International Journal of Quantum Chemistry

Cover image for Vol. 113 Issue 21

5 November 2013

Volume 113, Issue 21

Pages i–iv, 2333–2412

  1. Cover Image

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    1. You have free access to this content
      Cover Image, Volume 113, Issue 21 (pages i–ii)

      Version of Record online: 23 SEP 2013 | DOI: 10.1002/qua.24549

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      All-electron canonical molecular orbital calculations based on B3LYP density functional theory are applied on a model of carbonmonoxy myoglobin consisting of 2494 atoms and various sizes of quantum mechanics/molecular mechanics models. In the cover article by Kouji Chiba, Toshiyuki Hirano, Fumitoshi Sato, and Masahiro Okamoto on page 2345, the effect of proton tautomerization in distal histidine (His), especially influences on electrostatic potential inside the heme pocket, and the size dependency of the computational model on the electronic structure are investigated.

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      Inside Cover, Volume 113, Issue 21 (pages iii–iv)

      Version of Record online: 23 SEP 2013 | DOI: 10.1002/qua.24550

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      Molecular dynamics simulations were performed on the Hras-GTP complex and the Hras-GDP complex in water solvents by Takeshi Miyakawa et al. on page 2333. From the trajectories of the simulations, the radius distribution functions of the water molecules around each phosphorus atom in GTP and GDP were calculated. From these values, the first hydration spheres of the water molecules around each phosphorus atom were defined. The duration time of the water molecules of the first hydration spheres was calculated, and it was found that the occurrence ratio for the duration time is proportional to the power of the duration time when the duration time is shorter than 10 ps.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Molecular dynamics simulations of the Hras-GTP complex and the Hras-GDP complex (pages 2333–2337)

      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Taku Mizukami, Kazutomo Kawaguchi, Hiroaki Saito and Hidemi Nagao

      Version of Record online: 21 MAY 2013 | DOI: 10.1002/qua.24457

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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.

    2. A dual-level direct dynamics study on the hydrogen abstraction reaction of oxygen atom with methylhydrazine (pages 2338–2344)

      Li Wang, Jinmiao Wen, Hongqing He and Jinglai Zhang

      Version of Record online: 30 APR 2013 | DOI: 10.1002/qua.24458

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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.

    3. Clarification of the role of protein in carbonmonoxy myoglobin by investigating electronic states (pages 2345–2354)

      Kouji Chiba, Toshiyuki Hirano, Fumitoshi Sato and Masahiro Okamoto

      Version of Record online: 30 APR 2013 | DOI: 10.1002/qua.24459

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      The iron-containing protein myoglobin is commonly found in muscular tissue of vertebrate animals and is a reliable marker for the 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.

    4. Intermolecular interactions of formic acid with benzene: Energy decomposition analyses with ab initio MP2 and double-hybrid density functional computations (pages 2355–2360)

      Feng Yu

      Version of Record online: 9 MAY 2013 | DOI: 10.1002/qua.24460

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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 the B2PLYP functional. These are tested against a popular noncovalent complexation energies database. This work is expected to provide new insight into these important interactions.

    5. Intermolecular interactions in uracil–nitrous acid complexes: structures, binding energy, topological properties, and nuclear magnetic resonance study (pages 2361–2371)

      Batoul Makiabadi, Mohammad Zakarianejad, Sotoodeh Bagheri, Hamid Reza Masoodi and Raziyeh Sadaat Aghaie

      Version of Record online: 13 MAY 2013 | DOI: 10.1002/qua.24461

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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.

    6. Theoretical study on keto–enol tautomerism and isomerization in pyruvic acid (pages 2372–2378)

      Younes Valadbeigi and Hossein Farrokhpour

      Version of Record online: 16 MAY 2013 | DOI: 10.1002/qua.24467

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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 a tetragonal ring formed in the absence of water.

    7. Influence of collision energy and reagent vibrational excitation on the dynamics of the reaction H + LiH (pages 2379–2384)

      Dan Li, Yuliang Wang, Jun Wang and Yingtao Zhao

      Version of Record online: 22 MAY 2013 | DOI: 10.1002/qua.24468

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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 barrierless 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.

    8. Insight into the structural requirements of benzimidazole derivatives as interleukin-2 inducible t-cell kinase inhibitors by computational explorations (pages 2385–2396)

      Jinghui Wang, Feng Li, Yan Li, Yinfeng Yang, Bin Wang, Shuwei Zhang and Ling Yang

      Version of Record online: 16 MAY 2013 | DOI: 10.1002/qua.24470

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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 inducibleT-cell kinase. The developed models demonstrate good predictive ability and some key structural factors responsible for the activity.

    9. A theoretical study of the dihydrogen molecule confined inside carbon nanotubes (pages 2397–2404)

      Wiem Felah Gtari and Bahoueddine Tangour

      Version of Record online: 21 MAY 2013 | DOI: 10.1002/qua.24474

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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 catalyst.

    10. Potential energy and dipole moment of the Na2+ ionic molecule (pages 2405–2412)

      Hamid Berriche

      Version of Record online: 25 JUN 2013 | DOI: 10.1002/qua.24475

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      Ionic alkali pairs like Na2+ become immobilized and localized spatially in Coulomb crystals when translationally cooled to temperatures of a few mK. Accurate potential energy and dipole functions data are required to predict and guide the experimental studies. Potential energies, spectroscopic constants and dipole functions of ground and excited states of the Na2+ ionic molecule are calculated using a one-electron pseudopotential approach, where the Na2+ core is replaced by effective potential.