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

Syndromics: A Bioinformatics Approach for Neurotrauma Research

Substantial scientific progress has been made in the past 50 years in delineating many of the biological mechanisms involved in the primary and secondary injuries following trauma to the spinal cord and brain. These advances have highlighted numerous potential therapeutic approaches that may help restore function after injury. Despite these advances, bench-to-bedside translation has remained elusive. Translational testing of novel therapies requires standardized measures of function for comparison across different laboratories, paradigms, and species. Although numerous functional assessments have been developed in animal models, it remains unclear how to best integrate this information to describe the complete translational “syndrome” produced by neurotrauma. The present paper describes a multivariate statistical framework for integrating diverse neurotrauma data and reviews the few papers to date that have taken an information-intensive approach for basic neurotrauma research. We argue that these papers can be described as the seminal works of a new field that we call “syndromics”, which aim to apply informatics tools to disease models to characterize the full set of mechanistic inter-relationships from multi-scale data. In the future, centralized databases of raw neurotrauma data will enable better syndromic approaches and aid future translational research, leading to more efficient testing regimens and more clinically relevant findings

Regularized orbital-optimized second-order perturbation theory.

Orbital-optimized second-order perturbation theory (OOMP2) optimizes the zeroth order wave function in the presence of correlations, removing the dependence of the method on Hartree-Fock orbitals. This is particularly important for systems where mean field orbitals spin contaminate to artificially lower the zeroth order energy such as open shell molecules, highly conjugated systems, and organometallic compounds. Unfortunately, the promise of OOMP2 is hampered by the possibility of solutions being drawn into divergences, which can occur during the optimization procedure if HOMO and LUMO energies approach degeneracy. In this work, we regularize these divergences through the simple addition of a level shift parameter to the denominator of the MP2 amplitudes. We find that a large level shift parameter of 400 mEh removes divergent behavior while also improving the overall accuracy of the method for atomization energies, barrier heights, intermolecular interactions, radical stabilization energies, and metal binding energies

M2(m-dobdc) (M = Mg, Mn, Fe, Co, Ni) Metal-Organic Frameworks Exhibiting Increased Charge Density and Enhanced H2 Binding at the Open Metal Sites

The well-known frameworks of the type M2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate) have numerous potential applications in gas storage and separations, owing to their exceptionally high concentration of coordinatively unsaturated metal surface sites, which can interact strongly with small gas molecules such as H2. Employing a related meta-functionalized linker that is readily obtained from resorcinol, we now report a family of structural isomers of this framework, M2(m-dobdc) (M = Mg, Mn, Fe, Co, Ni; m-dobdc4– = 4,6-dioxido-1,3-benzenedicarboxylate), featuring exposed M2+ cation sites with a higher apparent charge density. The regioisomeric linker alters the symmetry of the ligand field at the metal sites, leading to increases of 0.4–1.5 kJ/mol in the H2 binding enthalpies relative to M2(dobdc). A variety of techniques, including powder X-ray and neutron diffraction, inelastic neutron scattering, infrared spectroscopy, and first-principles electronic structure calculations, are applied in elucidating how these subtle structural and electronic differences give rise to such increases. Importantly, similar enhancements can be anticipated for the gas storage and separation properties of this new family of robust and potentially inexpensive metal–organic frameworks

M2(m-dobdc) (M = Mg, Mn, Fe, Co, Ni) metal-organic frameworks exhibiting increased charge density and enhanced H2 binding at the open metal sites.

The well-known frameworks of the type M2(dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate) have numerous potential applications in gas storage and separations, owing to their exceptionally high concentration of coordinatively unsaturated metal surface sites, which can interact strongly with small gas molecules such as H2. Employing a related meta-functionalized linker that is readily obtained from resorcinol, we now report a family of structural isomers of this framework, M2(m-dobdc) (M = Mg, Mn, Fe, Co, Ni; m-dobdc(4-) = 4,6-dioxido-1,3-benzenedicarboxylate), featuring exposed M(2+) cation sites with a higher apparent charge density. The regioisomeric linker alters the symmetry of the ligand field at the metal sites, leading to increases of 0.4-1.5 kJ/mol in the H2 binding enthalpies relative to M2(dobdc). A variety of techniques, including powder X-ray and neutron diffraction, inelastic neutron scattering, infrared spectroscopy, and first-principles electronic structure calculations, are applied in elucidating how these subtle structural and electronic differences give rise to such increases. Importantly, similar enhancements can be anticipated for the gas storage and separation properties of this new family of robust and potentially inexpensive metal-organic frameworks

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.This article is from Molecular Physics: An International Journal at the Interface Between Chemistry and Physics 113 (2015): 184, doi:10.1080/00268976.2014.952696.</p