Journal of Computational Chemistry

Cover image for Vol. 36 Issue 20

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: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (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. 1 - 25
  1. Full Papers

    1. Libcint: An efficient general integral library for Gaussian basis functions

      Qiming Sun

      Article first published online: 30 JUN 2015 | DOI: 10.1002/jcc.23981

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      Integral evaluation can be as simple as building toy bricks. In this spirit, an open source library Libcint was developed to automatically implement integrals for Gaussian type basis functions. Libcint library is able to handle arbitrary integral expressions on top of p, r operators and Pauli matrices for various integral types (one-electron overlap, nuclear attraction, two-electron Coulomb, and Gaunt operators) for various basis types (Cartesian, spherical, and spinor), without loss of computational efficiency.

    2. H/D isotope effect on charge-inverted hydrogen-bonded systems: Systematic classification of three different types in H3XHYH3 (X = C, Si, or Ge, and Y = B, Al, or Ga) with multicomponent calculation

      Taro Udagawa and Masanori Tachikawa

      Article first published online: 30 JUN 2015 | DOI: 10.1002/jcc.23978

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      Geometrical isotope effect, which is induced by isotope-substitution of hydrogen, in various H3XHYH3 (X = C, Si, or Ge, and Y = B, Al, or Ga) hydrogen-bonded systems are systematically analyzed using the multicomponent MO method. Isotope effects of interaction energies and spatial distribution of nuclear wavefunctions are also analyzed. The GIEs in these HB systems can be classified into three types.

  2. Software News and Updates

    1. You have full text access to this OnlineOpen article
      SDA 7: A modular and parallel implementation of the simulation of diffusional association software

      Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter and Rebecca C. Wade

      Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23971

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      SDA 7 is the latest release of the Simulation of Diffusional Association software, a Brownian dynamics simulation package for the modeling of biomolecular systems. This release has been fully rewritten in Fortran 90, using an object-oriented programming approach, with improved parallelization on multi-core shared memory architectures. It consolidates the previously separate versions used for simulations of bimolecular and many-molecule systems, and allows modeling of solute flexibility.

  3. Full Papers

    1. Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling

      Chao Lv, Erick W. Aitchison, Dongsheng Wu, Lianqing Zheng, Xiaolin Cheng and Wei Yang

      Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23982

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      The orthogonal space tempering simulation shows that hydrogen sulfide is amphipathic, and thus is favorably localized at the interface between the head-group and acyl chain regions. Because the membrane binding affinity of H2S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the trans-membrane free energy barriers to encounter by this toxic molecule are very small.

    2. Is molecular alignment an indispensable requirement in the MIA-QSAR method?

      Stephen J. Barigye and Matheus P. Freitas

      Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23992

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      The 2D-Discrete Fourier Transform is introduced as a strategy for creating a common base to construct multivariate images for chemical structures using their magnitude spectra. Thus, for the first time, the modeling of structurally diverse noncongruent chemical images in the Multivariate Image Analysis-Quantitative Structure Activity Relationship context is possible.

    3. Fragment-based similarity searching with infinite color space

      Jakub Gunera and Peter Kolb

      Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23974

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      RedFrag is a fast and intuitive algorithm for similarity-based molecule screenings. It uses a reduced graph representation of molecules, with an infinite color space for each of the nodes. This makes it an evolved version of feature trees while retaining the efficiency of this concept. RedFrag is evaluated both retro- as well as prospectively, the latter leading to five novel binders of endothiapepsin.

    4. Statistical analysis of electronic excitation processes: Spatial location, compactness, charge transfer, and electron-hole correlation

      Felix Plasser, Benjamin Thomitzni, Stefanie A. Bäppler, Jan Wenzel, Dirk R. Rehn, Michael Wormit and Andreas Dreuw

      Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23975

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      A new methodology for the analysis of electronic excitations is introduced. The formalism, which is based on a statistical analysis of the wavefunction of the electron-hole pair, allows to quantify the spatial location and compactness of electronic excitations, as well as giving new insight into charge transfer and correlation effects. A special focus is laid on different ways to quantify charge separation. In the figure, the hole (red) and electron (blue) densities are shown for a Rydberg state of cytosine. The hole size σh, the electron size σe, and the distance between the charge centroids inline image are marked.

    5. Hydrogen bond–aromaticity cooperativity in self-assembling 4-pyridone chains

      Megha Anand, Israel Fernández, Henry F. Schaefer III and Judy I-Chia Wu

      Article first published online: 23 JUN 2015 | DOI: 10.1002/jcc.23976

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      Hydrogen bonding interactions can polarize the π-systems of 4-pyridones to increase cyclic (4n+2) π electron delocalization. The resulting H-bonded six-membered rings exhibit enhanced π-aromaticity and the corresponding N[BOND]H···O[DOUBLE BOND]C interactions are strengthened. Extended H-bonded 4-pyridone chains exhibit high degrees of such cooperativity, even when each of the neighboring 4-pyridone rings are twisted to preclude direct π-overlap between the H-bonded units.

