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Quantenchemie - Neueste Forschungsartikel der Fachverlage


 
Aktuelle Fachartikel zur Quantenchemie, sortiert nach Erscheinungsdatum.

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International Journal of Quantum Chemistry - published by Wiley-Interscience -
A journal devoted to Theory and Computation in Chemistry, Physics, and Molecular Biology



Aktuelle wissenschaftliche Fachartikel der genannten Journale:


Ab initio study of the π–π interactions between CO2 and benzene, pyridine, and pyrrole

The π–π interactions between CO2 and three aromatic molecules, namely benzene (C6H6), pyridine (C5H5N), and pyrrole (C4H5N), which represent common functional groups in metal-organic/zeoliticimidazolate framework materials, were characterized using high-level ab initio methods. The coupled-cluster with single and double excitations and perturbative treatment of triple excitations (CCSD(T)) method with a complete basis set (CBS) was used to calibrate Hartree–Fock, density functional theory, and second-order M⊘ller–Plesset (MP2) with resolution of the identity approximation calculations. Results at the MP2/def2-QZVPP level showed the smallest deviations (only about 1 kJ/mol) compared with those at the CCSD(T)/CBS level of theory. The strength of π–π binding energies (BEs) followed the order C4H5N > C6H6 ∼ C5H5N and was roughly correlated with the aromaticity and the charge transfer between CO2 and aromatic molecule in clusters. Compared with hydrogen-bond or electron donor–acceptor interactions observed during BE calculations at the MP2/def2-QZVPP level of theory, π–π interactions significantly contribute to the total interactions between CO2 and aromatic molecules. © 2013 Wiley Periodicals, Inc.

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The climatic effects of rising atmospheric levels of carbon have motivated extensive research into carbon sequestration using porous metal organic frameworks (MOFs). Weak intermolecular interactions between carbon dioxide (CO2) and MOFs largely determine their carbon uptake. This work studies these interactions between CO2 and aromatic species representing common building blocks of MOFs and finds an interesting correlation to molecular aromaticity. The results suggest design of efficient MOFs through use of linkers with enhanced aromaticity.

Quelle: International Journal of Quantum Chemistry | 24 May 2013 | 7:00 am CEST

Influence of collision energy and reagent vibrational excitation on the dynamics of the reaction H + LiH

We present a detailed quasiclassical trajectory (QCT) study of the dynamics corresponding to the reaction H + LiH inline image proceeding via depletion and H-exchange paths on a new potential energy surface of the electronic ground state. The effects of collision energy and reagent initial vibrational excitation on the reaction probability and cross sections are studied over a wide range of collision energies. The QCT-calculated reaction probability and cross sections are in good agreement with previous time-dependent wave packet results. More importantly, we found that the vibrational excitation of LiH molecule inhibits the LiH depletion reaction, whereas it promotes the H-exchange reaction. In addition, the differential cross sections calculated for the depletion reaction at different collision energies and excitation states indicate a strong forward scattering of the product molecule H2. © 2013 Wiley Periodicals, Inc.

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The lithium hydrogen (LiH) depletion reaction is significant in chemical studies of the early Universe. This work carries out a detailed quasiclassical trajectory study of the barrier-less reaction dynamics on a new potential energy surface of the electronic ground state. The results show that LiH vibrational excitation remarkably inhibits the depletion reaction, promotes the H-exchange reaction, and predicts a strong forward scattering of the hydrogen molecule.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 7:01 am CEST

Congested molecules. Where is the steric repulsion? An analysis of the electron density by the method of interacting quatum atoms

The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analyzed by the method of interacting quatum atoms (IQA). For all the molecules studied, the calculations show the existence of a bond path between the congested atoms and which, according to the quatum Theory of Atoms in Molecules, indicates that there is a stabilizing interaction between these atoms. The bond path is found to exist up to interatomic distances well-beyond the sum of the van der Waals radii. The IQA results indicate that steric hindrance is not a repulsive force between the congested atoms but that is the result of an increase in the intra-atomic or self-energy of the congested atoms. This increase in self-energy is caused by the deformation of the atomic basin of the congested atoms. © 2013 Wiley Periodicals, Inc.

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The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analysed by the method of Interacting quatum Atoms. The results indicate that steric hindrance is not a repulsive force between the congested atoms, but that it is the result of an increase in the self-energy those atoms. Neither bond paths, nor individual pair wise interaction energies are found to be useful indicators for the existence or absence of steric hindrance.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 6:46 am CEST

Intramolecular CH/π interactions in alkylaromatics: Monomer conformations for poly(3-alkylthiophene) atomistic models

In existing poly(3-alkylthiophenes) atomistic models, an extended conformation of the side chain is usually assumed. We report a first principle study of the side-chain energetics of 3-hexylthiophene, with the constraint of compatibility with crystal packing requirements. The first two torsion angles of the side chain closest to the ring were considered. Electron correlation is shown to be of great relevance in the assessment of the relative stability of folded conformers against extended ones. The roles of local charge-transfer, rehybridization, steric repulsion, and basis set superposition error, were all considered in the rationalization of our results. We extend our analysis to the thiophene/methane complex in order to elucidate the main differences between intermolecular and intramolecular CH/π phenomena. While in the noncovalent complex a single C[BOND]H bond mediates the interaction, folded arrangements of 3-alkylthiophenes require the collective effort of several aliphatic bonds. © 2013 Wiley Periodicals, Inc.

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A collective network of electron density delocalization effects in folded alkylaromatics gives them an edge over extended arrangements. This phenomenon is investigated in detail for the monomer of poly(3-hexylthiophene), the most commonly used semiconducting polymer. Side chain energetic and conformational aspects are explored by quantum chemical means in the long-term perspective of developing a more accurate crystal structure atomistic model for mobility and phase-transition simulations.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 6:45 am CEST

Molecular dynamics simulations of the Hras-GTP complex and the Hras-GDP complex

We study the structures of the Hras-GTP complex and the Hras-GDP complex in water to investigate the mechanism of GTP hydrolysis of the Hras-GTP complex. We performed molecular dynamics simulations of these complexes to investigate the structures of these complexes using the potential parameters of AMBER ff03 and our potential parameters around Mg2+. Our simulations show that the averaged structure differences between the Hras-GTP complex and Hras-GDP complex are found in the switch I and II regions. In particular, in the switch II region, the α2-helix of Hras-GDP is shorter than the α2-helix of Hras-GTP. The averaged number of water molecules in the first hydration sphere in Hras-GDP complex is larger than that in Hras-GTP complex. The occurrence ratio of the duration time of waters in the first hydration sphere of PA has long tail both in Hras-GTP and in Hras-GDP. In Hras-GDP complex, β-phosphate is hard to be hydrolyzed, while the number of waters in the first hydration sphere is larger than those in Hras-GTP. This suggests that there is a special direction for the hydrolysis. © 2013 Wiley Periodicals, Inc.

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Guanine nucleotide-binding proteins, like Hras, play an important role in many cell processes such as signal transduction, transportation, and secretion of proteins. The structures of Hras complexes with GTP and GDP complexes in aqueous solution are investigated in solution by molecular dynamics simulations. For the Hras-GDP complex, the number of water molecules in the first hydration sphere is larger than in the case of Hras-GTP, suggesting a special direction for the hydrolysis.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 6:45 am CEST

A theoretical study of the dihydrogen molecule confined inside carbon nanotubes

The aim of this work is to better understand the interaction between the confined dihydrogen molecule and armchair (2,2), (3,3) (4,4), (5,5), and (6,6) single-walled carbon nanotubes (SWNT) using Restricted Hartree–Fock (RHF) and Density Functional Theory (DFT) methods using B3LYP and CAM-B3LYP functionals. Depending on the calculation method and its orientation inside the nanotube, H2 binds differently. We found that H[BOND]H bond length increases when H2 is trapped in CNT (2,2) and decreases for CNT (3,3) and (4,4). The characteristics of confined H2 in (5,5) and (6,6) nanotubes are similar to H2 in a free state. © 2013 Wiley Periodicals, Inc.

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Dihydrogen is an extraordinary fuel source but its storage is an ongoing research challenge. This work examines the possibility of confinement of hydrogen inside carbon nanotubes and studies the energetics and bonding theoretically. The predicted activation of the H[BOND]H bond in one of the studied cases could be used in oxidative addition reactions or for alkene hydrogenation without a metal catalysts.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 6:44 am CEST

Gas storage of simple molecules in boron oxide nanocapsules

The capability of the B20O30 nanocapsule to store H2, N2, CO, CO2, NH3, CH4, and Cl2 molecules on the outer surface and inside of the cage was investigated using Monte Carlo simulations, long-range and dispersion corrected density functional theory, and Møller–Plesset second-order perturbation theory. Also, Monte Carlo simulations were employed to investigate the adsorption behavior of larger number of guest molecules inserted into and onto the larger B80O120 and B20O30@B80O120 cages. Absolute localized molecular orbitals energy decomposition analysis was used to describe the nature of intermolecular interactions in these endohedral and exohedral complexes. It is found that the hydrogen and ammonia gases are diffused to the inside of spherical B20O30 capsule, while other guest molecules prefer to interact with the outer surface of spherical and pyramidal capsules. For B80O120, up to 26 H2 and 11–14 N2, CO, CO2, NH3, and CH4 molecules are stored inside the capsule. The residual molecules are adsorbed on the outer surface of nanocapsule. © 2013 Wiley Periodicals, Inc.

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Encapsulation of atoms and molecules by fullerenes is a subject of current research interest, usually achieved experimentally with difficulty, under high pressure. This work examines the capability of boron oxide nanocapsules to store some simple gaseous molecules both endo- and exo-hedrally. The study finds that boron oxide complexes of different geometries have gas storage capabilities similar to C60. The results are expected to excite further experimental work in this field.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 6:40 am CEST

Inheritance and correlation of nucleic acid pyrimidine bases

Valence electronic structures of pyrimidine (P, C4N2H4) and nucleic acid (NA) pyrimidine bases, including cytosine (C, C4N3OH5), thymine (T, C5N2O2H6), and uracil (U, C4N2O2H4), are studied using B3LYP/aug-cc-pVTZ, B3LYP/TZVP, SAOP/et-pVQZ, and OVGF/TZVP. The highest occupied molecular orbital (HOMO) and the next HOMO (NHOMO) of pyrimidine are conclusively assigned as 7b2 and 2b1, respectively. The ionization energy spectra and valence orbital momentum distributions studies reveal that the NA bases, that is, cytosine, thymine, and uracil, exhibit a larger degree of similarity to each other than to pyrimidine, although they do inherit certain properties from pyrimidine. © 2013 Wiley Periodicals, Inc.

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Orbital momentum distributions reveal that pyrimidine exhibits less similarity to the nucleic acid (NA) bases (cytosine, thymine, and uracil) than the NA bases do to each other. The high symmetry of pyrimidine restricts interchanges between the x- and y-components of its orbitals, whereas the NA bases are more flexible as they do not possess such symmetry restriction. This may be one reason that pyrimidine does not appear in most of the RNA and DNA polymers.

Quelle: International Journal of Quantum Chemistry | 22 May 2013 | 6:40 am CEST

Inside Cover, Volume 113, Issue 13

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Quantum potential based theories present important insights into the quantum domain behavior of classically chaotic systems. The Review on page 1747 by Munmun Khatua, Debdutta Chakraborty, and Pratim Kumar Chattaraj discusses some representative examples of quantum signature of classical chaos through the study of quantum domain behavior of classical nonintegrable systems using quantum fluid dynamics, the quantum theory of motion and the quantum fluid density functional theory, and also the reactivity dynamics of various systems in free and confined environments. The solution of the relevant generalized non-linear Schrödinger equation provides the essential time-dependent density and current density and dynamical variants of different electronic structure principles become evident.

