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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The Fe(II) spin crossover complex [Fe{H B(pz) } (bipy)] (pz = pyrazol-1-yl, bipy = 2,2'-bipyridine) can be locked in a largely low-spin-state configuration over a temperature range that includes temperatures well above the thermal spin crossover temperature of 160 K. This locking of the spin state is achieved for nanometer thin films of this complex in two distinct ways: through substrate interactions with dielectric substrates such as SiO and Al O , or in powder samples by mixing with the strongly dipolar zwitterionic p-benzoquinonemonoimine C H (-⋯ NH ) (-⋯ O) . Remarkably, it is found in both cases that incident X-ray fluences then restore the [Fe{H B(pz) } (bipy)] moiety to an electronic state characteristic of the high spin state at temperatures of 200 K to above room temperature; that is, well above the spin crossover transition temperature for the pristine powder, and well above the temperatures characteristic of light- or X-ray-induced excited-spin-state trapping. Heating slightly above room temperature allows the initial locked state to be restored. These findings, supported by theory, show how the spin crossover transition can be manipulated reversibly around room temperature by appropriate design of the electrostatic and chemical environment.

NMR chemical shifts were calculated for semiconducting (n,0) single-walled carbon nanotubes (SWNTs) with n ranging from 7 to 17. Infinite isolated SWNTs were calculated using a gauge-including projector-augmented plane-wave (GIPAW) approach with periodic boundary conditions and density functional theory (DFT). In order to minimize intertube interactions in the GIPAW computations, an intertube distance of 8 A was chosen. For the infinite tubes, we found a chemical shift range of over 20 ppm for the systems considered here. The SWNT family with lambda = mod(n, 3) = 0 has much smaller chemical shifts compared to the other two families with lambda = 1 and lambda = 2. For all three families, the chemical shifts decrease roughly inversely proportional to the tube's diameter. The results were compared to calculations of finite capped SWNT fragments using a gauge-including atomic orbital (GIAO) basis. Direct comparison of the two types of calculations could be made if benzene was used as the internal (computational) reference. The NMR chemical shifts of finite SWNTs were found to converge very slowly, if at all, to the infinite limit, indicating that capping has a strong effect (at least for the (9,0) tubes) on the calculated properties. Our results suggest that (13)C NMR has the potential for becoming a useful tool in characterizing SWNT samples.

Evolutionary structure searches are used to predict stable phases with unique stoichiometries in the hydrogenrich region of the magnesium/hydrogen phase diagram under pressure. MgH4, MgH12 and MgH16 are found to be thermodynamically stable with respect to decomposition into MgH2 and H2 near 100 GPa, and all lie on the convex hull by 200 GPa. MgH4 contains two H − anions and one H2 molecule per Mg 2+ cation, whereas the hydrogenic sublattices of MgH12 and MgH16 are composed solely of H δ− 2 molecules. The high-hydrogen content stoichiometries have a large density of states at the Fermi level, and the Tc of MgH12 at 140 GPa is calculated to be nearly three times greater than that of the classic hydride, MgH2, at 180 GPa.