International Journal of Quantum Chemistry

Cover image for Vol. 113 Issue 6

Special Issue: 14th International Density Functional Theory Conference

15 March 2013

Volume 113, Issue 6

Pages i–iv, 745–879

Issue edited by: Nikitas I. Gidopoulos, Andreas K. Theophilou

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      Cover Image, Volume 113, Issue 6 (pages i–ii)

      Version of Record online: 7 FEB 2013 | DOI: 10.1002/qua.24403

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      Solvent is crucial for many chemical and physical processes of matter and needs to be taken into account in simulations. Recently implicit solvation models have been developed in which the solute cavity is defined via isosurfaces of the electronic density, and the molecular charge is polarized self-consistently by the dielectric continuum that surrounds the solute. On page 771, Chris-Kriton Skylaris and colleagues explore such a solvent model as implemented in the ONETEP linearscaling density functional theory (DFT) program that is capable of highly accurate first principles calculations with thousands of atoms. A 2602-atom protein-ligand complex is used as an example relevant to drug design applications.

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      Inside Cover, Volume 113, Issue 6 (pages iii–iv)

      Version of Record online: 7 FEB 2013 | DOI: 10.1002/qua.24404

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      In the cover article on page 808, Ursula Rothlisberger and co-workers compare the performance of different computational methods with respect to their ability to reproduce the relative energetics and to generate candidate structures for subsequent refinement at the higher level of theory for medium-sized biomolecules. A series of classical non-polarizable and polarizable force fields and a semiempirical method for this purpose are benchmarked against their capacity to predict the ground state structure of protonated gramicidin S, a cyclic decapeptide and natural antibiotic against bacteria and fungi, for which the native structure is unknown.

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    3. Full Papers
    1. Density functional theory study on magnetic interactions in the V3+ dimer complexes (pages 745–752)

      Hidenori Suzuki and Chikatoshi Satoko

      Version of Record online: 21 MAR 2012 | DOI: 10.1002/qua.24067

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      Theoretical studies of the magnetic interactions in transition metal dimer complexes are often based on the assumption that the d-electrons are localized near the metal centers. As this is not always the case a new theoretical framework is needed. An Effective Hamiltonian method, based on the DFT-based ligand field model, is used to overcome this limitation and applied in this article to the study of Vanadium dimer complexes.

    2. An analysis of unsupported triple and quadruple metal–metal bonds between two homonuclear group 6 transition elements based on the combined natural orbitals for chemical valence and extended transition state method (pages 753–761)

      Sylvester Ndambuki and Tom Ziegler

      Version of Record online: 17 APR 2012 | DOI: 10.1002/qua.24068

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      The understanding of chemical and physical properties of molecules in many chemical reactions is of fundamental importance, particularly in the characterization and prediction of the reactivity of molecular systems. Numerous schemes for chemical bond analysis exist that focus on different aspects of bonding. In this account, the energy and density decomposition scheme (ETS-NOCV) is applied to the study of selected multiple MAM bonds, and provides a qualitative and quantitative picture of the interactions that govern chemical bond formation.

    3. Correlation measures as benchmarks in reduced density matrix functional theory (pages 762–765)

      N. N. Lathiotakis

      Version of Record online: 27 MAR 2012 | DOI: 10.1002/qua.24069

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      Reduced density-matrix functional theory (RDMFT) is a promising alternative approach to the problem of electron correlation. Like standard density functional theory, RDMFT also requires the definition of an unknown exchange-correlation functional, for which several approximations have been proposed. In this article, correlation energies and entropies are calculated to benchmark some of these functionals and to compare their accuracy against the results of multi-determinants quantum chemical calculations.

    4. Separation of energies of the direct (through-space) and indirect (through-bridge) interactions in SCF LCAO MO theory (pages 766–770)

      Roman F. Nalewajski

      Version of Record online: 13 APR 2012 | DOI: 10.1002/qua.24070

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      The direct (“through-space”) bonding interaction between neighboring atoms implies the presence of the bond-charge between the two nuclei. For more distant atomic partners, e.g. in cross-ring p-interactions, such an accumulation of the valence electrons can be absent, and an indirect (“throughbridge”) mechanism is needed. This article introduces a recipe for partitioning the molecular electronic energy into components associated with pairs of atomic orbitals and identifying the contributions of the direct and indirect chemical bond types.

    5. Large-scale DFT calculations in implicit solvent—A case study on the T4 lysozyme L99A/M102Q protein (pages 771–785)

      Jacek Dziedzic, Stephen J. Fox, Thomas Fox, Christofer S. Tautermann and Chris-Kriton Skylaris

      Version of Record online: 28 MAR 2012 | DOI: 10.1002/qua.24075

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      When employing implicit solvation models great care is required in the selection of a number of numerical parameters in order to obtain accurate and physically relevant results. This article presents a detailed study of how these parameters can affect the calculation of solvation and binding energies of large biomolecules in solution and provides a recipe for their optimal selection for routine “production” calculations.

