International Journal of Quantum Chemistry

Cover image for Vol. 114 Issue 6

15 March 2014

Volume 114, Issue 6

Pages i–iv, 367–435

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. You have free access to this content
      Cover Image, Volume 114, Issue 6 (pages i–ii)

      Article first published online: 5 FEB 2014 | DOI: 10.1002/qua.24614

      Thumbnail image of graphical abstract

      The graphical representation of protein sequences is expected to have broad applications because of their constitutive role in all living cells and direct correlation with biological functions. The cover exhibits a highly compact 2D graphical representation of the ND5 protein of humans by assigning amino acids to the circumference of a unit circle with a cyclic order. This representation could visually reveal general composition features of protein sequences, and roughly exhibit major differences between similar protein sequences. Experiments by Yushuang Li, Qian Liu, Xiaoqi Zheng, and Ping-an He on page 409 show that the proposed graphical model is effective for investigating biological structures and evolutionary relationships.

    2. You have free access to this content
      Inside Cover, Volume 114, Issue 6 (pages iii–iv)

      Article first published online: 5 FEB 2014 | DOI: 10.1002/qua.24615

      Thumbnail image of graphical abstract

      B3LYP and MP2 methods are used to study the hydroxylation and dehydrogenation of thymine at different sites in the presence of hydroxyl radicals (·OH). The MP2 method captures a feature in the reaction of thymine with hydroxyl radicals that the B3LYP method misses. A transition state exists in the hydroxylation of thymine at its C6 site, according to the MP2 calculations by Rongri Tan, Dongqi Wang, Lin Hu, and Feng-Shou Zhang on page 367. This is consistent with the experimental observation that there is a larger population for the C5-hydroxylated product than for the C6-hydroxylated product.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Probing the Reactivity of Hydroxyl Radicals toward Isolated Thymine Using Theoretical Calculations (pages 367–374)

      Rongri Tan, Dongqi Wang, Lin Hu and Feng-Shou Zhang

      Article first published online: 10 OCT 2013 | DOI: 10.1002/qua.24567

      Thumbnail image of graphical abstract

      The exposure of living organisms to ionizing radiation and reactive oxygen species such as hydroxyl radicals results in damage to DNA. This work examines the reaction of the thymine nucleobase with these radicals, using quantum chemical calculations. A transition state in the hydroxylation of thymine is discovered, which is consistent with experimental observations.

    2. Theoretical investigation on the dissociation of (R)-benzoin catalyzed by benzaldehyde lyase (pages 375–382)

      Jing Zhang, Xiang Sheng, QianQian Hou and Yongjun Liu

      Article first published online: 5 NOV 2013 | DOI: 10.1002/qua.24573

      Thumbnail image of graphical abstract

      Benzaldehyde lyase (BAL) is an enzyme that catalyzes the reversible conversion of aromatic 2-hydroxy ketones like (R)-benzoin to benzaldehyde. The strict R-selectivity of BAL, which is taken advantage of in the kinetic resolution of racemic benzoins, is unique in this class of enzymes, and calls for a detailed mechanistic study of its catalytic activity.

    3. Ro-vibrational studies of diatomic molecules in a shifted Deng–Fan oscillator potential (pages 383–391)

      Amlan K. Roy

      Article first published online: 5 NOV 2013 | DOI: 10.1002/qua.24575

      Thumbnail image of graphical abstract

      The Deng–Fan empirical potential for diatomic molecules, also called generalized Morse potential, has interesting applications in molecular spectroscopy and calculations of electronic transitions. As the exact analytical solution of this potential for arbitrary quantum states is unknown, approximations of the nature of solutions in relativistic and non-relativistic domains need to be introduced. Here, accurate ro-vibrational states of the shifted Deng–Fan potential are obtained with a generalized pseudospectral method.

    4. Computational estimates of thermochemistry and pKa values of cyclopropenyl imine superbases (pages 392–399)

      Gökçen A. Çiftcioğlu and Carl Trindle

      Article first published online: 5 NOV 2013 | DOI: 10.1002/qua.24576

      Thumbnail image of graphical abstract

      Thermochemical properties of superbase species derived from cyclopropeneimine are estimated by modeling a series of isodesmic reactions. Proton affinities, gas phase basicities, and pKa values are well-represented by calculations. The relative base strengths in gas are enhanced by alkyl substitution, either by methyl groups or larger species. In acetonitrile solution, alkyl substitution instead seems to weaken the base.

    5. A comparative study of some lithium and hydrogen-bonded complexes: Ab initio and QTAIM studies (pages 400–408)

      Xueying Zhang, Xiaoyan Li, Yanli Zeng, Lingpeng Meng and Shijun Zheng

      Article first published online: 5 NOV 2013 | DOI: 10.1002/qua.24577

      Thumbnail image of graphical abstract

      Lithium is a small, monovalent, electropositive element with a single electron in an sorbital. As the closest congener to hydrogen, lithium can form weak interactions with electronegative proton acceptors analogous to the hydrogen bond. Common features and differences between properties of the lithium and hydrogen bond are investigated by first principles using the interactions of cyanide with lithium and hydrogen halides as a model system.

    6. UC-Curve: A highly compact 2D graphical representation of protein sequences (pages 409–415)

      Yushuang Li, Qian Liu, Xiaoqi Zheng and Ping-an He

      Article first published online: 21 NOV 2013 | DOI: 10.1002/qua.24581

      Thumbnail image of graphical abstract

      Graphical representations of DNA, RNA, and proteins represent fundamental tools for the analysis and understanding of their biological structure and evolution. While the field has focused on DNA, graphical representations of protein sequences, like the highly compact 2D representation introduced in this work, are increasingly useful in bioinformatics.

    7. Shape and location of multiple charge carriers in linear π-electron systems (pages 416–428)

      Oleg S. Nychyporenko, Olga P. Melnyk, Olexandr O. Viniychuk, Tetiana M. Pinchuk-Rugal, Volodymyr A. Brusentsov, Elena L. Pavlenko, Oksana P. Dmytrenko, Nikolay P. Kulish and Olexiy D. Kachkovsky

      Article first published online: 23 NOV 2013 | DOI: 10.1002/qua.24585

      Thumbnail image of graphical abstract

      Organic conjugated molecules, used as molecular wires and semiconductor devices, can be used as model systems in the study of electron-transfer processes. Ionic defects in such chain-like molecules are notable for being localized within a distance of several atoms and thus behaving like solitary waves (known as solitons). This work investigates the nature of charge and bond length distributions in these solitonic waves on the injection of up to five charge carriers.

    8. Theoretical study of the vibrational frequencies of carbon disulfide (pages 429–435)

      Zerong Daniel Wang, Meagan Hysmith, Motoko Yoshida, Ben George and Perla Cristina Quintana

      Article first published online: 25 NOV 2013 | DOI: 10.1002/qua.24586

      Thumbnail image of graphical abstract

      Model molecules are often used in benchmark calculations to identify the most appropriate computational approach for describing specific physical properties. Calculations of the vibrational frequencies of CS2 using a combination of theoretical methods and basis sets validate the use of B3LYP and MP2 as the most accurate approaches. Although Hartree–Fock generally overestimates the frequency, it outperforms MP2 and some DFT functionals in predicting the frequency for asymmetric stretching.

SEARCH

SEARCH BY CITATION