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.

/pdf/advances-in-molecular-quantum-chemistry-contained-in-the-q-3j7dwbtpjv.pdf

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

Determination of Relative Configuration in Organic Compounds by NMR Spectroscopy and Computational Methods

Fungus-growing ants engage in mutualistic associations with both the fungus they cultivate for food and actinobacteria (Pseudonocardia spp) that produce selective antibiotics to defend that fungus from specialized fungal parasites We have analyzed one such system at the molecular level and found that the bacterium associated with the ant Apterostigma dentigerum produces dentigerumycin, a cyclic depsipeptide with highly modified amino acids, to selectively inhibit the associated parasitic fungus (Escovopsis sp)

/pdf/dentigerumycin-a-bacterial-mediator-of-an-ant-fungus-3ekpe2l258.pdf

Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis

Apratoxin A (1), a potent cytotoxin with a novel skeleton, has been isolated from the marine cyanobacterium Lyngbya majuscula Harvey ex Gomont. This cyclodepsipeptide of mixed peptide-polyketide biogenesis bears a thiazoline ring flanked by polyketide portions, one of which possesses an unusual methylation pattern. Its gross structure has been elucidated by spectral analysis, including various 2D NMR techniques. The absolute configurations of the amino acid-derived units were determined by chiral HPLC analysis of hydrolysis products. The relative stereochemistry of the new dihydroxylated fatty acid unit, 3,7-dihydroxy-2,5,8,8-tetramethylnonanoic acid, was elucidated by successful application of the J-based configuration analysis originally developed for acyclic organic compounds using carbon-proton spin-coupling constants ((2,3)J(C,H)) and proton-proton spin-coupling constants ((3)J(H,H)); its absolute stereochemistry was established by Mosher analysis. The conformation of 1 in solution was mimicked by molecular modeling, employing a combination of distance geometry and restrained molecular dynamics. Apratoxin A (1) possesses IC(50) values for in vitro cytotoxicity against human tumor cell lines ranging from 0.36 to 0.52 nM; however, it was only marginally active in vivo against a colon tumor and ineffective against a mammary tumor.

Total structure determination of apratoxin A, a potent novel cytotoxin from the marine cyanobacterium Lyngbya majuscula.

A method for elucidating the relative configuration of acyclic organic compounds was developed on the basis of carbon-proton spin-coupling constants ((2,3)J(C,H)) and interproton spin-coupling constants ((3)J(H,H)). This method is based on the theory that, in acyclic systems, the conformation of adjacent asymmetric centers is represented by staggered rotamers, and their relative stereochemistry can be determined using (2,3)J(C,H) and (3)J(H,H), because the combined use of these J values enables the identification of the predominant staggered rotamer(s) out of the six possible derived from threo and erythro configurations. Detailed conformational analysis for model compounds 1-4 revealed that this method is useful in most cases for assignment of the configuration of acyclic structures occurring in natural products, in which stereogenic methine carbons are often substituted with a methyl or a hydroxy (alkoxy) group. This J-based configuration analysis was applied to the stereochemical elucidation of carboxylic acid 5 derived from zooxanthellatoxin and proven to be a practical method even for natural products with complicated structures.

Stereochemical Determination of Acyclic Structures Based on Carbon−Proton Spin-Coupling Constants. A Method of Configuration Analysis for Natural Products

Parr’s index to describe both electrophilicity and nucleophilicity

Intrinsic reactivity index as a single scale directed toward both electrophilicity and nucleophilicity using frontier molecular orbitals

As the first step to understand the reaction mechanism and diastereoselectivity of sodium borohydride reduction of ketones, ab initio Car−Parrinello molecular dynamics simulation has been performed on a solution of NaBH4 in liquid methanol. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, it was strongly suggested that Na+ and BH4− are associated in the solvent forming contact ion pairs. Thus we propose a new transition state structure model that contains complexation of the carbonyl oxygen with sodium cation. Predicted diastereoselectivity of the reduction of some substituted cyclohexanones applying this novel transition state model is in good agreement with experimental data, showing its validity and effectiveness to investigate the diastereoselectivity of NaBH4 reduction of other ketones.

Theoretical study on the mechanism and diastereoselectivity of NaBH4 reduction.

The “cis effect” is a phenomenon in which the cis isomer is more stable than the corresponding trans isomer or almost the same stability in some molecules with double bonds. In order to clarify the...

Daisuke Kaneno

Papers

Stereochemical Determination of Acyclic Structures Based on Carbon−Proton Spin-Coupling Constants. A Method of Configuration Analysis for Natural Products

Parr’s index to describe both electrophilicity and nucleophilicity

Intrinsic reactivity index as a single scale directed toward both electrophilicity and nucleophilicity using frontier molecular orbitals

Theoretical study on the mechanism and diastereoselectivity of NaBH4 reduction.

The Origin of Cis Effect in 1,2-Dihaloethenes : The Quantitative Comparison of Electron Delocalizations and Steric Exchange Repulsions