Journal of Computational Chemistry

Cover image for Vol. 34 Issue 15

5 June 2013

Volume 34, Issue 15

Pages i–iv, 1271–1362

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. You have free access to this content
      Cover Image, Volume 34, Issue 15 (pages i–ii)

      Version of Record online: 25 APR 2013 | DOI: 10.1002/jcc.23318

      Thumbnail image of graphical abstract

      Developable domains characteristic of columnar mesophases are seen when mixed-valent diruthenium tetracarboxylates are observed under a polarizing optical microscopy by Maria Castro, Adrian Roitberg, and Fabio Cukiernik on page 1283. Molecular dynamics simulations with an extended AMBER force field provide insights about the relative contributions of different intermolecular interactions to the supramolecular architecture of these coordination polymers in the liquid crystalline phase. The cover shows two snapshot views from the molecular dynamics calculation, which are overlaid onto an image from the microscope.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 15 (pages iii–iv)

      Version of Record online: 25 APR 2013 | DOI: 10.1002/jcc.23319

      Thumbnail image of graphical abstract

      Full configurational space quantum mechanics calculation results are used to develop van der Waals force field parameters for benzene and alkane. Using the novel partition function-based weighting method proposed by Yao Wu, Xiaodong Dai, Niu Huang, and Lifeng Zhao on page 1271, the huge amount of quantum mechanics interaction energies are automatically weighted and selected according to statistical importance. The new weighting scheme (orange) provides a different configurational energy distribution profile than the one resulting from the general Boltzmann weighting method (blue). The new method is verified to be effective in discriminating fitting errors and avoiding overfittings in force field parameterization.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space (pages 1271–1282)

      Yao Wu, Xiaodong Dai, Niu Huang and Lifeng Zhao

      Version of Record online: 19 FEB 2013 | DOI: 10.1002/jcc.23249

      Thumbnail image of graphical abstract

      Quantum mechanical potential energy surfaces are increasingly applied as target data in the development of nonbonded force field parameters. However, the fitted parameters heavily depend on the choice of the weighting factors. A novel partition function-based weighting scheme is developed to obtain physically reasonable parameters by reducing the overfitting. Since no prerequisite conditions are required, the weighting scheme is generally applicable in any type of force field parameterization.

    2. Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type (pages 1283–1290)

      Maria Ana Castro, Adrian E. Roitberg and Fabio D. Cukiernik

      Version of Record online: 22 FEB 2013 | DOI: 10.1002/jcc.23254

      Thumbnail image of graphical abstract

      New parameters for AMBER molecular force field are defined from experimental data and QM calculations, and validated against model systems of known structure. This modified force field is used to simulate different arrangements of polymeric diruthenium tetracarboxylates, Ru2 (O2CR) 4X, providing insights on the influence that the different molecular fragments have on the supramolecular structure of these materials. The developed force field is easily transferable to other MMX coordination polymers.

    3. Search of truncation of (N−1) electron basis containing full connected triple excitations in computing main and satellite ionization potentials via Fock-space coupled cluster approach (pages 1291–1310)

      Kalipada Adhikari, Sudip Chattopadhyay, Barin Kumar De, Amitava Sharma, Ranendu Kumar Nath and Dhiman Sinha

      Version of Record online: 9 MAR 2013 | DOI: 10.1002/jcc.23255

      Thumbnail image of graphical abstract

      The eigenvalue-independent partitioningvalence- universal multireference coupled cluster method is implemented with the full inclusion of triples excitations for computing and analyzing the entire main and several satellite peaks in the ionization potential spectra of several molecules.

    4. Local Hartree–Fock orbitals using a three-level optimization strategy for the energy (pages 1311–1320)

      Ida-Marie Høyvik, Branislav Jansik, Kasper Kristensen and Poul Jørgensen

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/jcc.23256

      Thumbnail image of graphical abstract

      How to efficiently generate a set of local occupied and unoccupied Hartree–Fock orbitals is shown by using the three-level optimization procedure for the energy combined with a refined version of the least-change strategy. The refined leastchange strategy includes a separation of core and valence spaces to avoid mixing of these spaces.

    5. Pseudosymmetry analysis of molecular orbitals (pages 1321–1331)

      David Casanova, Pere Alemany, Andrés Falceto, Abel Carreras and Santiago Alvarez

      Version of Record online: 22 FEB 2013 | DOI: 10.1002/jcc.23257

      Thumbnail image of graphical abstract

      The classical treatment of molecular symmetry, successful in explaining many aspects of the properties and reactivity of molecules, is helpless in those cases with an approximate symmetry. Crystallographers and chemists often use the terms “pseudosymmetry,” “approximate symmetry,” and “quasisymmetry.” The pseudosymmetry concept is rigorously defined for the analysis of pseudosymmetry properties of molecular orbitals by means of a simple decomposition in pseudosymmetry irreducible representations.

    6. Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane–water partition coefficients (pages 1332–1340)

      Sven Jakobtorweihen, Thomas Ingram and Irina Smirnova

      Version of Record online: 28 FEB 2013 | DOI: 10.1002/jcc.23262

      Thumbnail image of graphical abstract

      The extension of COSMO-RS to anisotropic systems, referred to as COSMOmic, needs structural information of these systems. This information can be obtained from molecular dynamics simulations. This combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies.

    7. Which density functional is close to CCSD accuracy to describe geometry and interaction energy of small noncovalent dimers? A benchmark study using Gaussian09 (pages 1341–1353)

      Karunakaran Remya and Cherumuttathu H. Suresh

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/jcc.23263

      Thumbnail image of graphical abstract

      A benchmark study on almost all possible DFT methods (total 382) in Gaussian09 is done to locate functionals that agree well with the CCSD/aug-cc-pVTZ geometry and the Ave-CCSD(T)/(Q-T) interaction energy (Eint) for noncovalently interacting molecular dimers in dispersion-dominated (class 1), dipole-induced dipole (class 2), and dipole-dipole (class 3) classes. Our results unambiguously show that M06L is the most trustworthy DFT method in Gaussian09 for the study of noncovalently interacting systems.

    8. Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules (pages 1354–1362)

      Silvia A. Martins and Sergio F. Sousa

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/jcc.23264

      Thumbnail image of graphical abstract

      Polarized continuum model methods and thermodynamic integration are evaluated in the determination of differences in solvation free energy on hydroxyl groups (HO) addition. Solvation model D (SMD) performs better among polarized continuum model (PCM) based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/ mol for both quantities. In solvation free energy changes on alkane-alcohol transformation, thermodynamic integration yielded better results, particularly for HO addition to aromatic rings (0.53 kcal/mol).