Quelle: International Journal of Quantum Chemistry | 21 May 2013 | 2:39 pm CEST

Cover Image, Volume 113, Issue 13

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Surprisingly differing NMR chemical shifts are obtained when a methyl acrylate or a vinyl acetate monomer, respectively, is incorporated into a neutral Ni(II) complex. According to Andrea Frank, Andreas Berkefeld, Matthias Drexler, Heiko M. Möller, and Thomas E. Exner on page 1787, these findings can be explained by unusual short distances between the Ni ion and the Ccarbonyl of the monomer as well as differential electron polarization effects as disclosed by natural bond orbital (NBO) analysis.

Quelle: International Journal of Quantum Chemistry | 21 May 2013 | 2:38 pm CEST

Global optimization of clusters using electronic structure methods

Over the past decade, there has been a significant growth in the development and application of methods for performing global optimization (GO) of cluster and nanoparticle structures using first-principles electronic structure methods coupled to sophisticated search algorithms. This has in part been driven by the desire to avoid the use of empirical potentials (EPs), especially in cases where no reliable potentials exist to guide the search toward reasonable regions of configuration space. This has been facilitated by improvements in the reliability of the search algorithms, increased efficiency of the electronic structure methods, and the development of faster, multiprocessor high-performance computing architectures. In this review, we give a brief overview of GO algorithms, though concentrating mainly on genetic algorithm and basin hopping techniques, first in combination with EPs. The major part of the review then deals with details of the implementation and application of these search methods to allow exploration for global minimum cluster structures directly using electronic structure methods and, in particular, density functional theory. Example applications are presented, ranging from isolated monometallic and bimetallic clusters to molecular clusters and ligated and surface supported metal clusters. Finally, some possible future developments are highlighted. © 2013 Wiley Periodicals, Inc.

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The development of more powerful global search algorithms and increasingly efficient electronic structure methods over the past decade, coupled with significant enhancements in computer power, has facilitated the exploration of clusters and nanoparticles at relatively high levels of theory. This review describes the implementation and application of global optimization algorithms to search for global minimum cluster structures directly using electronic structure methods. These methods are critically compared with search algorithms using empirical potentials and possible future trends are discussed.

Quelle: International Journal of Quantum Chemistry | 19 May 2013 | 6:21 am CEST

Theoretical study on keto–enol tautomerism and isomerization in pyruvic acid

Isomerization and tautomerism of 12 isomers of pyruvic acid including 4 keto and 8 enol forms were studied at the MP2 and B3LYP levels of theory using 6-311++G(2df,p) basis set, separately. Activation energy (Ea), imaginary frequency (υ), and Gibbs free energy (ΔG#) of the considered isomerization and tautomerism reactions were calculated. Interconversion of the enol forms proceeds through two paths: (i) proton transfer and (ii) internal rotation. Activation energies for the proton transfer paths were in the range of 125–145 kJ/mol and for the internal rotation paths were in the range of 5–45 kJ/mol. Keto–enol tautomerism of pyruvic acid proceeds only through proton transfer route and their activation energies were in the range of 200–300 kJ/mol. Effect of microhydration on the transition state structures and activation energies was also investigated. It was found that the presence of a water molecule catalyzes the isomerization and tautomerism reactions of pyruvic acid so that the activation energies decrease. © 2013 Wiley Periodicals, Inc.

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Pyruvic acid is involved in the metabolism of carbohydrates. Keto–-enol tautomerism in pyruvic acid can involve the transformation of the more stable keto form into the enol form. This is catalyzed by water, acting synchronously as a proton donor and proton acceptor. This study finds that a transition state structure with a hexagonal ring is formed which is more stable than tetragonal ring formed in the absence of water.

Quelle: International Journal of Quantum Chemistry | 17 May 2013 | 6:40 am CEST

Insight into the structural requirements of benzimidazole derivatives as interleukin-2 inducible t-cell kinase inhibitors by computational explorations

In the present work, a set of ligand- and receptor-based 3D-QSAR models were developed to explore the structure–activity relationship of 109 benzimidazole-based interleukin-2-inducible T-cell kinase (ITK) inhibitors. In order to reveal the requisite 3D structural features impacting the biological activities, a variety of in silico modeling approaches including the comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), docking, and molecular dynamics were applied. The results showed that the ligand-based CoMFA model (Q2 = 0.552, R2ncv = 0.908, R2pred = 0.787, SEE = 0.252, SEP = 0.558) and CoMSIA model (Q2 = 0.579, R2ncv = 0.914, R2pred = 0.893, SEE = 0.240, SEP = 0.538) were superior to other models with greater predictive power. In addition, a combined analysis between the 3D contour maps and docking results showed that: (1) Compounds with bulky or hydrophobic substituents near ring D and electropositive or hydrogen acceptor groups around rings C and D could increase the activity. (2) The key amino acids impacting the receptor–ligand interactions in the binding pocket are Met438, Asp500, Lys391, and Glu439. The results obtained from this work may provide helpful guidelines in design of novel benzimidazole analogs as inhibitors of ITK. © 2013 Wiley Periodicals, Inc.

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The activation of T-lymphocytes is critical for the initiation and regulation of the body's immune response to external pathogens. These cells are distinguished by the presence of a T-cell antigen receptor on the surface. This work uses three-dimensional quantitative structure-activity relationship methods to study a series of benzimidazole derivatives that exhibit activity against interleukin-2 inducible T-cell kinase. The developed models demonstrated good predictive ability and some key structural factors responsible for the activity.

Quelle: International Journal of Quantum Chemistry | 17 May 2013 | 6:32 am CEST

Electronic structure of francium

This article presents the first calculations of the electronic structure of francium for the bcc, fcc, and hcp structures, using the linearized augmented plane wave (LAPW) method. Both the local density approximation (LDA) and generalized gradient approximation (GGA) were used to calculate the electronic structure and total energy of francium (Fr). The GGA and LDA both found the total energy of the hcp structure to be slightly below that of the fcc and bcc structures, respectively. This is in agreement with similar results for the other alkali metals where the bcc structure is found not to be the ground state in contradiction to experiment. The equilibrium lattice constant, bulk modulus, and superconductivity parameters were calculated. Calculations of the enthalpy of the system suggest a structural transition from hcp to bcc under a pressure of 0.57 GPa. Using the McMillan-Gaspari-Gyorffy theories, we found that under further pressures, in the range of 3–14 GPa, Fr could be a superconductor with critical temperature up to 7 K. This is consistent with the other alkali metals and originates from an increase of the d-like density of states at the Fermi level, which makes the alkali metals behave like transition metals. © 2013 Wiley Periodicals, Inc.

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Little is known about the properties of the heaviest alkali metal, francium. This article provides the first electronic structure study of francium while completing a systematic study of the other alkalis. Theoretically, the alkalis should become superconductors under pressure. Lithium has been the only one experimentally verified. This study suggests that the increased d-character of the states at the Fermi level is the mechanism for superconductivity under pressure.

Quelle: International Journal of Quantum Chemistry | 13 May 2013 | 8:54 am CEST

Intermolecular interactions in uracil–nitrous acid complexes: structures, binding energy, topological properties, and nuclear magnetic resonance study

Molecular interactions between uracil and nitrous acid (U–NA) [C4N2O2H4[BOND]NO2H] have been studied using B3LYP, B3PW91, and MP2 methods with different basis sets. The optimized geometries, harmonic vibrational frequencies, charge transfer, topological properties of electron density, nucleus-independent chemical shift (NICS), and nuclear magnetic resonance one- and two-bonds spin–spin coupling constants were calculated for U–NA complexes. In interaction between U and NA, eight cyclic complexes were obtained with two intermolecular hydrogen bonds N(C)HU…N(O) and OHNA…OU. In these complexes, uracil (U) simultaneously acts as proton acceptor and proton donor. The most stable complexes labeled, UNA1 and UNA2, are formed via NH bond of U with highest acidity and CO group of U with lowest proton affinity. There is a relationship between hydrogen bond distances and the corresponding frequency shifts. The solvent effect on complexes stability was examined using B3LYP method with the aug-cc-pVDZ basis set by applying the polarizable continuum model (PCM). The binding energies in the gas phase have also been compared with solvation energies computed using the PCM. Natural bond orbital analysis shows that in all complexes, the charge transfer takes place from U to NA. The results predict that the Lone Pair (LP)(O)U → σ*(O[BOND]H) and LP(N(O)NA → σ*(N(C)[BOND]H)U donor–acceptor interactions are most important interactions in these complexes. Atom in molecule analysis confirms that hydrogen bond contacts are electrostatic in nature and covalent nature of proton donor groups decreases upon complexation. The relationship between spin–spin coupling constant (1hJHY and 2hJHY) with interaction energy and electronic density at corresponding hydrogen bond critical points and H-bonds distances are investigated. NICS used for indicating of aromaticity of U ring upon complexation. © 2013 Wiley Periodicals, Inc.

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Hydrogen bonds play important role in the structure and stability of biomolecular complexes by determining the relationship between reactivity of a molecule and its structure. This work analyzes the hydrogen bonding interaction in, and solvent stability of, uracil-nitrous acid complexes. Nitrous acid is an important indoor pollutant and expected to cause oxidative damage to RNA. The results are expected to improve the understanding of hydrogen bonding interactions in such complexes.

Quelle: International Journal of Quantum Chemistry | 13 May 2013 | 8:54 am CEST

Intermolecular interactions of formic acid with benzene: Energy decomposition analyses with ab initio MP2 and double-hybrid density functional computations

The intermolecular interactions of formic acid (HCOOH) with benzene (C6H6) have been investigated using localized molecular orbital energy decomposition analyses (LMO-EDA) with ab initio MP2 and several double-hybrid density functionals. The molecular geometries of five HCOOH…C6H6 complexes and corresponding benchmark total interaction energies at the CCSD(T)/CBS level are taken from literature (Zhao et al., J. Chem. Theory Comput. 2009, 5, 2726). According to the results of LMO-EDA with the MP2 method, the dispersion energies are found to be as important as the electrostatic energies for the total interaction energies of the five HCOOH…C6H6 complexes. Based on LMO-EDA with the double-hybrid density functionals of B2PLYP, B2K-PLYP, B2T-PLYP, and B2GP-PLYP computations, two new parameters for the framework of B2PLYP are extrapolated. These two new parameters are tested with other 10 complexes involving C6H6 (Crittenden, J. Phys. Chem. A 2009, 113, 1663), and they perform well on predicting the corresponding total interaction energies. Interestingly, these two new parameters for the framework of B2PLYP also perform well on the noncovalent complexation energies database (NCCE31/05) developed by Truhlar's group (Zhao and Truhlar, J. Phys. Chem. A 2005, 109, 5656). Therefore, these two new parameters appear to be suitable for investigating the noncovalent interactions, and they are denoted as B2N-PLYP, where N stands for the noncovalent interaction. This study is expected to provide new insight into the derivation of double-hybrid density functionals for studying the noncovalent interactions. © 2013 Wiley Periodicals, Inc.