    6. Saturn Systems

      Habib U. Rehman, Nida A. McKee and Michael L. McKee

      Article first published online: 19 JUN 2015 | DOI: 10.1002/jcc.23979

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      Nanohoops, such as cycloparaphenylenes [10]CPP, can bind to C60 and [Li@C60)]+ through noncovalent interactions with free energies of binding greater than 10 kcal/mol in nonpolar solvents. With the right size, the hoops bind around the equator of the fullerene and resemble the ring around Saturn. Density functional calculations can predict the binding constants and suggest new nanohoops as targets for synthesis. The graphic image is the HOMO of C60@(C6H4)10.

    7. QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)

      Ignacio Viciano, Raquel Castillo and Sergio Martí

      Article first published online: 19 JUN 2015 | DOI: 10.1002/jcc.23967

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      CYP19A1 aromatase is a Cytochrome P450 responsible for the final step of the androgens conversion into the corresponding estrogens, and thus can play a significant role in the hormone-dependent breast cancer development. The first of three oxidative subcycles of this enzyme consists of an initial hydrogen abstraction followed by an oxygen rebound step, giving place to a hydroxylated form of the androstenedione substrate via two possible electronic spin pathways.

    8. The role of induced current density in Steroelectronic effects: Perlin effect

      Joseelyne G. Hernández-Lima, Jose E. Barquera-Lozada, Gabriel Cuevas and Fernando Cortés-Guzmán

      Article first published online: 17 JUN 2015 | DOI: 10.1002/jcc.23965

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      Differing behavior of geminal hydrogen atoms of a cyclic structure is known as Perlin effect. In this article, the local and integrated properties of induced current density (which directly determines nuclear magnetic shielding) are used to understand the normal and reverse Perlin effect in several diheterocyclic structures.

    9. Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation

      Gregory R. Bowman

      Article first published online: 16 JUN 2015 | DOI: 10.1002/jcc.23973

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      This article assesses whether modern simulations accurately capture ps-ns timescales—as judged by their ability to predict order parameters—or if force fields are now a limiting factor. The results show microseconds of simulation with any of three force fields and a proper method for calculating order parameters are required for accuracy and precision. This has important implications for the extent of simulations required for slower processes and the utility of enhanced sampling methods.

    10. The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube

      Benjamin D. Jensen, Kristopher E. Wise and Gregory M. Odegard

      Article first published online: 12 JUN 2015 | DOI: 10.1002/jcc.23970

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      The Reactive Force Field was originally developed to model chemical reactions in a molecular dynamics framework. However, it is a promising candidate for modeling fracture in carbon-based materials because of its ability to treat covalent bond cleavage. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the predicted fracture behavior of graphene, diamond, and a carbon nanotube.

    11. Confined polyelectrolytes: The complexity of a simple system

      Sandra C. C. Nunes, Marie Skepö and Alberto A. C. C. Pais

      Article first published online: 12 JUN 2015 | DOI: 10.1002/jcc.23969

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      The effect of spherical confinement on conformation and counterion release is addressed. The condensation of monovalent and trivalent ions shows distinct trends, as space decreases. Different charge layers are found along the confining radius, which cannot be simply explained by polyelectrolyte electrostatic persistence. Regular structures were found for stiffer chains, even in the presence of monovalent counterions.

    12. Heats of formation of platonic hydrocarbon cages by means of high-level thermochemical procedures

      Amir Karton, Peter R. Schreiner and Jan M. L. Martin

      Article first published online: 12 JUN 2015 | DOI: 10.1002/jcc.23963

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      This work determines total atomization energies and heats of formation for platonic and prismatic polycyclic hydrocarbon cages by means of the W1-F12 and W2-F12 thermochemical protocols. Using these accurate reference data, the performance of computationally economical theoretical methods (e.g., density functional theory and composite ab initio methods) was evaluated via atomization and bond separation reactions for the calculation of these challenging thermochemical quantities.

    13. Nucleus-independent chemical shift analysis of the electronic states of the (CO)4, (CS)4, and (CSe)4 molecules

      Yunfei Zhou, Xiaoguang Bao and Weston Thatcher Borden

      Article first published online: 8 JUN 2015 | DOI: 10.1002/jcc.23962

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      The occupancy of the a2u MOs of (CO)4, (CS)4, and (CSe)4 control the NICS(1) values that are computed for these compounds.

    14. Multiscale enhanced sampling of intrinsically disordered protein conformations

      Kuo Hao Lee and Jianhan Chen

      Article first published online: 6 JUN 2015 | DOI: 10.1002/jcc.23957

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      Multiscale enhanced sampling (MSES) uses efficient coarse-grained (CG) models to accelerate sampling of atomistic protein conformations. The efficacy of MSES for simulating intrinsically disordered proteins (IDPs) is investigated, and refined MSES Hamiltonian/temperature replica exchange protocols are developed that involve additional parameters in the MSES coupling restraint potential. The refined protocols drive more conformational transitions to improve the convergence of simulated ensembles. Nonetheless, further improvement of MSES for simulating IDPs likely requires more detailed CG models.

