BackgroundThe 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.ResultsThe 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.ConclusionsAvogadro 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.

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From detailed assessments of electronic structure, we find that a combination of significantly quantal elements, six of seven atoms being hydrogen, becomes a stable metal at a pressure approximately 1/4 of that required to metalize pure hydrogen itself. The system, LiH6 (and other LiHn), may well have extensions beyond the constituent lithium. These hypothetical materials demonstrate that nontraditional stoichiometries can considerably expand the view of chemical combination under moderate pressure.high pressure ͉ hydrogen metallization ͉ lithium chemistry T hree lines of thought-call them obsessions-impelled this investigation: (i) thinking of new pathways to promote and enhance the metallization of hydrogen, (ii) more generally the potential stability of new compounds with unusual stoichiometries under high pressures, and (iii) proposals for the design of new superconductors. As will be seen, we find two surprising ways (making good chemical sense) for the first, as well as sound theoretical evidence for the second. Based upon what is already known about possible superconductivity in metallic hydrogen, we find indications for the third.LiH, crystallizing in the NaCl structure with a band gap of 4.99 eV (1), is one stable point in the Li/H phase diagram, the only one other than the elements at ambient conditions. It remains stable at higher pressures; the reaction Li ϩ 1 2 H 2 3 LiH is computed to be exothermic at all of the pressures we have considered. Calculations predict that pressure-induced metallization and transformation to the CsCl structure occur simultaneously at approximately 329 GPa (2). The results of our density functional theory (DFT) calculations on LiH are given in the supporting information (SI).Hydrogen also vehemently resists metallization.

A detailed molecular orbital (MO) analysis of the structure and electronic properties of the great variety of species in lithium-ammonia solutions is provided. In the odd-electron, doublet states we have considered: e-@(NH3)n (the solvated electron, likely to be a dynamic ensemble of molecules), the Li(NH3)4 monomer, and the [Li(NH3)4+.e-@(NH3)n] ion-pairs, the Li 2s electron enters a diffuse orbital built up largely from the lowest unoccupied MOs of the ammonia molecules. The singly occupied MOs are bonding between the hydrogen atoms; we call this stabilizing interaction H-->H bonding. In e-@(NH3)n the odd electron is not located in the center of the cavities formed by the ammonia molecules. Possible species with two or more weakly interacting electrons also exhibit H-->H bonding. For these, we find that the singlet (S=0) states are slightly lower in energy than those with unpaired (S=1, 2...) spins. TD-DFT calculations on various ion-pairs show that the three most intense electronic excitations arise from the transition between the SOMO (of s pseudosymmetry) into the lowest lying p-like levels. The optical absorption spectra are relatively metal-independent, and account for the absorption tail which extends into the visible. This is the source of Sir Humphry Davy's "fine blue colour" first observed just over 200 years ago.

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