    6. Hydrogen sulfide adsorption on a defective graphene (pages 786–791)

      Dobrina Borisova, Vladislav Antonov and Ana Proykova

      Version of Record online: 24 MAR 2012 | DOI: 10.1002/qua.24077

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      Vacancies in graphene attract hydrogen sulphide molecules. The result is sulphur chemisorption and hydrogen molecule release. Density functional theory computations indicate that graphene with vacancies is a metal, and becomes a semiconductor upon the adsorption of sulphur. It is found that vacancies induce a ferromagnetic state, in agreement with experimental observations.

    7. Vacancy spatial distribution causes different magnetism in graphene (pages 792–796)

      Vladislav Antonov, Dobrina Borisova and Ana Proykova

      Version of Record online: 24 MAR 2012 | DOI: 10.1002/qua.24078

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      Although the pristine form is nonmagnetic, magnetism has been reported in defective graphene. Both vacancy concentration and relative spatial distribution are found to play a crucial role in determining the orientation and magnitude of the induced magnetic moment in graphene. Depending on the vacancy distribution both ferromagnetic and antiferromagnetic states are possible.

    8. First-principles study of vanadium adsorption and diffusion on the AlN(0001) surface (pages 797–801)

      Jagger Rivera-Julio, William López-Pérez, Rafael González-Hernández, Gene E. Escorcia-Salas and José Sierra-Ortega

      Version of Record online: 28 MAR 2012 | DOI: 10.1002/qua.24079

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      In order to improve the quality of the transition-metal (TM) films on AlN surfaces, it is essential to understand the structural and electronic properties of the AlN surface and the underlying kinetic processes on it (such as adsorption, desorption, and surface diffusion). In particular, the TM adsorption energy and the TM diffusion energy barrier on the AlN surfaces are considered key parameters for controlling the growth rate and the material quality.

    9. Density functional theory study of the multimode Jahn-Teller problem in the fullerene anion (pages 802–807)

      Harry Ramanantoanina, Maja Gruden-Pavlovic, Matija Zlatar and Claude Daul

      Version of Record online: 28 MAR 2012 | DOI: 10.1002/qua.24080

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      To tackle the multimode problem in the C60 ion, multideterminantal density functional theory and the intrinsic distortion path analysis, in which the distortion is represented as a superposition of all totally symmetric normal modes in the low symmetry point groups, has been performed. Completely theoretical models give further insight into the microscopic origin of vibronic coupling in the fullerene anion.

    10. Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide (pages 808–814)

      Manuel Doemer, Matteo Guglielmi, Prashanth Athri, Natalia S. Nagornova, Thomas R. Rizzo, Oleg V. Boyarkin, Ivano Tavernelli and Ursula Rothlisberger

      Version of Record online: 5 APR 2012 | DOI: 10.1002/qua.24085

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      The theoretical prediction of low energy-structures of gas-phase biomolecular ions is of great practical importance for the interpretation of cold ion spectroscopic data. A series of classical non-polarizable and polarizable force fields and a semi-empirical method for this purpose is benchmarked in this article. Their performance is discussed in relation to their potential use to efficiently explore conformational space and generate candidate structures for subsequent refinement at the DFT level.

    11. Polarized–unpolarized ground state of small polycyclic aromatic hydrocarbons (pages 815–819)

      E. San-Fabiín and F. Moscardó

      Version of Record online: 4 APR 2012 | DOI: 10.1002/qua.24090

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      The question of whether graphene nanoribbons and related structures show a spin polarized ground state is still open. Hartree-Fock and density functional theory calculations suggest that a nonpolarized (antiferromagnetic) ground state should be found in these systems. However, antiferromagnetism is no longer observed when multideterminantal calculations, based on both perturbative and variational wavefunctions, are performed instead.

    12. Magnetic, kinetic, and optical properties of new high-pressure phases in the system Cr–GaSb: Ab initio density functional theory study (pages 820–829)

      Erkin Kulatov, Maria Magnitskaya, Yurii Uspenskii, Svetlana Popova, Vadim Brazhkin and Evgenii Maksimov

      Version of Record online: 7 APR 2012 | DOI: 10.1002/qua.24097

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      New high-pressure synthesized compounds CrGaSb and CrGa2Sb2 are at the edge between metal and semiconductor and, in addition, CrGa2Sb2 is an above-room-temperature ferromagnet. The density of states of CrGa2Sb2 exhibits a pseudogap, which becomes wider when the semi-local MBJ exchange-correlation potential is used instead of GGA functionals. The obtained results imply that CrGa2Sb2 is close to a semiconducting or half-metallic state, which makes this compound potentially interesting for spintronics applications.

