Eva Zurek

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

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.

A little bit of lithium does a lot for hydrogen

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.

XtalOpt: An Open-Source Evolutionary Algorithm for Crystal Structure Prediction

The implementation and testing of XtalOpt, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XtalOpt are optimized using a novel benchmarking scheme. XtalOpt is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface.

Rubidium Polyhydrides Under Pressure: Emergence of the Linear H3− Species

The structures of compressed rubidium polyhydrides, RbH(n) with n>1, and their evolution under pressure are studied using density functional theory calculations. These phases, which start to stabilize at only P = 2 GPa, consist of Rb(+) cations and one or more of the following species: H(-) anions, H(2) molecules, and H(3)(-) molecules. The latter motif, the simplest example of a three-center four-electron bond, is found in the most stable structures, RbH(5) and RbH(3) , which metallize above 200 GPa. At the highest pressures studied, our evolutionary searches find an RbH(6) phase which contains polymeric (H(3)(-))(∞) chains that show signs of one-dimensional liquid-like behavior.

Surface state engineering of molecule-molecule interactions.

Engineering the electronic structure of organics through interface manipulation, particularly the interface dipole and the barriers to charge carrier injection, is of essential importance to improve organic devices. This requires the meticulous fabrication of desired organic structures by precisely controlling the interactions between molecules. The well-known principles of organic coordination chemistry cannot be applied without proper consideration of extra molecular hybridization, charge transfer and dipole formation at the interfaces. Here we identify the interplay between energy level alignment, charge transfer, surface dipole and charge pillow effect and show how these effects collectively determine the net force between adsorbed porphyrin 2H-TPP on Cu(111). We show that the forces between supported porphyrins can be altered by controlling the amount of charge transferred across the interface accurately through the relative alignment of molecular electronic levels with respect to the Shockley surface state of the metal substrate, and hence govern the self-assembly of the molecules.

Enantioselective Copper‐Catalyzed Carboetherification of Unactivated Alkenes

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein reported is a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols which terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, thus yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition-state calculations support a cis-oxycupration stereochemistry-determining step.

Compressed cesium polyhydrides: Cs+ sublattices and H3(-) three-connected nets.

The cesium polyhydrides (CsH(n), n > 1) are predicted to become stable, with respect to decomposition into CsH and H2, at pressures as low as 2 GPa. The CsH3 stoichiometry is found to have the lowest enthalpy of formation from CsH and H2 between 30 and 200 GPa. Evolutionary algorithms predict five distinct, mechanically stable, nearly isoenthalpic CsH3 phases consisting of H3(–) molecules and Cs+ atoms. The H3(–) sublattices in two of these adopt a hexagonal three-connected net; in the other three the net is twisted, like the silicon sublattice in the α-ThSi2 structure. The former emerge as being metallic below 100 GPa in our screened hybrid density functional theory calculations, whereas the latter remain insulating up to pressures greater than 250 GPa. The Cs+ cations in the most-stable I4(1)/amd CsH3 phase adopt the positions of the Cs atoms in Cs-IV, and the H3(–) molecules are found in the (interstitial) regions which display a maximum in the electron density.

Metallization of magnesium polyhydrides under pressure

Evolutionary structure searches are used to predict stable phases with unique stoichiometries in the hydrogen-rich region of the magnesium/hydrogen phase diagram under pressure. MgH

Decomposition Products of Phosphine Under Pressure: PH2 Stable and Superconducting?

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Identifying duplicate crystal structures: XtalComp, an open-source solution☆

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