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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
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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.
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.
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.
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.
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.
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 HH bond in one of the studied cases could be used in oxidative addition reactions or for alkene hydrogenation without a metal catalysts.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 d and s ± condensate symmetries.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.