    15. The Reaction between Bromine and the Water Dimer and the Highly Exothermic Reverse Reaction

      Guoliang Li, Hui Wang, Qian-Shu Li, Yaoming Xie and Henry F. Schaefer III

      Article first published online: 4 JUN 2015 | DOI: 10.1002/jcc.23951

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      The entrance complex, transition state, and exit complex for the Br + (H2O)2 [RIGHTWARDS ARROW] HBr + (H2O)OH reaction have been investigated using the CCSD(T) method with correlation consistent basis sets up to cc-pVQZ-PP. Both zero-point vibrational energies and spin-orbit coupling effects are found to be important. The potential energy surface for the Br + (H2O)2 reaction is compared with the related Br + H2O, Cl + (H2O)2 and F + (H2O)2 reactions.

    16. An analytical bond-order potential for carbon

      X. W. Zhou, D. K. Ward and M. E. Foster

      Article first published online: 27 MAY 2015 | DOI: 10.1002/jcc.23949

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      A new parameterization of Pettifor's bond order potential has been performed for carbon. The method captures the property trends of important carbon phases and passes stringent molecular dynamics simulation tests: not only allowing for the crystalline growth of graphene, graphite, and carbon nanotubes, but also the transformation of graphite to diamond at high pressure.

    17. The origins of the directionality of noncovalent intermolecular interactions#

      Changwei Wang, Liangyu Guan, David Danovich, Sason Shaik and Yirong Mo

      Article first published online: 25 MAY 2015 | DOI: 10.1002/jcc.23946

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      The block-localized wavefunction method, which can derive hypothetical structures without the charge transfer effect and conduct intermolecular energy decomposition analysis, is used to probe the origins of the directionality of weak noncovalent bonds. While the overall steric energy exhibits certain angular dependency, in all cases the charge transfer exhibits the strongest directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the bond covalency.

    18. A comparative computationally study about the defined m(II) pincer hydrogenation catalysts (m = fe, ru, os)

      Haijun Jiao, Kathrin Junge, Elisabetta Alberico and Matthias Beller

      Article first published online: 17 MAY 2015 | DOI: 10.1002/jcc.23944

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      DFT studies on the defined pincer-type catalysts M(H)2(CO)[NH(C2H4PiPr2)2] (1M) and M(H)(CO)[N(C2H4PiPr2)2] (2M) (M = Fe, Ru, Os) reveal remarkable differences in electronic structures and hydrogenation reactivity of nitriles, ester, and ketones. For acetonitrile hydrogenation, Fe- and Ru-based catalysts are best. For methyl benzoate hydrogenation and dehydrogenation of benzyl alcohol, Ru-based catalysts are best. In contrast, Os-based catalysts are least active.

    19. Inter- and intramolecular CF···c[DOUBLE BOND]o interactions on aliphatic and cyclohexane carbonyl derivatives

      Rodrigo A. Cormanich, Roberto Rittner, David O'Hagan and Michael Bühl

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23918

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      Prototypical inter- and intramolecular CF···C[DOUBLE BOND]O interactions are assessed computationally at the B3LYP-D3 level. The interactions are noticeable in intermolecular complexes 1, where they can amount to stabilizations around about 1 kcal mol, however, they are not strong enough to dominate conformational preferences in organofluorine derivatives such as 2 - 4.

    20. Theoretical and experimental investigation of crown/ammonium complexes in solution

      Andreas J. Achazi, Larissa K. S. von Krbek, Christoph A. Schalley and Beate Paulus

      Article first published online: 13 APR 2015 | DOI: 10.1002/jcc.23914

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      Gibbs energies of association inline image of monovalent crown/ammonium complexes in solution are calculated with DFT-D3(BJ) and the continuum solvation model COSMO-RS. For comparison, experimental data are obtained by isothermal titration calorimetry. Calculated and measured Gibbs energies of association inline image in solution agree well.

    21. From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg–Coxeter fullerenes up to C980

      Lukas N. Wirz, Ralf Tonner, Andreas Hermann, Rebecca Sure and Peter Schwerdtfeger

      Article first published online: 26 MAR 2015 | DOI: 10.1002/jcc.23894

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      A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C20.

    22. Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material

      Jose L. Mendoza-Cortes, Qi An, William A. Goddard III, Caichao Ye and Sergey Zybin

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23893

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      The two most stable isomers of Di-tetrazine-tetroxide (DTTO), c1 and c2, were used to predict the most stable polymorphs of DTTO. For the c1 isomer, the most stable polymorph has P212121 space group with a density of 1.96 g/cm3. Conversely, for the c2 isomer, the most stable polymorph has Pbca space group with a density of 1.98 g/cm3. These predicted densities are among the highest of current energetic materials.

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