the structural demands of this coordination center with a structure of the in vitro model of a beryllium immunoprotein complex determined previously by protein crystallography (Clayton & al., Cell 2014, 158, 132). 9Be NMR chemical shielding values, quadrupole coupling constants and asymmetry parameters (η) have been calculated

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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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 <url>http://avogadro.openmolecules.net</url>.</p