    13. Comparative assessment of QSTR models based on density functional, hartree–fock, AM1, and PM3 methods for acute toxicity of aliphatic compounds toward Vibrio fischeri (pages 830–839)

      Altaf Hussain Pandith and Nasarul Islam

      Version of Record online: 17 APR 2012 | DOI: 10.1002/qua.24133

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      Quantitative-structure-toxicity relationship (QSTR) models are used to predict the toxicity of chemical compounds toward various types of biological systems. This allows researchers to save human and financial resources in in vitro testing of toxicity of a large number of new chemical compounds of unknown toxicity. This article evaluates the comparative efficiency of different theoretical methods in formulating the QSTR model equations for predicting acute toxicity of different classes of aliphatic compounds toward Vibrio fischeri bacteria

    14. Lead adsorption on the pseudo-10-fold surface of the Al13Co4 complex metallic alloy: A first principle study (pages 840–846)

      S. Alarcón Villaseca, J.-M. Dubois and É. Gaudry

      Version of Record online: 9 MAY 2012 | DOI: 10.1002/qua.24142

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      Al13Co4 is a very efficient and highly selective catalyst for the semihydrogenation of acetylene. The absorption of lead atoms on the pseudo-10-fold surface of Al13Co4 is studied using a combination of experimental and simulated scanning tunneling microscopy images. The ab initio calculations are fundamental for the detailed understanding of the experimental observations for the different lead coverages.

    15. First-principles investigation of magnetic property and defect formation energy in Ni-Mn-Ga ferromagnetic shape memory alloy (pages 847–851)

      Jing Bai, Nan Xu, Jean-Marc Raulot, Claude Esling, Xiang Zhao and Liang Zuo

      Version of Record online: 22 MAY 2012 | DOI: 10.1002/qua.24158

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      First-principle calculations can be used to investigate micro-magnetic properties of materials. Isosurface plots indicate that when extra Mn occupies one Ni site in Ni2MnGa ferromagnetic shape memory alloy, most of the free electrons gather around the extra Mn; whereas the charges in perfect Ni2MnGa are regularly distributed between two neighboring Ni atoms functioning as bridge.

    16. Effect of the molecular structure in the prediction of thermodynamic properties for 1-butyl-3-methylimidazolium chloride ionic liquid (pages 852–858)

      Lourdes del Olmo, Rafael López and José M. García de la Vega

      Version of Record online: 30 MAY 2012 | DOI: 10.1002/qua.24177

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      Ionic liquids (ILs) are of great interest as green solvents and may display very different properties depending on their molecular structure. Density functional theory in combination with COSMO-RS calculations are used in this article to study the influence of conformers in the estimation of physicochemical properties of the 1-butyl-3-methylimidazolium IL.

    17. The choice of the exchange-correlation functional for the determination of the jahn–teller parameters by the density functional theory (pages 859–864)

      Ljubica Andjelković, Maja Gruden-Pavlović, Claude Daul and Matija Zlatar

      Version of Record online: 22 JUN 2012 | DOI: 10.1002/qua.24245

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      The importance of the proper choice of the exchange-correlation functional in the analysis of Jahn–Teller effects by means of multideterminantal DFT is highlighted in this article. The choice of the functional strongly depends on the chemical system at hand, but to obtain fast and qualitatively reliable results, the local density approximation can be considered appropriate for a wide range of Jahn–Teller molecular systems.

    18. Optoelectronic properties of KDP by first principle calculations (pages 865–872)

      Hossein Asghar Rahnamaye Aliabad, Marjan Fathabadi and Iftikhar Ahmad

      Version of Record online: 26 JUN 2012 | DOI: 10.1002/qua.24258

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      Potassium dihydrogen phosphate, KH2PO4 (KDP) has extensive use in optoelectronic applications, for example, in second and third harmonic generation in Nd:YAG lasers. The structure and optoelectronic properties of KDP in its orthorhombic and tetragonal phases are investigated in this work using DFT. The PO4 tetrahedric building blocks in this material are found to be symmetric in the tetragonal phase, whereas this symmetry is broken in the orthorhombic structure.

    19. Exchange, correlation, and the effective mass m* of electrons in two-dimensional layers calculated via a DFT-based classical map (pages 873–879)

      M. W. C. Dharma-wardana

      Version of Record online: 12 JUL 2012 | DOI: 10.1002/qua.24273

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      The electron mass in two-dimensional layers is modified to an “effective mass” m* by many-body effects. Experiments, theories or simulations for this very central Fermi-liquid “Landau parameter” disagree. This article evaluates m* using an extension of finite-temperature density functional ideas.