Journal of Computational Chemistry

Cover image for Vol. 36 Issue 5

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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  1. Full Papers

    1. Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids

      Caleb Carlin and Mark S. Gordon

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

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      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.

    2. H2 adsorption on Ag-nanocluster/single-walled carbon nanotube composites: A molecular dynamics study on the effects of nanocluster size, diameter, and chirality of nanotube

      Hamed Akbarzadeh and Amir Nasser Shamkhali

      Article first published online: 13 JAN 2015 | DOI: 10.1002/jcc.23817

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      H2 adsorption on (Ag-nanocluster)/(single-walled carbon nanotube) composites are studied by molecular dynamics simulation to investigate effects of nanocluster size, diameter, and chirality of nanotube. The results show that increase of nanocluster size and nanotube diameter decreases adsorption. Also, H2 adsorbates have more tendencies to the nanoclusters located on nanotubes with armchair chirality. Moreover, the effect of nanocluster size is more important than chirality of nanotube.

    3. Theoretical prediction of the host–guest interactions between novel photoresponsive nanorings and C60: A strategy for facile encapsulation and release of fullerene

      Kun Yuan, Jing-Shuang Dang, Yi-Jun Guo and Xiang Zhao

      Article first published online: 8 JAN 2015 | DOI: 10.1002/jcc.23824

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      A series of photoresponsive nanorings was designed by employing different numbers of azobenze groups as construction units of host molecules. The complexes formed with guest C60 and these hosts were investigated theoretically. Host 7, which is composed by seven azo groups and seven phenyls, is the most feasible host molecule for the encapsulation of guest C60 among all candidates; the guest C60 would be facile released from the cavity of the host 7 by configuration transformation under the 563 nm photoirradiation.

    4. van der Waals interactions are critical in Car–Parrinello molecular dynamics simulations of porphyrin–fullerene dyads

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

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

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      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, used 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. Energy decomposition analysis of cation–π, metal ion–lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π–π interactions

      Bhaskar Sharma, Hemant Kumar Srivastava, Gaddamanugu Gayatri and Garikapati Narahari Sastry

      Article first published online: 8 JAN 2015 | DOI: 10.1002/jcc.23827

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      The nature of cation–π, metal ion–lone pair (M–LP), hydrogen bonding (HB), charge-assisted hydrogen bonding (CAHB), and π–π interactions, has been probed through energy decomposition schemes. Although there is a mix of electrostatic, polarization, and dispersion components in all noncovalent interactions, their nature can be contrasted by comparing and contrasting the percentage contributions of these three components.

    6. Single-ended transition state finding with the growing string method

      Paul M. Zimmerman

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

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      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.

    7. Accuracy assessment of the linear Poisson–Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid–protein complexes

      Federico Fogolari, Alessandra Corazza and Gennaro Esposito

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

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      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.

    8. Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach

      Siladitya Padhi, Siddabattula Ramakrishna and U. Deva Priyakumar

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23828

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      A method has been proposed for generating putative initial structural models of membrane proteins, which can be considered for further molecular dynamics simulations. The initial models developed for the proteins M2, BM2, and ErbB2 provide structures close to the experimental structures via two independent sampling schemes.

  2. Software News and Updates

    1. The development of an artificial organic networks toolkit for LabVIEW

      Hiram Ponce, Pedro Ponce and Arturo Molina

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23818

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      This article reviews the development process of the Artificial Organic Networks Toolkit, a graphical software package that implements the machine learning technique so-called artificial organic networks which it is inspired on chemical organic compounds. In addition, this work presents two practical case studies (sensor characterization and blood–brain barrier partitioning model) to show the usage of the toolkit.

  3. Full Papers

    1. Application of polarizable ellipsoidal force field model to pnicogen bonds

      Fang Liu, Likai Du, Jun Gao, Lili Wang, Bo Song and Chengbu Liu

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23819

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      A modification of the polarizable ellipsoidal force field (PEff) model was proposed to understand the anisotropic characters of pnicogen bonds. The results indicate that the modified PEff model can precisely characterize pnicogen bonds. The root mean squared error between PESs obtained with PEff and MP2 models is less than 0.5 kcal/mol. This model may be applied to other noncovalent bond interactions to understand the role of anisotropic intermolecular interactions.