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Complexes of formic acid and benzene exhibit a rich variety of noncovalent interactions and are thus reasonable prototypes for understanding such interactions between small organic molecules and aromatic compounds. This article uses a combination of ab initio and density functional theory (DFT)-based methods to find two new parameters related to B2PLYP functional. These are tested against a popular noncovalent complexation energies database. This work is expected to provide new insight into these important interactions.

Quelle: International Journal of Quantum Chemistry | 9 May 2013 | 1:00 pm CEST

Clarification of the role of protein in carbonmonoxy myoglobin by investigating electronic states

This article reports the proton tautomerization effects of distal histidine residues in carbonmonoxy myoglobin according to the density functional calculations of the whole protein. The electron eigenstates and electrostatic potential (ESP) distributed around heme and its pocket vary significantly depending on the protonation positions of the distal histidine residues. To investigate the range over which the electronic structures are affected by the proton tautomerization, the quantum mechanics/molecular mechanics (QM/MM) method is applied to probe the QM size to reproduce the atomic partial charges and ESP around the active center. Consequently, we show that these properties converged for the 300 pm QM/MM system in this study. During the analysis, we also find that amino residues such as Phe43, Val68, and Phe138 interact strongly with heme through orbital mixing, indicating that the protein is a medium not only interacting with the reaction center, but also buffering on electrons. © 2013 Wiley Periodicals, Inc.

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The iron-containing protein myoglobin is commonly found in muscular tissue of vertebrate animals and is a reliable marker for presence of tissue injury, including cardiac problems. Despite extensive studies, the effect of the protein on heme is still not sufficiently understood. This work studies the effect of proton tautomerization in distal histidine.

Quelle: International Journal of Quantum Chemistry | 30 Apr 2013 | 9:06 am CEST

A dual-level direct dynamics study on the hydrogen abstraction reaction of oxygen atom with methylhydrazine

The mechanism of the multichannel reaction CH3NHNH2 (SC1 and SC2) + O → products is investigated theoretically using ab initio and density functional theory, and dynamics properties are explored by a dual-level direct dynamics method. The calculation of the potential energy surface is carried out at the BMC-CCSD//MPW1K/6-311G(d,p) level. Using canonical variational transition state theory with a small-curvature tunneling correction, the rate constants of each channel are evaluated over a wide temperature range of 200–2000 K on the basis of obtained electronic structures and energy information. The total rate constants are calculated from the sum of the individual rate constants taking into account the Boltzmann distribution of two conformers. The reactivity of the H atom located in different groups is compared. © 2013 Wiley Periodicals, Inc.

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Diamine-based compounds such as methylhydrazine are used as rocket fuels, thereby making the relevant oxidation and hydrogen abstraction reactions interesting. This work calculates the rate constants and studies the mechanism of the hydrogen abstraction. In absence of experimental data, these results are expected to provide an insight into the dynamical properties of the reaction over a wide temperature range.

Quelle: International Journal of Quantum Chemistry | 30 Apr 2013 | 9:06 am CEST

The 13th V. A. fock meeting on quantum and computational chemistry

Quelle: International Journal of Quantum Chemistry | 30 Apr 2013 | 9:06 am CEST

Gas storage of simple molecules in boron oxide nanocapsules

The capability of the B20O30 nanocapsule to store H2, N2, CO, CO2, NH3, CH4, and Cl2 molecules on the outer surface and inside of the cage was investigated using Monte Carlo simulations, long-range and dispersion corrected density functional theory, and Møller–Plesset second-order perturbation theory. Also, Monte Carlo simulations were employed to investigate the adsorption behavior of larger number of guest molecules inserted into and onto the larger B80O120 and B20O30@B80O120 cages. Absolute localized molecular orbitals energy decomposition analysis was used to describe the nature of intermolecular interactions in these endohedral and exohedral complexes. It is found that the hydrogen and ammonia gases are diffused to the inside of spherical B20O30 capsule, while other guest molecules prefer to interact with the outer surface of spherical and pyramidal capsules. For B80O120, up to 26 H2 and 11–14 N2, CO, CO2, NH3, and CH4 molecules are stored inside the capsule. The residual molecules are adsorbed on the outer surface of nanocapsule. © 2013 Wiley Periodicals, Inc.

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Encapsulation of atoms and molecules by fullerenes is a subject of current research interest, usually achieved experimentally with difficulty, under high pressure. This work examines the capability of boron oxide nanocapsules to store some simple gaseous molecules both endo- and exo-hedrally. The study finds that boron oxide complexes of different geometries have gas storage capabilities similar to C60. The results are expected to excite further experimental work in this field.

Quelle: International Journal of Quantum Chemistry | 25 Apr 2013 | 1:49 pm CEST

Inheritance and correlation of nucleic acid pyrimidine bases

Valence electronic structures of pyrimidine (P, C4N2H4) and nucleic acid (NA) pyrimidine bases, including cytosine (C, C4N3OH5), thymine (T, C5N2O2H6), and uracil (U, C4N2O2H4), are studied using B3LYP/aug-cc-pVTZ, B3LYP/TZVP, SAOP/et-pVQZ, and OVGF/TZVP. The highest occupied molecular orbital (HOMO) and the next HOMO (NHOMO) of pyrimidine are conclusively assigned as 7b2 and 2b1, respectively. The ionization energy spectra and valence orbital momentum distributions studies reveal that the NA bases, that is, cytosine, thymine, and uracil, exhibit a larger degree of similarity to each other than to pyrimidine, although they do inherit certain properties from pyrimidine. © 2013 Wiley Periodicals, Inc.

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Orbital momentum distributions reveal that pyrimidine exhibits less similarity to the nucleic acid (NA) bases (cytosine, thymine, and uracil) than the NA bases do to each other. The high symmetry of pyrimidine restricts interchanges between the x- and y-components of its orbitals, whereas the NA bases are more flexible as they do not possess such symmetry restriction. This may be one reason that pyrimidine does not appear in most of the RNA and DNA polymers.

Quelle: International Journal of Quantum Chemistry | 25 Apr 2013 | 1:49 pm CEST

Theoretical study of enantiomeric and geometric control in chiral guanidine-catalyzed asymmetric 1,4-addition of 5H-oxazol-4-ones

Abstract

Density functional theory calculations are used to study the reaction mechanism and origins of high stereoselectivity in chiral guanidine-catalyzed asymmetric 1,4-addition of 5H-oxazol-4-ones. The reaction involves proton abstraction of 5H-oxazol-4-one, C[BOND]C bond formation, and proton transfer. N1 atom of chiral guanidine exchanges its character as base and acid to activate 5H-oxazol-4-one and to facilitate the product formation. The role of N2[BOND]H2 is not only H-bond donor for 5H-oxazol-4-one but also electron accepter for N1. The enantioselectivity related with rate-limiting step 1 and Z/E selectivity determined in step 2 are primarily influenced by a five to six-membered ring link in the backbone of chiral guanidine. The reaction proceeds along the favorable path with smaller rotations of the linked bonds. The enantioselectivity is improved with guanidine involving an electron-deficient and bulky substituent. With methyl ether-protected hydroxy in structure, the catalytic ability and enantioselective control of guanidine are extraordinarily low, affording the opposite enantiomer as major product. Z-isomers are preferred in all cases. © 2013 Wiley Periodicals, Inc.

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Chiral guanidine catalysts are widely used in various asymmetric reactions to obtain high enantioselectivity. However, the reaction of asymmetric 1,4-addition catalyzed by bicyclic chiral guanidine is not well-understood. This article presents the origin of high enantiomeric and geometric control for this type of guanidine. The results are expected to contribute to the design and modification of guanidine catalysts.

Quelle: International Journal of Quantum Chemistry | 10 Apr 2013 | 5:43 am CEST

Generalized relativistic effective core potential calculations of the adiabatic potential curve and spectroscopic constants for the ground electronic state of the Ca2 molecule

Abstract

The potential curve, dissociation energy, equilibrium internuclear distance, and spectroscopic constants for the 1Σmath image ground state of the Ca2 molecule are calculated with the help of the generalized relativistic effective core potential method, which allows one to exclude the inner core electrons from the calculations and to take the relativistic effects into account effectively. Extensive generalized correlation basis sets were constructed and used. The scalar relativistic coupled cluster method with corrections for high-order cluster amplitudes is used for the correlation treatment. The results are analyzed and compared with the experimental data and corresponding all-electron results. © 2013 Wiley Periodicals, Inc.

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The Ca2 molecule is a difficult system for ab initio modeling due to multiconfigurational nature of the ground state, weak interatomic interaction, and noticeable relativistic corrections. To estimate the computational accuracy of the quantum chemical methods used, the calculated results are compared with the corresponding experimental data. The potential energy curve, dissociation energy, equilibrium internuclear distance, and spectroscopic constants for this molecule are obtained.

Quelle: International Journal of Quantum Chemistry | 10 Apr 2013 | 5:43 am CEST

DNA sequencing with titanium nitride electrodes

Abstract

We construct a hydrogen-bond based metal–molecule–metal junction, which contains two identical “reader” molecules, one single DNA base as a bridged molecule, and two titanium nitride electrodes. Hydrogen bonds are formed between “reader” molecules and DNA base, whereas titanium–sulfur bonds are formed between “reader” molecules and titanium nitride electrodes. We perform electronic structure calculations for both the bare bridged molecule and the full metal–molecule–metal system. The projected density of states shows that when the molecule is connected to the titanium nitride electrode, the energy levels of the bridged molecule are shifted, with an indirect effect on the hydrogen bonds. This is similar to the case for a gold electrode but with a more pronounced effect. We also calculate the current–voltage characteristics for the molecular junctions containing each DNA base. Results show that titanium nitride as an electrode can generate distinct conductance for each DNA base, providing an alternative electrode for DNA sequencing. © 2013 Wiley Periodicals, Inc.

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The extraction of human genomic information is expected to lead to a revolution in development of individualized medical therapies. Electron transport through DNA-based molecular junctions opens the door to fast and cheap DNA sequencing, on the basis of distinct current–voltage characteristics. This work studies two kinds of sequencing devices with titanium nitride and gold electrodes theoretically. The molecular conductances obtained suggest that these are viable candidate devices for fast DNA sequencing.

Quelle: International Journal of Quantum Chemistry | 10 Apr 2013 | 5:43 am CEST

TD-DFT benchmarks: A review

Abstract

Time-Dependent Density Functional Theory (TD-DFT) has become the most widely-used theoretical approach to simulate the optical properties of both organic and inorganic molecules. In this contribution, we review TD-DFT benchmarks that have been performed during the last decade. The aim is often to pinpoint the most accurate or adequate exchange-correlation functional(s). We present both the different strategies used to assess the functionals and the main results obtained in terms of accuracy. In particular, we discuss both vertical and adiabatic benchmarks and comparisons with both experimental and theoretical reference transition energies. More specific benchmarks (oscillator strengths, excited-state geometries, dipole moments, vibronic shapes, etc.) are summarized as well. © 2013 Wiley Periodicals, Inc.

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Time-dependent density functional theory has become the most widely used tool to investigate excited state properties. However, the selection of an adequate exchange-correlation functional remains a major issue. In this review, the results obtained through recent benchmarks are summarized and several properties considered: vertical and adiabatic transition energies, dipoles, geometries, oscillator strengths, and vibrational signatures. The review concludes with a set of general guidelines for active practitioners.

