Journal of Computational Chemistry

Cover image for Vol. 36 Issue 9

April 5, 2015

Volume 36, Issue 9

Pages i–iv, 585–693

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 36, Issue 9 (pages i–ii)

      Article first published online: 24 FEB 2015 | DOI: 10.1002/jcc.23888

      Thumbnail image of graphical abstract

      Using the accurate Wn-F12 thermochemical protocols, Amir Karton and Lars Goerigk show on page 622 (DOI: 10.1002/jcc.23837) that the widely used and popular CBS-QB3 composite method produces unusually large deviations for pericyclic reaction barrier heights. This unexpected finding has a significant impact on benchmark studies carried out for the assessment of density-functional-theory methods. Several related key issues are discussed in this context. These examples are a reminder to be cautious in the application of CBS-type composite methods in similar situations.

    2. You have free access to this content
      Cover Image, Volume 36, Issue 9 (pages iii–iv)

      Article first published online: 24 FEB 2015 | DOI: 10.1002/jcc.23889

      Thumbnail image of graphical abstract

      The image depicts the efficacy of Unitary Group Adapted State-Specific Multireference Perturbation Theory (UGA-SSMRPT2) for computing in an intruder-free manner the potential energy surface of “difficult” molecular states requiring a balanced inclusion of static and dynamic correlation. On page 670 (DOI: 10.1002/jcc.23851), Avijit Sen, Sangita Sen, Pradipta Kumar Samanta, and Debashis Mukherjee report the working equations are simple and incur low computational cost, yet are founded on sound physics involving a multireference starting function (CASSCF) and inclusion of dynamical correlation via perturbation, while maintaining the size extensivity and size-consistency of the energy. The perturbative wave function is a spin-eigenfunction due to the UGA formulation of the theory.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Accuracy assessment of the linear Poisson–Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid–protein complexes (pages 585–596)

      Federico Fogolari, Alessandra Corazza and Gennaro Esposito

      Article first published online: 8 JAN 2015 | DOI: 10.1002/jcc.23832

      Thumbnail image of graphical abstract

      The generalized Born model in the Onufriev, Bashford, and Case (OBC) implementation has emerged as one of the best compromises between accuracy and speed of computation. The linearization of the Poisson–Boltmann equation is shown to have mild effects on computed forces. With optimal choice of the OBC model parameters, the solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson–Boltzmann model.

    2. Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids (pages 597–600)

      Caleb Carlin and Mark S. Gordon

      Article first published online: 23 JAN 2015 | DOI: 10.1002/jcc.23838

      Thumbnail image of graphical abstract

      A comparison of the accuracy of MP2 and the high level coupled cluster method [CR-CC(2,3)] in predicting ionization potential and proton affinity of anions is made. The results show an increase in accuracy using CR-CC(2,3) for ionization potentials over MP2, but no significant difference in accuracy for proton affinities.

    3. Single-ended transition state finding with the growing string method (pages 601–611)

      Paul M. Zimmerman

      Article first published online: 8 JAN 2015 | DOI: 10.1002/jcc.23833

      Thumbnail image of graphical abstract

      Single-ended transition state findings are now possible in the growing string method, which allows a simultaneous search for reaction paths and transition states without knowledge of the product structure. This new method is shown to rapidly uncover detailed mechanistic information at a low cost and with low user effort.

    4. van der Waals interactions are critical in Car–Parrinello molecular dynamics simulations of porphyrin–fullerene dyads (pages 612–621)

      Topi Karilainen, Oana Cramariuc, Mikael Kuisma, Kirsi Tappura and Terttu I. Hukka

      Article first published online: 8 JAN 2015 | DOI: 10.1002/jcc.23834

      Thumbnail image of graphical abstract

      The interplay between electrostatic and van der Waals (vdW) interactions in the formation of porphyrin-fullerene (Ph–C60) dimers is still under debate despite its importance in determining the structural characteristics of these complexes, which are extensively as artificial photosynthesis centers in organic solar cells. Car–Parrinello molecular dynamics (CPMD) simulations with and without empirical vdW corrections are used to study the geometry and physical properties of a Ph–C60 dyad.

    5. Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS-QB3 composite method and their consequences in DFT benchmark studies (pages 622–632)

      Amir Karton and Lars Goerigk

      Article first published online: 3 FEB 2015 | DOI: 10.1002/jcc.23837

      Thumbnail image of graphical abstract

      Using the accurate Wn-F12 thermochemical protocols, it is shown that the widely used and popular CBS-QB3 composite method produces unusually large deviations for pericyclic reaction barrier heights. This unexpected finding has a significant impact on benchmark studies carried out for the assessment of density-functional-theory methods. Several related key issues are discussed in this context. These examples are a reminder to be cautious in the application of CBS-type composite methods in similar situations.

    6. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages (pages 633–648)

      Letif Mones, Andrew Jones, Andreas W. Götz, Teodoro Laino, Ross C. Walker, Ben Leimkuhler, Gábor Csányi and Noam Bernstein

      Article first published online: 3 FEB 2015 | DOI: 10.1002/jcc.23839

      Thumbnail image of graphical abstract

      Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives.

    7. Quantifying electro/nucleophilicity by partitioning the dual descriptor (pages 649–659)

      Vincent Tognetti, Christophe Morell and Laurent Joubert

      Article first published online: 3 FEB 2015 | DOI: 10.1002/jcc.23840

      Thumbnail image of graphical abstract

      Electrophilic and nucleophilic regions inside a molecule are delimited in real space and quantified using the dual descriptor. This partition scheme is applied to the reactivity of carbocations and to the prediction of the strength of halogen bonds.

    8. A DFT study on Cu(I) coordination in Cu-ZSM-5: Effects of the functional choice and tuning of the ONIOM approach (pages 660–669)

      Simone Morpurgo

      Article first published online: 13 FEB 2015 | DOI: 10.1002/jcc.23843

      Thumbnail image of graphical abstract

      The coordination of Cu+ to the T1 and T7 sites of Cu-ZSM-5 was investigated. ONIOM-2 calculations were performed at the DFT level by the B3LYP, BLYP, PBE1PBE, PBE, M06, and M062X functionals with extended basis set. Cu+ coordination and the energetics of NO adsorption are affected by the functional choice. The computational approach to the low-level part of ONIOM-2 calculations is also discussed.

    9. Unitary group adapted state specific multireference perturbation theory: Formulation and pilot applications (pages 670–688)

      Avijit Sen, Sangita Sen, Pradipta Kumar Samanta and Debashis Mukherjee

      Article first published online: 16 FEB 2015 | DOI: 10.1002/jcc.23851

      Thumbnail image of graphical abstract

      Diagrammatic depiction of the structure of the working equations for the cluster amplitudes inline image and inline image is presented. The shaded blocks are the composites, G, obtained by connecting the unperturbed Hamiltonian, H0, and the cluster operators, Tμ, as well as the perturbation, V, for a given partitioning and when acting on a model function inline image. The block diagrams clearly indicate that the amplitudes of only the proportional G-blocks are added together.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules—a GPU solver using the fast multipole method and statistical thermodynamics (pages 689–693)

      Alexander A. Kantardjiev

      Article first published online: 3 FEB 2015 | DOI: 10.1002/jcc.23842

      Thumbnail image of graphical abstract

      IrGPU.proton.Net combines both theoretical rigor and practical flavor to help scientists elicit subtle issues in biomolecule physics.

SEARCH

SEARCH BY CITATION