Journal of Computational Chemistry

Cover image for Vol. 34 Issue 8

30 March 2013

Volume 34, Issue 8

Pages i–iv, 611–705

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    1. You have free access to this content
      Cover Image, Volume 34, Issue 8 (pages i–ii)

      Article first published online: 21 FEB 2013 | DOI: 10.1002/jcc.23258

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      A new approach (PICVib) to compute selected vibrational frequencies at high levels or of large systems is presented by Marcus V. P. dos Santos, Eduardo C. Aguiar, João Bosco P. da Silva, and Ricardo L. Longo on page 611. The image illustrates this approach applied to the water dimer where the green circles represent the selected vibration and the arrows the harmonically displaced structures along the corresponding normal mode. Only single-point calculations are used to accurately predict the vibrational frequency. Thus, high level methods, including coupled-cluster, can be employed and large systems can be viably treated, as represented in the background by many interacting molecules.

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      Inside Cover, Volume 34, Issue 8 (pages iii–iv)

      Article first published online: 21 FEB 2013 | DOI: 10.1002/jcc.23259

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      A new geometric-flow based approach is used to self-consistently solve the Poisson equation and determine the dielectric profile around the small molecule glycerol triacetate, as presented by Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guowei Wei, and Nathan A. Baker on page 687. This approach is applied to a set of small molecules and produces solvation energy results that are in good agreement with experimental measurements. More importantly, the self-consistent nature of the geometric flow method removes the ambiguity associated with the functional form of the solute–solvent interface, a source of confusion and error in many implicit solvent electrostatics calculations.

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    1. PICVib: An accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels (pages 611–621)

      Marcus V. P. dos Santos, Eduardo C. Aguiar, João Bosco P. da Silva and Ricardo L. Longo

      Article first published online: 23 NOV 2012 | DOI: 10.1002/jcc.23166

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      A new approach (PICVib) was developed to provide vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level. The approach has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. It is general, robust and was validated for a wide range of frequency values (20–4800 cm1) and large systems.

    2. Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules (pages 622–639)

      Satoru G. Itoh and Hisashi Okumura

      Article first published online: 29 NOV 2012 | DOI: 10.1002/jcc.23167

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      A new type of the Hamiltonian replicaexchange method was proposed for molecular dynamics and Monte Carlo simulations, referred to as the Coulomb replicaexchange method. In this method, electrostatic charge parameters are exchanged among replicas. This method was applied to a fragment of an amyloid-β peptide in an explicit water solvent. β-Helix, α-helix, 310-helix, β-hairpin, and β-sheet structures were obtained, and the conformational transition pathways among these structures from the free-energy landscape were deduced.

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    1. Free energy simulation of helical transitions (pages 640–645)

      Ning Ma, Ying-Hua Chung and Arjan van der Vaart

      Article first published online: 5 NOV 2012 | DOI: 10.1002/jcc.23174

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      A new umbrella sampling method was developed to calculate free energies of helical transitions. With this method, the free energy landscape as a function of the helical radius and pitch was calculated for four peptides using the AMBER and CHARMM force fields.

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    1. Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene (pages 646–655)

      Goran Kovacevic and Aleksandar Sabljic

      Article first published online: 5 NOV 2012 | DOI: 10.1002/jcc.23175

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      The main atmospheric degradation pathway for aromatic pollutants like fluorobenzene is initiated by hydroxyl radical due to its high oxidation potential. The transition state for the formation of prereaction complex was determined for the first time. G3 calculations correctly predicted that atmospheric oxidation of fluorobenzene is dominated by the ortho and para reaction channels. The experimental reaction rates and their unusual temperature dependence were successfully reproduced by RRKM theory in the temperature range of environmental concern.

    2. Cationic closo-carboranes 2. Do computed 11B and 13C NMR chemical shifts support their experimental availability? (pages 656–661)

      Drahomír Hnyk and Elambalassery G. Jayasree

      Article first published online: 23 NOV 2012 | DOI: 10.1002/jcc.23176

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      Computationally predicted closo-tricarbaboranes C3Bn–3Hn+ (n 5 5, 6, 7, 10, 12) are further analyzed in terms of computing their 11B and 13C chemical shifts. The data obtained for these potentially weakly coordinating cations do not show any substantial deviations from known values of chemical shifts in the area of boron cluster chemistry, and on that basis their experimental availability is possible.

    3. Hardness potential derivatives and their relation to Fukui indices (pages 662–672)

      Soumen Saha, Rituparna Bhattacharjee and Ram Kinkar Roy

      Article first published online: 23 NOV 2012 | DOI: 10.1002/jcc.23177

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      Electrophilic (Δ+ h(k)) and nucleophilic (Δh(k)) hardness potential [h (r)] can address the N-dependence problem of the local hardness descriptor and at the same time can, in principle, explain the intermolecular and intramolecular reactivities toward nucleophilic and electrophilic attacks on systems, where the electronic factor plays the deciding role of reactivity.

    4. Ab initio calculations of the Ar–ethane intermolecular potential energy surface using bond function basis sets (pages 673–680)

      Jian-Dong Zhang, Shu-Jin Li and Fu-Ming Tao

      Article first published online: 23 NOV 2012 | DOI: 10.1002/jcc.23179

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      The intermolecular potential energy surface (PES) of argon-ethane was studied. The PES of argon-ethane was characterized by a global minimum at a near Tshaped configuration, and a second minimum at a collinear configuration. An augmented correlation-consistent basis set with a set of bond functions can effectively produce results equivalent to the next larger augmented correlation-consistent basis set. The use of bond functions improved the PES, resulting in accurate potential anisotropy.

    5. An efficient method for computing the QTAIM topology of a scalar field: The electron density case (pages 681–686)

      Juan I. Rodríguez

      Article first published online: 23 NOV 2012 | DOI: 10.1002/jcc.23180

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      The Bader's quantum theory of atoms in molecules (QTAIM) was used in a wide range of applications from solid state physics and X-ray crystallography to drug design and biochemistry. However, it has not always been feasible to apply QTAIM to large systems due to its computational cost. This article presents a vectorized and parallel algorithm for computing the QTAIM topology of the electron density that scales linearly with the system size and quasi-linearly with the number of processors. The method is applied to a series of representative molecules.

    6. Parameterization of a geometric flow implicit solvation model (pages 687–695)

      Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guowei Wei and Nathan A. Baker

      Article first published online: 5 DEC 2012 | DOI: 10.1002/jcc.23181

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      A geometric flow implicit solvent model with a self-consistent treatment of polar and nonpolar energetics was used to study properties of a series of small molecules. The graphical abstract figure illustrates the solute–solvent interface obtained from this implicit solvent model.

    7. Complexes of 4-substituted phenolates with HF and HCN: Energy decomposition and electronic structure analyses of hydrogen bonding (pages 696–705)

      Halina Szatyłowicz, Tadeusz M. Krygowski, Célia Fonseca Guerra and F. Matthias Bickelhaupt

      Article first published online: 23 NOV 2012 | DOI: 10.1002/jcc.23182

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      Electron-donating and weakly electronaccepting substituents affect H-bond strengths (and related properties) more strongly than electron-accepting ones.

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