International Journal of Quantum Chemistry

Cover image for Vol. 113 Issue 12

15 June 2013

Volume 113, Issue 12

Pages i–iv, 1669–1746

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Perspectives
    4. Tutorial Reviews
    5. Full Papers
    1. You have free access to this content
      Cover Image, Volume 113, Issue 12 (pages i–ii)

      Article first published online: 6 MAY 2013 | DOI: 10.1002/qua.24464

      Thumbnail image of graphical abstract

      In 2012, high-resolution structures were available for about 800 ligand binding pockets in human proteins, frequently in multiple conformations. As presented on page 1669 by Andrey V. Ilatovskiy et al., the background bubble plot schematically represents each pocket in the human structural pocketome as a sphere whose size is proportional to the size of the corresponding conformational ensemble. This rapidly growing data set creates remarkable opportunities for computational prediction of novel protein-ligand interactions in the drug research applications outlined in the foreground image. While ab initio quantum mechanical approaches are known to provide unprecedented accuracy in structure-based binding energy calculations, they are limited to only small systems of dozens of atoms. In the structural chemogenomics era, it is critical that new approaches are developed that enable application of QM methodologies to non-covalent interactions in systems as large as protein-ligand complexes and conformational ensembles.

    2. You have free access to this content
      Inside Cover, Volume 113, Issue 12 (pages iii–iv)

      Article first published online: 6 MAY 2013 | DOI: 10.1002/qua.24465

      Thumbnail image of graphical abstract

      In a fashion similar to how the periodic table is used to characterize elements, a set of variables can be used to characterize chemical compounds and determine their quantum mechanical properties. For each element in the periodic table, all possible stoichiometries are displayed that can be obtained by repartitioning onto multiple atomic sites with variable atomic numbers, nuclear charges, and the Np protons that make up the atomic number. As presented by O. Anatole von Lilienfeld on page 1676, the cover image exemplifies the case of Np = 10 protons. Here, NI, ZI, and i are number of atoms in a given compound, nuclear charge of atom I, and stoichiometry index (sorted by increasing NI), respectively. Thus, each column corresponds to a different stoichiometry, various familiar compositions are pointed out, and in the limit of NI [RIGHTWARDS ARROW]1 the stoichiometry corresponds to Ne, while H10 is recovered for NI [RIGHTWARDS ARROW] Np

  2. Perspectives

    1. Top of page
    2. Cover Image
    3. Perspectives
    4. Tutorial Reviews
    5. Full Papers
    1. You have free access to this content
      Quantum mechanics approaches to drug research in the era of structural chemogenomics (pages 1669–1675)

      Andrey V. Ilatovskiy, Ruben Abagyan and Irina Kufareva

      Article first published online: 20 FEB 2013 | DOI: 10.1002/qua.24400

      Thumbnail image of graphical abstract

      The rapid growth of 3D information about proteins and binding pockets creates remarkable opportunities for computational prediction of protein-ligand interactions. While ab initio QM approaches provide unprecedented accuracy in binding energy calculations, they are limited to only small systems. In the structural chemogenomics era, new approaches are needed that enable QM methodology application to systems as large as protein-ligand complex ensembles. This Perspective highlights recent advances towards bridging a gap between high-accuracy and high-volume computations in drug research.

  3. Tutorial Reviews

    1. Top of page
    2. Cover Image
    3. Perspectives
    4. Tutorial Reviews
    5. Full Papers
    1. You have full text access to this OnlineOpen article
      First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties (pages 1676–1689)

      O. Anatole von Lilienfeld

      Article first published online: 26 FEB 2013 | DOI: 10.1002/qua.24375

      Thumbnail image of graphical abstract

      This tutorial deals with chemical compound space from first principles, that is, the set of variables which characterize chemical compounds and determine all their quantum mechanical properties. Drawing from the periodic table of the elements, the challenge consists of navigating the many possibilities to combine different assemblies of atoms for the purpose of molecular design. Two complementary approaches, based on deductive (variational) and inductive (correlational) reasoning, are discussed.