Quelle: International Journal of Quantum Chemistry | 9 Apr 2013 | 7:29 am CEST

A molecular study of tetrakis(p-methoxyphenyl)porphyrin and its Zn(II) complex as discotic liquid crystals

Abstract

A theoretical study has been carried out on two methoxyphenyl derivatives (tetrakis-(p-methoxyphenyl)- porphyrin and the Zn-containing complex), which are the reduced size representation of the alkyl peripheral substituent systems. The aim is to study the electronic interactions on these aromatic cores which is one of the most important properties in discotic liquid crystals. Their face-to-face dimeric conformation systems were studied in order to evaluate charge transport properties, by assessing the intermolecular charge transfer integrals “t” in the context of the Marcus electron transfer theory. The intermolecular transfer integral has been calculated from the matrix elements of the Kohn–Sham Hamiltonian including dispersion correction for noncovalent interacting systems. The results indicate that the effect of the Zn center in these porphyrins is nearly negligible and both studied systems can act as electron carriers, which are also seen in the bonding interaction of the LUMO orbitals. © 2013 Wiley Periodicals, Inc.

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Two macrocyclic molecules, tetrakis-(p-methoxyphenyl)porphyrin and its Zn-containing complex, represent model structures for the study of the charge-transfer processes in non-covalent π-stacking systems. Density functional theory calculations, incorporating dispersion corrections, suggest that the effect of the metallic center over the electron transfer property is nearly negligible in these systems.

Quelle: International Journal of Quantum Chemistry | 9 Apr 2013 | 7:20 am CEST

Proper quantization rule approach to three-dimensional quantum dots

Abstract

In this article, we develop a formalism to obtain the energy levels of the electron in a central force potential confined in a spherical quantum dot with radius rC by the proper quantization rule and the Wentzel-Kramers-Brillouin approximation. It is shown that the numerical results are in good agreement with exact solutions. To illustrate this method, we consider the linear harmonic oscillator and Coulomb potential confined within an impenetrable sphere of radius rC in three dimensions. © 2013 Wiley Periodicals, Inc.

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A formalism is developed to calculate the energy levels of an electron subject to a central force potential confined in a spherical quantum dot with radius rC using proper quantization rule. Obtained numerical results are in good agreement with exact solutions. The case of a three-dimensionally confined linear harmonic oscillator subjected to a Coulomb force-field is used as an illustrative example. The rule illustrates its simplicity in calculations and beauty of symmetrical expression.

Quelle: International Journal of Quantum Chemistry | 3 Apr 2013 | 6:55 am CEST

Comparison of various types of coherence and emergent coherent systems†

Abstract

Coherence is a collective property that is present in Bose–Einstein condensates (BEC), an example of which when charged is superconductivity (SC). Coherence is also believed to be present to a degree in highly efficient energy transfer in certain biological systems. Attributes of coherent systems are examined in BEC, superfluidity and Bardeen, Cooper, and Schrieffer SC and a laser in part 1. Part 2 consists of examination of various proposals for coherence including “emergent coherent systems” where there may be coherence but no phase transition. We discuss “cold” atomic gases, the Casimir effect, an extended version of Förster's resonance energy transfer, Fröhlich's model, exciton-coupled quantum wells, and conceptually “old” polaritons rejuvenated by new developments. A discussion about highly efficient energy transfer in photosynthesis along with our proposal for a possible new model for this system is the last of the examples. We finish with a discussion about emergent coherent systems and attempt to classify the examples of parts 1 and 2. © 2013 Wiley Periodicals, Inc.

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Coherence in molecular systems has evolved considerably since the fundamental insights of London and Penrose and Onsager and the first “cold atom” studies of the 1990s. This article provides a comprehensive review of the most important examples of coherent systems, from Bose-Einstein condensates, to superfluidity, to “cold” atomic gases. The role of coherence in the highly efficient energy transfer in photosynthesis and possible new models for it are also discussed.

Quelle: International Journal of Quantum Chemistry | 2 Apr 2013 | 9:21 am CEST

Electronic and magnetic properties of all 3d transition-metal doped ZnO monolayers

Abstract

Stable geometries, electronic structures, and magnetic properties of the ZnO monolayer doped with 3d transition-metal (TM) (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) atoms substituting the cation Zn have been investigated using first-principles pseudopotential plane wave method within density functional theory (DFT). It is found that these nine atomic species can be effectively doped in the ZnO monolayer with formation energies ranging from −6.319 to −0.132 eV. Furthermore, electronic structures and magnetic properties of ZnO monolayer can be modified by such doping. The results show that the doping of Cr, Mn, Fe, Co, Ni, and Cu atoms can induce magnetization, while no magnetism is observed when Sc, Ti, and V atoms are doped into the ZnO monolayer. The magnetic moment is mainly due to the strong p–d mixing of O and TM (Cr, Mn, Fe, Co, Ni, and Cu) orbitals. These results are potentially useful for spintronic applications and the development of magnetic nanostructures. © 2013 Wiley Periodicals, Inc.

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Doping is often used to tune the physical properties of semiconductor materials. In this work, the effect of substitutionally doping 3d transition-metal (TM) atoms into zinc oxide (ZnO) monolayers is studied theoretically. While doping with Cr, Mn, Fe, Co, Ni, and Cu is seen to induce magnetization, no such effect is observed in the case of Sc, Ti, and V. The results are expected to help in the design of spintronic devices based on ZnO.

Quelle: International Journal of Quantum Chemistry | 29 Mar 2013 | 1:45 pm CET

Plasmon resonances and plasmon-induced charge transport in linear atomic chains

Abstract

In linear hydrogen atomic chains, plasmon resonances and plasmon-induced charge transport are studied by time-dependent density functional theory. For the large linear chain, it is a general phenomenon that, in the longitudinal excitation, there are high-energy resonances and a large low-energy resonance. The energy of the large low-energy resonance conforms to the results calculated by the classical Drude model. In order to explain the formation mechanism of the high-energy resonances, we present a simple harmonic oscillator model. This model may reasonably account for the relationship between low-energy and high-energy resonances, and has a certain degree of universality. As the interatomic distance decreases, the current shows a gradual transition from insulator to metal. The current enhancement mainly depends on the local field enhancement associated with plasmon excitation, and the enhanced electron delocalization effect as a result of the decrease of the interatomic distance. © 2013 Wiley Periodicals, Inc.

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For a large linear hydrogen chain, generally, in the longitudinal excitation, there are high-energy resonances and a large low-energy resonance. As the interatomic distance decreases, the current response shows a gradual insulator to metal transition. The current enhancement mainly depends on the local field enhancement associated with plasmon excitation, and the enhanced electron delocalization effect as a result of the decrease of the interatomic distance.

Quelle: International Journal of Quantum Chemistry | 29 Mar 2013 | 1:45 pm CET

Superconductivity from repulsive electronic correlations on alternant cuprate and iron-based lattices

Abstract

A key question in the theory of high-temperature superconductivity is whether off-diagonal long-range order can be induced wholly or in large part by repulsive electronic correlations. Electron pairs on cuprate and the iron-based pnictide and chalcogenide alternant lattices may interact with a strong short-range Coulomb repulsion and much weaker longer range attractive tail. Here, we show that such interacting electrons can cooperate to produce a superconducting state in which time-reversed electron pairs effectively avoid the repulsive part but reside predominantly in the attractive region of the potential. The alternant lattice structure is a key feature of such a stabilization mechanism leading to the occurrence of high-temperature superconductivity with dmath image or sign alternating s-wave or s ± condensate symmetries. © 2013 Wiley Periodicals, Inc.

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High-temperature superconductivity can be induced by repulsive electronic correlations. Time-reversed electron pairs on cuprate and iron-based pnictide and chalcogenide alternant lattices can interact with a short-range Coulomb repulsion and a weaker longer range attractive tail. Such interacting electrons can collectively correlate to produce superconductivity. The alternant lattice structure is the key stabilizing feature of such a mechanism giving high-temperature superconductivity with dmath image and s ± condensate symmetries.

Quelle: International Journal of Quantum Chemistry | 23 Mar 2013 | 8:20 am CET

Theoretical investigation of the alloxan—dialuric acid redox cycle

Abstract

The redox cycle between alloxan, a mild oxidizing agent, and its reduction partner, dialuric acid, is investigated using density functional theory. It is found that the initial step is the one-electron reduction of alloxan followed by protonation, yielding a stable neutral radical, AH·. The radical can then accept another electron to form the dialuric acid anion. The formation of this anion is thermodynamically favored in both the gas phase and in solution. The radical may also undergo dimerization to alloxantin, followed by the transfer of a proton from one moiety to another, yielding alloxan and dialuric acid. This reduction is thermodynamically feasible in the gas phase, but not in aqueous solution. In the case of reduction of alloxan by glutathione at the physiological pH, computed redox potentials indicate that a two-electron reduction is the favored course of reaction, yielding directly the dialuric acid anion, which then undergoes aerial oxidation to yield the superoxide radical. The redox cycling between alloxan and dialuric acid is responsible for the diabetogenic activity of alloxan, producing cytotoxic radicals on reoxidation of dialuric acid. © 2013 Wiley Periodicals, Inc.

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Alloxan has long been used to induce diabetes in experimental animals in studies on diabetes mellitus, a metabolic disorder that affects several million people worldwide. The alloxan–dialuric acid redox cycle is believed to be responsible for the diabetogenecity of alloxan. Herein, the mechanism involved in this redox cycling is investigated, and it is found that alloxan is reduced by glutathione to the dialuric acid anion, which undergoes aerial oxidation to generate cytotoxic superoxide radicals, causing β-cell toxicity.

Quelle: International Journal of Quantum Chemistry | 23 Mar 2013 | 8:20 am CET

Theoretical characterization of hydrogen pentoxide, H2O5

Abstract

Following our investigations on hydrogen polyoxides, herein we employed coupled cluster theory in conjunction with Dunning's correlation consistent basis sets and density functional theory to study HOOOOOH (H2O5). The infrared spectra of H2O5 and its three deuterated isotopologues, as well as those of the five single-substituted 18O isotopologues are discussed in detail. Internal valence coordinates were employed to classify the vibrational modes. The Raman activity is reported to help in the identification of hydrogen pentoxide. The suggested enthalpy of formation is ΔHf,298° (HOOOOH) = 1.4 ± 1.5 kcal/mol. This value includes corrections for relativistic and core-valence effects as well as anharmonic corrections to Zero-point energy corrections. © 2013 Wiley Periodicals, Inc.

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Hydrogen polyoxides present challenges for theoretical chemists because of their highly correlated nature. A combination of high-level quantum chemical approaches is therefore employed in this work to study the structure, enthalpy of formation, and infrared spectrum of hydrogen pentoxide. The obtained results are intended to motivate and help experimentalists with the detection and characterization of H2O5.

Quelle: International Journal of Quantum Chemistry | 20 Mar 2013 | 9:38 am CET

Intermolecular interactions of a size-expanded guanine analogue with gold nanoclusters

Abstract

The interactions between a size-expanded Guanine analogue x-Guanine (xG) and gold nanoclusters, Aun (n = 2, 4, 6, and 8), were studied theoretically using density functional theory. Geometries of neutral complexes were optimized using the B3LYP functional with the 6-31+G(d,p) basis set for xG and the LANL2DZ basis set for gold clusters. The binding modes, interaction strength, and the charge-transfer properties of different Aun-xG complexes were investigated. Natural population analysis was performed for natural bond order charges. It was found that gold nanoclusters form stable complexes with xG and these binding results in a substantial amount of electronic charge being transferred from xG to the gold clusters. The vertical first ionization potential, electron affinity, Fermi Level, and the HOMO–LUMO gap of xG and its complexes with gold nanoclusters were also analyzed. © 2013 Wiley Periodicals, Inc.