    2. Ionic bonding of lanthanides, as influenced by d- and f-AOs, by core–shells and by relativity

      Wen-Xin Ji, Wei Xu, W. H. Eugen Schwarz and Shu-Guang Wang

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23820

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      The closed Lu 4f14 and 5s25p6 shells in LuX3 are not inert but influence the bonding, reproducible by wavefunction approaches. Accidental Ln-4f/F-2p near-degeneracy and AO-mixing is no evidence for covalence by noninteracting AOs. Fluorine causes overbinding with various DFs.

  4. Software News and Updates

    1. Etomica: An object-oriented framework for molecular simulation

      Andrew J. Schultz and David A. Kofke

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23823

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      Molecular simulation methods find application to an extremely broad set of materials and phenomena, yet underlying this diversity is a unifying structure that can allow such variety to be realized using a relatively small set of software components. Ideas for the design of such a framework are discussed as is the implementation of it in a package we call etomica.

  5. Full Papers

    1. Theoretical investigation of enantioselectivity of cage-like supramolecular assembly: The insights into the shape complementarity and host–guest interaction

      Yusuke Ootani, Yoshinobu Akinaga and Takahito Nakajima

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23821

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      The insights into the shape complementarity and host–guest interactions are important to design the supramolecular assemblies with high enantioselectivity. DFT investigation reveals that the reaction barriers and the stabilities of the prochiral structures of the aza-Cope rearrangement differed in the supramolecular assembly [Ga4L6]12−, resulting that the substrate with an R structure is favorably produced in the Δ-structure [Ga4L6]12−. The effects of the shape complementarity and host–guest interactions were analyzed.

    2. Internal coordinate density of state from molecular dynamics simulation

      Pin-Kuang Lai and Shiang-Tai Lin

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23822

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      The Wilson's B-matrix method is generalized to calculate internal coordinate density of state (DoS) of macromolecules. Compared with the Cartesian DoS where the normal modes are superposition of various internal modes, the internal DoS allows for a clear association of each vibrational modes with the dynamic behavior of a system, and thus provides a more natural way to describe molecular motion.

    3. Essential dynamics for the study of microstructures in liquids

      Maira D'Alessando, Andrea Amadei, Mauro Stener and Massimiliano Aschi

      Article first published online: 24 DEC 2014 | DOI: 10.1002/jcc.23814

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      A simple method, based on Essential Dynamics, is proposed for performing conformational analysis on clusters of arbitrary dimensions as provided by molecular dynamics (MD) simulations of liquids and solutions. The validity of the method is tested by modelling spectral observables of liquid water using a sequential procedure of configuration extraction from MD simulation and subsequent Quantum Chemical calculations.

  6. Obituary

    1. Paul Schleyer 1930–2014

      Article first published online: 24 DEC 2014 | DOI: 10.1002/jcc.23826

  7. Full Papers

    1. Persistent homology for the quantitative prediction of fullerene stability

      Kelin Xia, Xin Feng, Yiying Tong and Guo Wei Wei

      Article first published online: 19 DEC 2014 | DOI: 10.1002/jcc.23816

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      Geometric models often involve too much structural detail to be computationally efficient while topological models typically bear too little structural information to be quantitatively accurate. Persistent homology, a new branch of topology, bridges the gap between geometry and topology and offers a new strategy for handling big data. This work introduces persistent homology for qualitative analysis of fullerene topological fingerprints and quantitative prediction of fullerene stability.

    2. An incremental isoconversional method for kinetic analysis based on the orthogonal distance regression

      Tibor Dubaj, Zuzana Cibulková and Peter Šimon

      Article first published online: 18 DEC 2014 | DOI: 10.1002/jcc.23813

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      The parameters obtained from a kinetic analysis of thermoanalytical data often exhibit a conversion-dependent behavior. Modern isoconversional methods designed to deal with this problem are increasingly precise when applied to simulated data. Conversely, they do not take the errors of the measured data into account. The proposed incremental isoconversional method follows the error structure of the thermoanalytical measurements and the data are processed using the orthogonal distance regression without transformations.