  4. Full Papers

    1. Top of page
    2. Cover Image
    3. Perspectives
    4. Tutorial Reviews
    5. Full Papers
    1. Fock space multireference coupled cluster theory: Study of shape resonance (pages 1690–1695)

      Sumantra Bhattacharya, Nayana Vaval and Sourav Pal

      Article first published online: 8 JAN 2013 | DOI: 10.1002/qua.24387

      Thumbnail image of graphical abstract

      Metastable resonant states play an important role in the response of charged and highly excited molecular species. In this work, a complex absorbing potential has been used in conjunction with the Fock space multi-reference coupled cluster method. The choice of the basis set is found to be an important factor in the study of shape resonance of charged gaseous molecules.

    2. Computational investigation of the adsorption and reactions of SiHx (x = 0–4) on TiO2 anatase (101) and rutile (110) surfaces (pages 1696–1708)

      Wen-Fei Huang, Hsin-Tsung Chen and M.C. Lin

      Article first published online: 8 JAN 2013 | DOI: 10.1002/qua.24388

      Thumbnail image of graphical abstract

      SiHx (x = 0–4) has been used as a precursor with Ar as a carrier gas to grow silicon quantum dots (QD) over TiO2 by crystal vapor deposition. Density functional theory is used to increase the understanding of the complex Si-QDs growth process, and to elucidate the reaction mechanism of the SiHx decomposition over the anatase (101) and rutile (110) surfaces.

    3. Chemiluminescence of 1,2-dioxetanone studied by a closed-shell DFT approach (pages 1709–1716)

      Luís Pinto da Silva and Joaquim C.G. Esteves da Silva

      Article first published online: 8 JAN 2013 | DOI: 10.1002/qua.24389

      Thumbnail image of graphical abstract

      The open question of the mechanism of the chemiluminescence of simple 1,2-dioxetanone is revisited by means of a DFT approach. Calculations suggest that the thermal decomposition of this molecule occurs due to a concerted mechanism and not due to a step-wise biradical process. The use of a closed-shell, instead of an open-shell, approach in the study of simple 1,2-dioxetanone is also suggested in this work.

    4. DFT, CBS-Q, W1BD and G4MP2 calculation of the proton and electron affinities, gas phase basicities and ionization energies of saturated and unsaturated carboxylic acids (C1–C4) (pages 1717–1721)

      Younes Valadbeigi and Hossein Farrokhpour

      Article first published online: 12 JAN 2013 | DOI: 10.1002/qua.24391

      Thumbnail image of graphical abstract

      Protonation and ionization processes play an important role in atmospheric chemistry, biochemistry and other fields related to chemistry. Adiabatic ionization energy and electron affinity can be calculated as the energy difference between the neutral molecule and its cation and anion when all species are in their ground electronic states, respectively. Here, proton affinities, gas phase basicities, ionization energies, and electron affinities are calculated for C1–C4 carboxylic acids.

    5. Deep nuclear resonant tunneling thermal rate constant calculations (pages 1722–1734)

      Salvatore Mandrà, Stéphanie Valleau and Michele Ceotto

      Article first published online: 28 FEB 2013 | DOI: 10.1002/qua.24395

      Thumbnail image of graphical abstract

      Calculations of thermal rate constants in deep tunneling regimes remain a computationally challenging problem, even for one-dimensional systems. Here, a fast and robust time-independent algorithm for arbitrary one-dimensional potentials is presented. The method is able to deal with extreme resonance conditions, where several quasi-bound states are present and the standard log-derivative method fails. The generalization to multi-channel scattering is reported and an implementation of the method using Mathematica is included in the supplementary materials.

    6. Ab initio chemical kinetics for reactions of H atoms with SiHx (x = 1–3) radicals and related unimolecular decomposition processes (pages 1735–1746)

      Putikam Raghunath, Yun-Min Lee, Shang-Ying Wu, Jong-Shinn Wu and Ming-Chang Lin

      Article first published online: 22 FEB 2013 | DOI: 10.1002/qua.24396

      Thumbnail image of graphical abstract

      Chemical vapor deposition (CVD) of hydrogenated amorphous silicon thin films is an important process for thin-film solar cells and thin-film transistors. In this work, the mechanisms for the reaction of hydrogen atoms with SiHx radicals (x = 1–3) and related unimolecular decomposition processes are investigated. The rate constants for the forward and unimolecular reactions are predicted by solving the master equation covering the P,T-conditions commonly used in industrial CVD processes.

SEARCH

SEARCH BY CITATION