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Interactions of gold with DNA bases constitute an important area of research in the development of potential miniature devices and biotechnology. In this work, a comprehensive theoretical study of the interactions between the newly designed size-expanded guanine analogue x-Guanine and gold clusters was performed and compared to natural guanine. The results may provide useful guidance for design of devices incorporating nanowires.

Quelle: International Journal of Quantum Chemistry | 20 Mar 2013 | 9:37 am CET

Mechanism of aziridination of styrene catalyzed by copper(I) bis(oxazoline)

Abstract

Experimental studies show that copper complexes can be effectively anchored onto the pores of mesoporous solids, having a good catalytic performance in several reactions, among them the aziridination of olefins and in particular, styrene. In this work, the mechanism of the aziridination of styrene catalyzed by a bis(oxazoline) copper(I) complex was studied in detail by means of density functional theory (DFT) calculations. For such reactions in the homogeneous phase, our calculations revealed a wide diversity of reaction-pathways, which have not been considered in previous studies, and should be taken into account due to the small energy differences between them. What is more, our results show that there is a strong dependence on the chosen DFT functional. This has profound implications on the way the heterogeneous reaction is studied. © 2013 Wiley Periodicals, Inc.

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Experimental studies show that copper complexes can be effectively anchored into the pores of mesoporous solids, showing promising catalytic performances in several reactions, as for example the aziridination of olefins and in particular, styrene. The mechanism of this reaction catalyzed by a bis(oxazoline) copper(I) complex is studied here in detail by means of DFT calculations in the homogeneous phase. The calculations reveal a wide diversity of reaction-pathways with comparable energetic profiles.

Quelle: International Journal of Quantum Chemistry | 16 Mar 2013 | 7:45 am CET

Nature of closed- and open-shell interactions between noble metals and rare gas atoms

Abstract

Interactions between noble metals and rare gases have become an interesting topic over the last few years. In this work, a computational study of the open-shell (d10s1) and closed-shell (d10s and d10s2) noble metals (M = Cu, Ag, and Au) with three heaviest rare gas atoms (Rg = Kr, Xe, and Rn) has been performed. Potential energy curves based on ab initio [MP2, MP4, QCISD, and CCSD(T)] and DFT functionals (M06-2X and CAM-B3LYP) were obtained for ionic and neutral AuXe complexes. Dissociation energies indicate that neutral metals have the lowest and cationic metals have the highest affinities for interaction with rare gas atoms. For the same metals, there is a continuous increase in dissociation energies (De) from Kr to Rn. The nature of bonding and the trend of De and equilibrium bond lengths (Re) have been interpreted by means of quantum theory of atoms in molecules, natural bond orbital, and energy decomposition analysis. © 2013 Wiley Periodicals, Inc.

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Understanding the nature of binding between open-shell and closed-shell noble metal and noble gas atoms has become of great interest due to their respective noble character. Theoretical calculations have been expanded to characterize these systems. In this account, the nature of bonding is analyzed based on electronic charge and density distribution, and the energy decomposition method to provide a qualitative and quantitative scheme that can be helpful for investigating these interactions.

Quelle: International Journal of Quantum Chemistry | 16 Mar 2013 | 6:23 am CET

Computation of screened two-electron matrix elements

Abstract

Computational studies are presented for atoms in screening environments. Numerical solution of atomic Hartree–Fock equations in the Slater type orbitals basis are presented for screened Debye electron–electron as well as electron–nucleus interaction. Slater integrals are evaluated using a Gauss–Laguerre quadrature. Detailed numerical results are presented for various atoms and Debye lengths establishing the method as well as showing the opposing effects of electron–nucleus and electron–electron screening that may induce ambiguity in physical properties extracted from experimental plasma data. A detailed discussion of convergence properties is given. The relevant outcome of the present study revealed the fact that the present expansion method and the previously published Legendre expansion method (Winkler, Int. J. Quantum Chem. 2010, 110, 3129) have their best convergence properties in different regions of the Debye screening length. This is important for applications. In addition, the new expansion method can be implemented for other screening potentials, where other approaches fail. © 2013 Wiley Periodicals, Inc.

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Computational studies are presented for atoms in screening environments. Numerical results are presented for various atoms and Debye lengths showing the opposing effects of electron–nucleus and electron–electron screening that may induce ambiguity in physical properties extracted from experimental plasma data. Different expansion methods have their best convergence properties in vastly different regions of the Debye screening length. This is important for applications. The new expansion method can also be implemented for other screening potentials.

Quelle: International Journal of Quantum Chemistry | 16 Mar 2013 | 6:23 am CET

Structures, energetics, and isomerism of [Be,C,O,S]: Stability of triply bonded sulfur

Abstract

Multiply bonded sulfur has continued to attract attention both experimentally and theoretically. Triply sulfur-bonded compounds are still rare, due to either the lack of suitable generation precursors or the conversion instability toward doubly sulfur-bonded structures. A detailed computational study was performed on the structures and stability of various [Be,C,O,S] isomers at the coupled cluster singles doubles (triple excitations) (CCSD(T))/aug-cc-pVTZ//B3LYP/6-311+G(d)+ZPVE level to predict intrinsically stable isomers with triply bonded sulfur. The molecular orbital, bond distance, and harmonic vibrational frequency analysis were carried out at aug-cc-pVTZ-B3LYP, M06-2X, and CCSD(T) levels to investigate the bonding nature of linear structures. It was shown that two low-lying isomers are linear SBeCO 01 (0.0 kcal/mol) and SBeOC 02 (15.7 kcal/mol), both of which possess the S[TRIPLE BOND]Be triple bonding. The Lewis acid–base association of SBe + CO can barrierlessly form 01 and 02, with the former more abundant, while the insertion reaction of SCO + Be might generate more 02 than 01 via photochemical processes. By contrast, formation of the S[TRIPLE BOND]C-bearing isomer SCBeO 04 (39.4 kcal/mol) seems unlikely due to its higher energy and less kinetic competition than that of 01 and 02, via either simple association or insertion reactions. The new stable isomers SBeCO 01 and SBeOC 02 add to the number of S[TRIPLE BOND]Be triply bonded species. Their unique structures and varied branching ratios under association and insertion processes deserve future experimental study. © 2013 Wiley Periodicals, Inc.

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Despite the existence of carbon disulfide, sulfur exhibits a low tendency to form multiple bonds in its molecules. However, a rich set of chemical possibilities may exist for hypothetical multiply bonded sulfur-containing compounds. This work presents a detailed computational study on the structures and stability of various tetra-atomic [Be,C,O,S] isomers, which may exhibit triply bonded SC and SBe structures. The study predicts that two linear isomers SBeCO and SBeOC, with a unique triple SBe bonding, may be synthesizable via suitable Lewis acid–base reactions.

Quelle: International Journal of Quantum Chemistry | 16 Mar 2013 | 6:23 am CET

A computational investigation on the geometries, stabilities, antioxidant activity, and the substituent effects of the L-ascorbic acid and their derivatives

Abstract

The geometries, stabilities, and antioxidant activities of L-Ascorbic acid (1a), D-erythroascorbate (2a), and D-erythroascorbate glucoside (3a) as well as their sulfur and selenium derivatives are systematically investigated by using density functional theory. Emphasis is placed on studies of the two main mechanisms, that is, hydrogen atom donation and single-electron transfer, and the O[BOND]H bond dissociation enthalpy and the ionization potential are computed in the gas phase and water solution. The calculated results indicate that the 2-OH group in the five-membered ring acts as an important H atom donor to free radicals. The 2-OH radical spin density distribution shows that the unpaired electron is mostly located at the C3 atom of the five-membered ring and partially at the vicinal O atoms, proving that a certain delocalization of the odd electron is effective in the five-membered ring. In water aqueous solution, the antioxidant capacity and the electron donating ability are increased as the O atom in the five-membered ring of 1a, 2a, and 3a is replaced by S and Se, respectively, in good agreement with experimental measurements; Furthermore, their antioxidant capacities are enhanced as compared with the standard antioxidant (resveratrol). © 2013 Wiley Periodicals, Inc.

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Free radicals are continuously produced in the body's metabolic processes and ingested through exposure to contaminated environment. These chemical species mediate oxidative damage of the body's DNA and tissues, resulting in diseases like cancer, heart disease, and so on. Antioxidants found in many food groups and supplements help combat this damage. This work studies the antioxidant activity of vitamin C and related compounds and suggests synthesis of novel antioxidants.

Quelle: International Journal of Quantum Chemistry | 16 Mar 2013 | 6:23 am CET

Theoretical analyses of the host–guest interaction within chlorine hydrate

Abstract

The host–guest interaction is necessary for the stabilization of hydrates. Using Density Function Theory methods, the host–guest interaction within an unconventional chlorine hydrate was investigated, in combination with typical noncovalent analyses. The host–guest interaction energy was predicted to be as high as 17.51 kcal/mol, which was stronger than the typical van der Waals (vdW) interaction, due to an involvement of up to 20 Cl…O interactions. Polarization and dispersion energies made up the main contribution to the total interaction energy. Further visualization of the host–guest interaction validated, together with the general Cl…O interaction, another vdW interaction between the guest-Cl atom and the five-membered H2O cluster. Isosurfaces associated with two patterns of vdW interactions yielded a better “fit” in shape, suggesting their cooperativity in stabilizing the steric configuration. The σ-region on the guest-Cl atom was verified to regulate the electron redistribution over the molecular space. These results are useful for understanding specific halogen behavior, and the origin and nature of host–guest interaction in hydrates. © 2013 Wiley Periodicals, Inc.

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The host-guest interaction is fundamental for formation and stability of ice-liked hydrates. Understanding binding behavior between the guest-Cl and host water cage within unconventional chlorine hydrate is helpful for design and preparation of hydrates. Multiple noncovalent analyses, in conjunction with the active chlorine, have been used to explore the origin and feature of such intramolecular interaction. This work provides a comprehensive insight into the nature of host-guest interaction, which is necessary complement to conventional hydrates.

Quelle: International Journal of Quantum Chemistry | 16 Mar 2013 | 6:23 am CET

Conformational preference and mechanism of decarboxylation of levodopa. A quantum dynamics/quantum mechanics study

Abstract

The present study addresses the conformational preferences and the mechanism of decarboxylation of levodopa (LD). LD is used to increase dopamine concentrations in the treatment of Parkinson's disease. LD crosses the protective blood–brain barrier, where it is converted into dopamine by the process of decarboxylation. Molecular dynamics simulation has been carried out at the DFT/6-31++G level of theory to identify the global minimum structure of LD. Conformational preferences of the amino acid side chain of LD has been investigated at the B3LYP/6-311++G** level of theory. Fourier transform analysis has been performed to identify the origin of the rotational barriers. Electrostatic dipole moment and bond interactions underlie the observed potential energy barriers for rotation of the amino acid side chain of LD. The vital biological process of decarboxylation of LD has been examined in the gas phase and in aqueous solution. Without the presence of water, there is only one possible route for the decarboxylation of LD. In this concerted mechanism, a proton transfer and breakage of the C10[BOND]C18 bond, take place simultaneously (ΔE# = 73.2 kcal/mol). In solution, however, two possible decarboxylation routes are available for LD. The first involve the formation of a zwitterionic intermediate (ΔE# = 72.4 kcal/mol). The zwitterionic form of LD have been localized using explicitly bound water molecules to model short-range solvent effects and self-consistent reaction field polarized continuum model to estimate long-range solvent interactions. The second route involve the formation of a cyclic structure in which a water molecule acts as a bridge linking the anticarboxylic hydrogen and α-position carbon atom (ΔE# = 59.8 kcal/mol). Natural bond orbital (NBO) analysis reveals that the conformational and overall stability of the amino acid side chain is facilitated by the antiperiplanar interactions between the phenyl moiety C[BOND]H and C[BOND]C bonds and C[BOND]X bonds of the amino acid side chain. However, much of the major donor–acceptor interactions is of the lone pair type and is localized within the amino acid side chain itself. Results of the present work reveal that NBO data reflect nicely and identify clearly reaction coordinates at the transition species. © 2013 Wiley Periodicals, Inc.

