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

Molpro (available at http://www.molpro.net) is a general-purpose quantum chemical program. The original focus was on high-accuracy wave function calculations for small molecules, but using local approximations combined with explicit correlation treatments, highly accurate coupled-cluster calculations are now possible for molecules with up to approximately 100 atoms. Recently, multireference correlation treatments were also made applicable to larger molecules. Furthermore, an efficient implementation of density functional theory is available.

Molpro: a general-purpose quantum chemistry program package

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.

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

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.

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

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

A new explicitly correlated CCSD(T)-F12 approximation is presented and tested for 23 molecules and 15 chemical reactions. The F12 correction strongly improves the basis set convergence of correlation and reaction energies. Errors of the Hartree-Fock contributions are effectively removed by including MP2 single excitations into the auxiliary basis set. Using aug-cc-pVTZ basis sets the CCSD(T)-F12 calculations are more accurate and two orders of magnitude faster than standard CCSD(T)/aug-cc-pV5Z calculations.

A simple and efficient CCSD(T)-F12 approximation.

The simple and efficient CCSD(T)-F12x approximations (x = a,b) we proposed in a recent communication [T. B. Adler, G. Knizia, and H.-J. Werner, J. Chem. Phys. 127, 221106 (2007)] are explained in more detail and extended to open-shell systems. Extensive benchmark calculations are presented, which demonstrate great improvements in basis set convergence for a wide variety of applications. These include reaction energies of both open- and closed-shell reactions, atomization energies, electron affinities, ionization potentials, equilibrium geometries, and harmonic vibrational frequencies. For all these quantities, results better than the AV5Z quality are obtained already with AVTZ basis sets, and usually AVDZ treatments reach at least the conventional AVQZ quality. For larger molecules, the additional cost for these improvements is only a few percent of the time for a standard CCSD(T) calculation. For the first time ever, total reaction energies with chemical accuracy are obtained using valence-double-zeta basis sets.

Simplified CCSD(T)-F12 methods: Theory and benchmarks

Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.

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Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

We introduce density matrix embedding theory (DMET), a quantum embedding theory for computing frequency-independent quantities, such as ground-state properties, of infinite systems Like dynamical mean-field theory, DMET maps the bulk interacting system to a simpler impurity model and is exact in the noninteracting and atomic limits Unlike dynamical mean-field theory, DMET is formulated in terms of the frequency-independent local density matrix, rather than the local Green's function In addition, it features a finite, algebraically constructible bath of only one bath site per impurity site, with no bath discretization error Frequency independence and the minimal bath make DMET a computationally simple and efficient method We test the theory in the one-dimensional and two-dimensional Hubbard models at and away from half filling, and we find that compared to benchmark data, total energies, correlation functions, and metal-insulator transitions are well reproduced, at a tiny computational cost

Gerald Knizia

Papers

Molpro: a general-purpose quantum chemistry program package

A simple and efficient CCSD(T)-F12 approximation.

Simplified CCSD(T)-F12 methods: Theory and benchmarks

Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

Density matrix embedding: a simple alternative to dynamical mean-field theory.