    3. Search for the global minimum structures of AlB3H2n (n = 0 − 6) clusters

      İskender Muz, Osman Canko, Murat Atiş and Erdem Kamil Yıldırım

      Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23812

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      The global minimum structures of AlB3H2n (n = 0–6) clusters are investigated and the chemical bonding patterns of the most stable isomers are analyzed by the adaptive natural density partitioning method.

    4. New insights into the meaning and usefulness of principal component analysis of concatenated trajectories

      Gustavo Pierdominici-Sottile and Juliana Palma

      Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23811

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      Combined principal component analysis (combined-PCA) is a technique usually employed to analyze structural and dynamical differences between alternative conformations of a given protein. However, analytical formulas showing what is to be expected and what is not to be expected from a combined-PCA have never been provided. Here, we present and discuss such formulas. We believe that they will be useful to enlighten the discussions of the results of combined-PCA.

  8. Software News and Updates

    1. STOCK: Structure mapper and online coarse-graining kit for molecular simulations

      Staš Bevc, Christoph Junghans and Matej Praprotnik

      Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23806

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      STOCK is a web-based toolkit for setting up coarse-grained molecular simulations. One can define a molecular mapping from high to low resolution with the aid of a molecular visualizer. Additionally, one may generate effective potentials for coarse-grained simulations preserving structural properties of the underlying higher resolution model. The tool is available at http://stock.cmm.ki.si

  9. Full Papers

    1. k-Nearest neighbors optimization-based outlier removal

      Abraham Yosipof and Hanoch Senderowitz

      Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23803

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      A new iterative method for the identification and removal of outliers from quantitative structure activity relationship (QSAR) datasets is described. This method is based on a kNN optimization algorithm, and named kNN optimization-based outlier removal. The method is able to maintain the internal diversity of the parent dataset and at the same time produce QSAR models with better prediction statistics than other outlier removal methods.

    2. Force field development for organic molecules: Modifying dihedral and 1–n pair interaction parameters

      Siyan Chen, Shasha Yi, Wenmei Gao, Chuncheng Zuo and Zhonghan Hu

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23808

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      The energy correlation map between calculations from molecular mechanics force fields and quantum mechanical calculations illustrating the quality of the developed force field to describe the transition energies for condensed matter systems of ethane (right) and 3-hydroxypropionic acid (left). Especially for the 3-hydroxypropionic acid molecule, the parameters for the dihedral angle and 1−n interaction potentials in the new force field (MM) significantly help to improve the results in comparison to QM studies.

    3. Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer

      Víctor Duarte Alaniz, Tomás Rocha-Rinza and Gabriel Cuevas

      Article first published online: 2 DEC 2014 | DOI: 10.1002/jcc.23798

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      Eleven relative orientations of (CH4)2 were investigated through the topology of inline image and Symmetry Adapted Perturbation Theory (SAPT). The relations found between the components of SAPT and the properties of inline image are exploited to construct Mollier-like diagrams to evaluate the importance of hydrophobic interactions (HIs) in representative examples. These diagrams might prove useful in analyzing HIs, especially when ab-initio or SAPT calculations are unfeasible or prohibitively expensive.

    4. Pentaatomic planar tetracoordinate silicon with 14 valence electrons: A large-scale global search of SiXnYmq (n + m = 4; q = 0, ±1, −2; X, Y = main group elements from H to Br)

      Jing Xu and Yi-hong Ding

      Article first published online: 27 NOV 2014 | DOI: 10.1002/jcc.23792

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      The 14 electrons of planar tetracoordinate silicon were systematically searched for the first time, finding nine global minimum ptSi, that is, Li3SiAs2−, HSiY3 (Y = Al/Ga), Ca3SiAl, Mg4Si2−, C2LiSi, Si3Y2 (Y = Li/Na/K). The former six systems represent the first prediction. In light of the very limited global ptSi examples, the presently designed six systems with 14e are expected to enrich the exotic ptSi chemistry and welcome future laboratory confirmation.

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