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Aqueous protein chemistry is responsible for regulating vital biological functions in living beings. One of the major mechanisms for the irreversible destruction of amino acids is decarboxylation. This work examines the kinetics and mechanism of this decarboxylation process for Levodopa using quantum chemical methods.

Quelle: International Journal of Quantum Chemistry | 8 Mar 2013 | 11:32 am CET

Interaction of copernicium with gold: Assessment of applicability of simple density functional theories

Abstract

Interactions of Cn (element 112) atom with small Au clusters are studied using accurate ab initio scalar relativistic coupled cluster method for correlation treatment and two-component relativistic density functional theory (RDFT) to take account of spin-dependent relativistic effects. The results demonstrate the failure of RDFT with simple generalized-gradient and hybrid functionals in describing Cn–Au bonds in complex systems. © 2013 Wiley Periodicals, Inc.

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The accurate description of the interactions of copernicium atoms with gold is of primary importance for building adequate theoretical models of its thermochromatographic registration. Relativistic density functional theory with simple generalized-gradient and hybrid functionals, normally used for such models, fails to accurately describe Cn–Au bonds in complex systems. This failure is attributed to the difficulties in describing the aurophilic-like interactions of filled d-shells of Cn and Au.

Quelle: International Journal of Quantum Chemistry | 8 Mar 2013 | 11:31 am CET

Structural and charge-transfer properties of indolylfulgides

Abstract

The structural and electronic properties of a photochromic molecule dictate their potential photochemical activity. To gain insight into these influences, the ground-state structure and excited state properties of six indolylgulgides were calculated using several time dependent-density functional theory (DFT) (TD-DFT)//DFT methods, second-order Møller–Plesset (MP2), and CIS(D). These methods simulated the charge-transfer properties and the conformation of the ground-state structure for each molecule. Generally, TD-DFT accurately simulated the expected charge-transfer state. The degree of spatial overlap of the occupied and virtual molecular orbitals involved in the S1 transition of indolylfulgides quantitatively assessed their charge-transfer character and was qualitatively useful in assessing their photochromic activity. The M06, M06-2X, and M11 structures were quite similar to those calculated by MP2. Structural differences, similarities, and functional trends are compared and discussed. © 2013 Wiley Periodicals, Inc.

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The structural and electronic properties of a photochromic molecule dictate their photochemical activity. This communication assesses the efficacy of DFT and TD-DFT model the charge-transfer properties of the vertical excitations and the conformation of the ground-state structures of six model indolylgulgides. The use of meta-hybrid functionals (M06 family) are recommended in both structure and charge-transfer calculations for accuracy and consistency of results.

Quelle: International Journal of Quantum Chemistry | 5 Mar 2013 | 10:49 am CET

Bimolecular nature of boron trifluoride catalyzed glycosylation of a galactosyl donor: The role of the acceptor

Abstract

Density functional theory (DFT) computations disclose the mechanism of a crucial neighboring participation step in BF3 catalyzed stereoselective glycosylation of 1,2-cyclopropaneacetylated galactosyl donor. Two tandem SN2 displacements comprise this step: first, the glycosyl acceptor attacks the BF3-activated donor to break the donor's 1,2-cyclopropane ring; then, the donor's 2-acetyl oxygen substitutes the acceptor to accomplish the neighboring participation. A donor–acceptor hydrogen bond has been found to lower the overall activation free energy. This mechanism is preferred over a 2-acetyl oxygen coface SN2 displacement mechanism, in which no glycosyl acceptor is involved. © 2013 Wiley Periodicals, Inc.

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Catalyzed glycosylation of galactosyl donor may allow us to synthesize many potentially useful and biologically important carbohydrates. However, the microscopic process behind it remains unclear. In this work, its core mechanism, a neighboring participation step, is computationally resolved. While seemingly this step involves only one reactant—the glycosyl donor; but surprisingly, it is catalyzed by another reactant—the alcohol-like glycosyl acceptor. That means that the reaction is actually bimolecular in nature.

Quelle: International Journal of Quantum Chemistry | 5 Mar 2013 | 10:48 am CET

H2S splitting on Cu(110): Insight from combined periodic density functional theory calculations and microkinetic simulation

Abstract

Practical copper (Cu)-based catalysts for the water–gas shift (WGS) reaction was long believed to expose a large proportion of Cu(110) planes. In this work, as an important first step toward addressing sulfur poisoning of these catalysts, the detailed mechanism for the splitting of hydrogen sulfide (H2S) on the open Cu(110) facet has been investigated in the framework of periodic, self-consistent density functional theory (DFT-GGA). The microkinetic model based on the first-principles calculations has also been developed to quantitatively evaluate the two considered decomposition routes for yielding surface atomic sulfur (S*): (1) H2S → H2S* → SH* → S* and (2) 2H2S → 2H2S* → 2SH* → S* + H2S* → S* + H2S. The first pathway proceeding through unimolecular SH* dissociation was identified to be feasible, whereas the second pathway involving bimolecular SH* disproportionation made no contribution to S* formation. The molecular adsorption of H2S is the slowest elementary step of its full decomposition, being related with the large entropy term of the gas-phase reactant under realistic reaction conditions. A comparison of thermodynamic and kinetic reactivity between the substrate and the close-packed Cu(111) surface further shows that a loosely packed facet can promote the S* formation from H2S on Cu, thus revealing that the reaction process is structure sensitive. The present DFT and microkinetic modeling results provide a reasonably complete picture for the chemistry of H2S on the Cu(110) surface, which is a necessary basis for the design of new sulfur-tolerant WGS catalysts. © 2013 Wiley Periodicals, Inc.

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Copper (Cu)-based catalysts for the water–gas shift reaction are believed to expose a large proportion of Cu(110) planes. Sulfur poisoning is an issue in these catalysts. The present microkinetic investigation based on first-principles calculations represents the first theoretical attempt to map out the complete reaction network for hydrogen sulfide decomposition into S and H2 on Cu(110). All surface sites are covered by the S adatoms, produced from the direct dissociation of the SH intermediate.

Quelle: International Journal of Quantum Chemistry | 5 Mar 2013 | 10:47 am CET

Probing actinide electronic structure through pu cluster calculations

Abstract

Calculations of the electronic structure of clusters of plutonium have been performed, within the framework of the relativistic discrete-variational method. These theoretical results and those calculated earlier for related systems have been compared to spectroscopic data produced in the experimental investigations of bulk systems, including photoelectron spectroscopy. Observation of the changes in the Pu electronic structure as a function of size provides powerful insight for aspects of bulk Pu electronic structure. © 2013 Wiley Periodicals, Inc.

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Metallic plutonium is a unique material from a chemical point of view. A clear understanding of the electron distribution over s, p, d, and f states could increase the ability of scientists to explain some of its important chemical and physical properties. This article presents the results of cluster calculations of the changes in the Pu atomic configurations as a function of cluster size in cubic crystal using fully relativistic method.

Quelle: International Journal of Quantum Chemistry | 26 Feb 2013 | 10:20 am CET

A theoretical study of the effects of transition metal dopants on the adsorption and dissociation of hydrogen on nickel clusters

Abstract

The structure, stability, adsorption, and dissociation of H2 on nickel clusters doped with late transition metals were investigated using density functional theory with the BP86 functional. Molecular hydrogen physisorption occurred at a vertex atom with a low coordination number. Charge transfer between clusters and the H2 molecule stabilized the physisorption. The chemisorption of H2 occurred at the bridge sites, without any structural or spin change of the clusters. Among the pentamer clusters, Cd, Zn, and Au had the lowest chemisorption energies, while Ir and Pt had higher chemisorption energies for hydrogen. The computed reaction energies and activation barriers for the dissociation mechanism showed that dopants such as Rh, Pd, Pt, and Au have endothermic reaction energies and low activation barriers. This facilitates the reversible adsorption/dissociation of the H2 molecule on these metal-doped clusters. The dopant atoms play a major role in modulating the physisorption, chemisorption, and dissociation mechanism of H2 on nickel clusters. © 2013 Wiley Periodicals, Inc.

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Dopant atoms can play an important role in enhancing chemisorption on Ni clusters doped with late transition metal atoms. Molecular hydrogen physisorption occurs at the vertex atom with a low coordination number. This is mainly due to the interaction between the s orbital of H2 and the LUMO orbital of the clusters. The dopant determines the shape of LUMO orbital and the approach of H2 molecule. Furthermore, a charge transfer is found between the cluster and the H2 molecule which stabilizes the physisorption.

Quelle: International Journal of Quantum Chemistry | 26 Feb 2013 | 10:19 am CET

Quantum chemistry in studies of fluorescent and photosensing proteins

Abstract

This Perspective describes some of the recent successes in modeling properties of chromophore containing domains of proteins capable to respond to visible light by using quantum chemistry methods. Applications to two distinctively different classes of such proteins are considered: those of the green fluorescent protein family with the chromophores derived from the hydroxybenzylidene-imidazolinone moiety and those containing the flavin-based chromophore. The major emphasis is on applications of economic computational strategies to estimate geometry configurations and electronic excitation energies. We show that using the molecular cluster approach and the “black-box” methods ZINDO and SOS-CIS(D) proves to be efficient for characterization of protein spectra. © 2013 Wiley Periodicals, Inc.

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This Perspective describes some of the recent successes in modeling properties of chromophore containing domains of proteins capable to respond to visible light by using quantum chemistry methods. Applications to two classes of such proteins are considered: those of the green fluorescent protein family with the chromophores derived from the hydroxybenzylidene-imidazolinone and those containing the flavin-based chromophore. The major emphasis is on applications of economic computational strategies to estimate geometry configurations and electronic excitation energies.

Quelle: International Journal of Quantum Chemistry | 26 Feb 2013 | 10:17 am CET

A theoretical study of conformational flexibility, magnetic properties, and polarizabilities of trimethylnaphthalenes

Abstract

For almost all trimethylnaphthalenes (TMNs), the transition from a planar equilibrium ring conformation to a nonplanar conformation characterized by the torsional angle of 20° results in an energy increase of less than 2.5 kcal/mol. For some of them, it is less than 1.6 kcal/mol, which indicates that these molecules can change their conformation easily through intermolecular interactions. The results of the calculations reveal a linear relationship between the averaged rigidity constant and the relative energy for all planar TMNs. The changes of rings deformational energy imposed on π-electron systems of TMNs by medium polarity are negligible (less than 0.05 kcal/mol). The aromaticity indices, based on nucleus-independent chemical shifts, indicate aromatic character of TMNs. The α substitution increases the ring area more than the β substitution. The increase of anisotropy of dipole polarizabilities with the decrease of the area of rings for all planar TMNs, dimethylnaphthalenes and methylnaphthalenes is noticed. © 2013 Wiley Periodicals, Inc.

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Trimethylnaphthalenes (TMNs) are widespread pollutants. This article takes a look at the flexibility of TMNs aromatic rings, which is related to their binding to the cavity of enzymes. TMNs can change their conformation easily and calculations reveal a linear relationship between the averaged rigidity constant and the relative energy for planar TMNs. An inverse relationship between the anisotropy of the polarizability and the area of the rings in planar TMNs and dimethylnaphthalenes also is found.

Quelle: International Journal of Quantum Chemistry | 22 Feb 2013 | 11:33 am CET

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane

Abstract

Naproxen and relafen, as nonsteroidal antiinflammatory drugs, were simulated in neutral and charged forms and their effects on a lipid bilayer membrane were investigated by molecular dynamics simulation using Groningen machine for chemical simulations software (GROMACS). Simulation of 10 systems was performed, which included different dosages of the drug molecules, naproxen and Relafen, in charged and neutral forms, and a mixture of naproxen and Relafen in neutral forms. The effects of the mixture and the individual drugs' dosages on membrane properties, such as electrostatic potential, order parameter, diffusion coefficients, and hydrogen bond formation, were analyzed. Hydration of the drugs in the membrane system was investigated using radial distribution function analysis. Using fully hydrated dimyristoylphosphatidylcholine (DMPC) as a reference system, 128 lipid molecules and water molecules were simulated exclusively, and the same simulation technique was performed on 10 other systems, including drug mixtures and a DMPC membrane. Angular distributions of lipid chains of the membrane were calculated, and the effects of the drug insertion and chain orientation in the membrane were evaluated. © 2013 Wiley Periodicals, Inc.

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Nonsteoridal antiinflammatory drugs, such as naproxen and relafen, are commonly prescribed in a variety of pathologies. This article studies relafen and its mixture with naproxen, which is compared to naproxen in charged and neutral forms. The effect of level of these drugs' dosage on their diffusion coefficients, electrostatic potentials, hydrogen bond formations, order parameters, mass densities, and radial distribution functions are studied. It is found that a maximal diffusion coefficient must exist at some intermediate levels of dosage.

Quelle: International Journal of Quantum Chemistry | 22 Feb 2013 | 11:33 am CET

Removal of 4-chlorophenol using graphene, graphene oxide, and a-doped graphene (A = N, B): A computational study

Abstract

Density functional theory (including van der Waals correction with the PBE-D functional) is applied to the study of 4-chlorophenol (4-CP) adsorption on graphene oxide (GO), A-doped graphene (A = N, B), and pristine graphene and test their possible application for 4-CP removal. Results show that on GO adsorption is improved by the hydrogen bond interactions between the adsorbents and 4-CP, suggesting that functionalized graphene is a preferable alternative than pristine graphene for 4-CP removal. In addition, the stability of hydrogen bonds is confirmed by molecular dynamics calculations using the PM6 potential. Without hydrogen bonds, A-doped graphene models show a comparable performance for 4-CP removal than pristine graphene. Finally, even in a solvent medium, 4-CP adsorption is strong. © 2013 Wiley Periodicals, Inc.

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4-chlorophenol (4-CP) is an organic pollutant, frequently discharged in industrial wastewater, with high toxic/mutagenic activity. Graphene has shown its utility in the removal of 4-CP. This article discusses if the use of graphene oxide and doped graphene would further improve the adsorption process and thus these materials represent an advantage over pristine graphene in the elimination process of 4-CP.

Quelle: International Journal of Quantum Chemistry | 22 Feb 2013 | 11:32 am CET

Density dynamics in some quantum systems

Abstract

The quantum domain behavior of classical nonintegrable systems is well-understood by the implementation of quantum fluid dynamics and quantum theory of motion. These approaches properly explain the quantum analogs of the classical Kolmogorov–Arnold–Moser type transitions from regular to chaotic domain in different anharmonic oscillators. Field-induced tunneling and chaotic ionization in Rydberg atoms are also analyzed with the help of these theories. Quantum fluid density functional theory may be used to understand different time-dependent processes like ion-atom/molecule collisions, atom-field interactions, and so forth. Regioselectivity as well as confined atomic/molecular systems and their reactivity dynamics have also been explained. © 2013 Wiley Periodicals, Inc.

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Quantum potential based theories present important insights into the quantum domain behavior of classically chaotic systems. This review discusses some representative examples of quantum signature of classical chaos through the study of quantum domain behavior of classical nonintegrable systems using the quantum fluid dynamics, the quantum theory of motion and the quantum fluid density functional theory, as well as the reactivity dynamics of various systems in free and confined environments.

Quelle: International Journal of Quantum Chemistry | 21 Feb 2013 | 5:11 am CET

Direct delocalization for calculating electron transfer in fullerenes

Abstract

A method is introduced for simple calculation of charge transfer between very large solvated organic dimers (fullerenes here) from isolated dimer calculations. The individual monomers in noncentrosymmetric dimers experience different chemical environments, so that the dimers do not necessarily represent bulk-like molecules. Therefore, we apply a delocalizing bias directly to the Fock matrix of the dimer system, and verify that this is almost as accurate as self-consistent solvation. As large molecules like fullerenes have a plethora of excited states, the initially excited state orbitals are thermally populated, so that the rate is obtained as a thermal average over Marcus thermal transfers. © 2013 Wiley Periodicals, Inc.

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The study presents a simple and efficient method for calculating electron transfer in large organic dimers (fullerenes here). The method uses a potential, applied directly to the Fock matrix, to delocalize the frontier orbitals over a dimer. The electron transfer rates are then calculated using a Marcus theory formalism.

Quelle: International Journal of Quantum Chemistry | 21 Feb 2013 | 5:11 am CET

Crystal band structure from the embedded cluster

Abstract

The embedded cluster method for ion–covalent crystal band structure calculations is proposed. This method uses the results of embedded cluster electronic structure calculations within one-determinant Hartree–Fock approximations. The band structure of high-temperature cubic phase ZrO2 crystal is calculated and found to be in good agreement with calculations in the literature, which applied periodic boundary conditions at the same theory level. © 2013 Wiley Periodicals, Inc.

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An embedded cluster method for the calculation of the band structure of ion-covalent crystals is introduced. This new method employs solutions within the framework of the one-determinant Hartree–Fock approximation. In the case of the high-temperature cubic phase of ZrO2 crystals the resulting band structure is found to be in good agreement with that obtained by applying periodic boundary conditions at the same level of theory.

Quelle: International Journal of Quantum Chemistry | 21 Feb 2013 | 5:10 am CET

Performance of numerical atom-centered basis sets in the ground-state correlated calculations of noncovalent interactions: Water and methane dimer cases

Abstract

Numerical atom-centered basis sets (orbitals) (NAO) are known for their compactness and rapid convergence in the Hartree–Fock and density-functional theory (DFT) molecular electronic-structure calculations. To date, not much is known about the performance of the numerical sets against the well-studied Gaussian-type bases in correlated calculations. In this study, one instance of NAO [Blum et al., The Fritz Haber Institute ab initio Molecular Simulations Package (FHI-aims), 2009] was thoroughly examined in comparison to the correlation-consistent basis sets in the ground-state correlated calculations on the hydrogen-bonded water and dispersion-dominated methane dimers. It was shown that these NAO demonstrate improved, comparing to the unaugmented correlation-consistent based, convergence of interaction energies in correlated calculations. However, the present version of NAO constructed in the DFT calculations on covalently-bound diatomics exhibits enormous basis-set superposition error (BSSE)—even with the largest bases. Moreover, these basis sets are essentially unable to capture diffuse character of the wave function, necessary for example, for the complete convergence of correlated interaction energies of the weakly-bound complexes. The problem is usually treated by addition of the external Gaussian diffuse functions to the NAO part, what indeed allows to obtain accurate results. However, the operation increases BSSE with the resulting hybrid basis sets even further and breaks down the initial concept of NAO (i.e., improved compactness) due to the significant increase in their size. These findings clearly point at the need in the alternative strategies for the construction of sufficiently-delocalized and BSSE-balanced purely-numerical bases adapted for correlated calculations, possible ones were outlined here. For comparison with the considered NAOs, a complementary study on the convergence properties of the correlation-consistent basis sets, with a special emphasis on BSSE, was also performed. Some of its conclusions may represent independent interest. © 2013 Wiley Periodicals, Inc.

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Basis-set effects are a notorious source of error in quantum-chemical computations. The use of analytical Gaussian atomic-centered basis sets is commonplace due to their computational convenience. An alternative approach: the numerical atomic-centred basis sets (NAO), can provide greater flexibility but should be used with caution in correlated calculations. Using water and methane dimers as model systems, this article benchmarks NAOs and suggests strategies that take full advantage of their numerical construction procedure.

Quelle: International Journal of Quantum Chemistry | 18 Feb 2013 | 5:18 am CET

Importance of Pd and Pt excited states in N2O capture and activation: A comparative study with Rh and Au atoms

Abstract

Nitrous oxide (N2O) is an intermediate compound formed during catalysis occurring in automobile exhaust pipes. In this work, the N2O capture and activation by Pt and Pd atoms in the ground and excited states of many multiplicities are studied. Pt and Pd + N2O reactions are studied at multireference second-order perturbation level of theory using Cs symmetry. The PtN2O (1A′, 5A′, and 5A″) species are spontaneously created from excited states. Only the 5A′ and 5A″ states exhibit N2O activation reaction paths when N2O approaches Pt end-on by the N or O atoms side or side-on yielding NO or N2 as products, respectively. Pt+ cations ground and excited states, capture N2O, although only Pt+ (6A′ and 6A″) states show N2O activation yielding O and N2 as products. In the Pd atom case, PdN2O (1A′ and 5A″) species are also spontaneously created from excited states. The 5A″ state exhibits N2O activation yielding N2 + O as products. Pd+ cations in both ground and excited states capture N2O; however, only the [PdN2O]+ (4A′, 4A″, 6A′, and 6A″) states in side-on approaches and (6A′) in end-on approach activate the N2O and yield the N2 bounded to the metal and O as product. The results obtained in this work are discussed and compared with previous calculations of Rh and Au atoms. The reaction paths show a metal–gas dative covalent bonding character. Löwdin charge population analyses for Pt and Pd active states show a binding done through charge donation and retrodonation between the metals and N2O. © 2013 Wiley Periodicals, Inc.

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Nitrogen oxides are common exhaust gases from automobiles and a host of industrial processes. These gases have significantly negative effects on human health. Their reduction can produce in N2O in several cases. The capture and activation of this nitrous oxide by Pt and Pd atoms, and the relative efficacy of Pt, Pd, Rh, and Au for this purpose, is investigated here by quantum chemical methods.

Quelle: International Journal of Quantum Chemistry | 12 Feb 2013 | 9:06 am CET

Assessing the performance of density functional theory for the dynamic polarizabilities of amino acids: Treatment of correlation and role of exact exchange

Abstract

The theoretical determination of electric response properties of the biological systems is a field where the application of density functional theory (DFT) appears to be quite promising. In this work, the performance of 41 density functional methods is evaluated in predicting dynamic polarizabilities of an experimental benchmark set of 20 proteinogenic amino acids. The behavior of a large number of density functionals, including various types of the local spin density approximation (LSDA), generalized gradient approximation (GGA), meta-GGA (m-GGA), hybrid-GGA (h-GGA), hybrid meta-GGA (hm-GGA), and range-separated hybrid-GGA (rsh-GGA), has been assessed for the purpose. Analyzing the results of our DFT benchmarking, we found that these computationally economical methods show very diverse predictive capability and a careful selection of DFT functionals is very important in the polarizability calculations. Considering the role of exchange, correlation, dispersion and long-range corrections, it turned out that in the LSDA class, SVWN3 gives better results than SPL and SVWN5 toward the reference values. Of the GGA methods, OPBE outperforms all other functionals. The M06-L is the best method of m-GGA class. The B3LYP and TPSSh are the best functionals of h-GGA and hm-GGA lineages, respectively. Finally, CAM-B3LYP is the best method of rsh-GGA functionals that predicts the most accurate polarizability for amino acids by a large margin with respect to others. Overall, the best performing functionals turn out to be hm-GGAs TPSSh, TPSS1KCIS, M05, tau-HCTHhyb, and h-GGA B3LYP. Hopefully, the results of this investigation might provide the useful guidance to propose a new exchange-correlation functional for calculating the optical properties of biomolecular materials. © 2013 Wiley Periodicals, Inc.

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The performance of density functional theory methods is evaluated in predicting dynamic polarizabilities of an experimental benchmark set of proteinogenic amino acids. The results of this investigation might provide the useful guidance to propose new exchange-correlation functionals for calculating the optical properties of biomolecular materials.

Quelle: International Journal of Quantum Chemistry | 12 Feb 2013 | 9:05 am CET

Unpaired electrons at the second-order reduced density matrix level: Covalent bonding, and coulomb and fermi correlations in closed shell systems

Abstract

The usual one-electron populations in atomic orbitals of closed shell systems are split into unpaired and paired at the (spin-dependent) second-order reduced density matrix level. The unpaired electron in an orbital is defined as the “simultaneous occurrence of an electron and an electron hole of opposite spins in the same spatial orbital,” which for simplicity is called “electropon.” The electropon population in a given orbital reveals whether and to what degree the Coulomb correlations, and hence, the chemical bonding between this orbital and the remaining orbitals of the system are globally favorable or unfavorable. The interaction of two electropons in two target orbitals reveals the quality (favorable or unfavorable) and the strength of the covalent bonding between these orbitals; this establish a bridge between the notion of “unpaired electrons” and the traditional covalent structure of valence-bond (VB) theory. Favorable/unfavorable bonding between two orbitals is characterized by the positive/negative (Coulomb) correlation of two electropons of opposite spins, or alternatively, by the negative/positive (Fermi) correlation of two parallel spin electropons. A spin-free index is defined, and the relationship between the electropon viewpoint for chemical bonding and the well-known two-electron Coulomb and Fermi correlations is established. Benchmark calculations are achieved for ethylene, hexatriene, benzene, pyrrole, methylamine, and ammonia molecules on the basis of physically meaningful natural orbitals. The results, obtained in the framework of both orthogonal and nonorthogonal population analysis methods, provide the same conceptual pictures, which are in very good agreement with elementary chemical knowledge and VB theory. © 2013 Wiley Periodicals, Inc.

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The unpaired population in an orbital is defined as the “simultaneous occurrence of an electron and an electron hole of opposite spins in the same spatial orbital,” which for simplicity is called “electropon.” The electropon population represents the fraction of the conventional one-electron population that is responsible for covalent bonding. Favorable/unfavorable bonding between two orbitals is characterized by the positive/negative (Coulomb) correlation of two electropons of opposite spins, or alternatively, by the negative/positive (Fermi) correlation of two parallel spins.

Quelle: International Journal of Quantum Chemistry | 6 Feb 2013 | 1:33 pm CET

Resonance theory of catalytic action of transition-metal complexes: Isomerization of quadricyclane to norbornadiene catalyzed by metal porphyrins

Abstract

The theory of catalytic activity of transition-metal compounds is a fascinating problem especially if a comparison of different catalysts is necessary. The isomerization of quadricyclane (QC) to norbornadiene (NB) catalyzed by transition-metal porphyrins is a challenge and incidentally a suitable benchmark for various theories of catalysis. We analyze this process in detail using a valence bond-like scheme adjusted for the description of reaction centers containing transition-metal atoms. A qualitative explanation of contrasting catalytic behavior of Mn-phthalocyanine and Co-tetraphenylporphyrin is obtained from the analysis of the spectra of local many electron states of free catalysts and their complexes with the reactant/product. This picture is supported by the numerical analysis of potential energy profiles for the QC to NB isomerization in the presence of a catalyst performed in the effective Hamiltonian approximation. This exemplary reaction is put in a more general perspective of theories of catalytic activity of transition-metal complexes and in relation with oxygenation reactions. © 2013 Wiley Periodicals, Inc.

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A Google “catalysis theory” search results in rather dull entries such as “DFT application to specific cases of catalysis” rather than “theory of catalysis”. Here, instead, a general theory of catalysis of Woodward-Hoffmann restricted reactions by transition-metal complexes based on a) valence-bond ideas of chemical reactivity and b) entanglement of electronic states of reactants and catalyst described by c) an effective Hamiltonian for the reaction center, is provided. The novel approach is exemplified by the catalytic transformation of quadricyclane to norbornadiene.

Quelle: International Journal of Quantum Chemistry | 6 Feb 2013 | 12:51 pm CET

Small changes—Huge influences: NMR chemical shifts of Ni(II) complexes with polar substrates

Abstract

Neutral Ni(II) complexes have been shown to be highly valuable as robust and versatile catalysts in olefin polymerization. But they show reduced reactivity when the polar monomers methyl acrylate and vinyl acetate are incorporated. To get further insight into this behavior, NMR chemical shift calculations were performed on the system [(N,O) Ni (H) (PMe3)] 1 (N,O = equation image-N,O-{2,6-(3,5-(F3C)2C6H3)2C6H3)[BOND]N[DOUBLE BOND]C(H)-3,5-I2-2-O-C6H2}). The chemical shifts show reasonable agreement with experiment but are also extremely influenced by geometrical features of the complex as well as the inserted substrate. The first prominent feature, the low-field shift of the Ccarbonyl in the incorporated monomer, can only be reproduced when it is in close proximity to the Ni and in this way hinders the attack of a new monomer. Second, the almost 100 ppm difference in the chemical shift of the carbon of the two substrates directly bound to Ni can be reasoned by the different directionality of polarization as disclosed by natural bond orbital (NBO) analysis. © 2013 Wiley Periodicals, Inc.

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Neutral Ni(II) complexes have been shown to be highly valuable as robust and versatile catalysts in olefin polymerization. However, they show reduced reactivity when the polar monomers methyl acrylate and vinyl acetate are incorporated. NMR chemical shift calculations are performed on model systems to gain further insight into this behavior. The chemical shifts strongly depend on the geometrical features of the complex as well as the inserted substrate and the directionality of polarization.

Quelle: International Journal of Quantum Chemistry | 6 Feb 2013 | 12:48 pm CET

Dioxygen spectra and bioactivation

Abstract

Intensities of spin-forbidden transitions in electronic absorption and emission spectra of molecular oxygen are analyzed in order to understand the key mechanisms of spin-states mixing induced by spin-orbit coupling (SOC) and the ways to overcome spin prohibition for various photophysical and biochemical processes. Multireference configuration interaction calculations with SOC account are used to generalize spin-selection rules for the oxygen atmospheric and Herzberg bands in free O2 molecule and in collision complexes. Intensity enhancement of the atmospheric a1ΔgX3Σmath image, b1Σmath imageX3Σmath image, and Noxon b1Σmath imagea1Δg transitions upon bimolecular collisions are compared with those for Herzberg III transitions A′3ΔuX3Σmath image. Electric quadrupole, dipole, and magnetic approximations are used for transition probability calculations. Intensity distribution in rotational lines is also considered. With this background, we propose some simple spin-selection rules for dioxygen activation in enzymatic reactions. © 2013 Wiley Periodicals, Inc.

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This review discusses the key mechanisms of spin-states mixing induced by spin-orbit coupling in dioxygen and proposes ways to overcome spin prohibition for various photophysical and biochemical processes involving dioxygen.

Quelle: International Journal of Quantum Chemistry | 25 Jan 2013 | 9:15 am CET

Can coupled-cluster methods be used to describe excited states of the building blocks of DNA?

Abstract

Recent developments in Coupled-Cluster (CC) theory of excited states, which allow the application of these expensive methods for nucleobases and even for their complexes, are overviewed. Accuracy of the methods is analyzed and some recent encouraging results summarized. Finally, we speculate about possible directions of future research and how the CC calculations can be extended to the electric properties of DNA, in particular transport properties. © 2013 Wiley Periodicals, Inc.

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Recent developments in coupled-cluster (CC) theory of excited states allow the application of these expensive methods to a study of nucleobases and even their complexes. In this perspective, some of the recent encouraging results are summarized. This is followed by speculations of possible future applications of CC methods in study of spectroscopy and charge transport in DNA.

Quelle: International Journal of Quantum Chemistry | 25 Jan 2013 | 9:15 am CET

Analyzing the electronic structure of molecules using continuous symmetry measures

Abstract

The introduction of symmetry-related arguments in scientific theories since its early development has led to an apparent paradox: highly symmetric models are routinely being applied to situations where this symmetry is not present (or only present in an approximate way). In this article, the formalism of continuous symmetry measures is presented as a solution to this situation, making a special emphasis on its application to problems related to quantum chemistry. © 2012 Wiley Periodicals, Inc.

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Highly symmetric models are routinely being applied in theoretical chemistry to situations where this symmetry is not present (or only present in an approximate way). In this article, the formalism of Continuous Symmetry Measures is presented as a possible solution to problems arising from this contradiction.

Quelle: International Journal of Quantum Chemistry | 7 Dec 2012 | 5:57 am CET

Localized directed orbitals representing chemical bonds in ion-covalent crystals

Abstract

We propose a new method for decomposing electron density of a crystal into contributions associated with pair-wise chemical bonds. To this end, an ion-covalent crystal is represented using a neutral, closed shell cluster assembled from identical structural elements (SE) and embedded into the lattice electrostatic potential. The wave function of this cluster is calculated using the one determinant approximation. Then, a set of orthonormal, noncanonical, multicenter orbitals of the cluster valence states is generated, so as each orbital is localized on one structural element. The projection operators technique is used here, the valence molecular orbitals of the cluster being taken for the orthonormal basis set. In this construction, the first-order reduced density matrix of the cluster valence electrons is exactly the sum of the first-order reduced density matrices of the SE, and the latter is the exact sum of localized on this cluster orbitals densities. The localized orbitals are then transformed into directed orbitals corresponding to the ion-covalent bonds in each structural element. The first-order reduced density matrix of each structural element is exactly the sum of densities of all such corresponding directed orbitals. This method is demonstrated on the examples of MgO, cubic ZrO2, and rutile TiO2 crystals. © 2012 Wiley Periodicals, Inc.

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Localized Directed Orbitals Representing Chemical Bonds in Ion-Covalent Crystals Abarenkov I.V., Boyko M.A., and Sushko P.V. Clusters can be used as model of infinite crystal in electronic structure calculations, especially in the case of metal oxides, if they are embedded in a properly constructed potential. By introducing a new method for decomposing electron density of a crystal into contributions associated with pair-wise chemical bonds, this work suggests that relatively simple embedding potentials and small clusters can be sufficient to generate local orbitals that accurately represent bond orbitals in the infinite crystal.

Quelle: International Journal of Quantum Chemistry | 6 Dec 2012 | 12:37 pm CET




 


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