Journal of Computational Chemistry

Cover image for Vol. 36 Issue 25

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. Full Papers

    1. Application of a BOSS—Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

      Jonah Z. Vilseck, Jakub Kostal, Julian Tirado-Rives and William L. Jorgensen

      Article first published online: 27 AUG 2015 | DOI: 10.1002/jcc.24045

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      The introduction of ab initio and density function methods into on-the-fly quantum mechanics and molecular mechanics (QM/MM) simulations is accomplished with a program interface whereby the Gaussian and BOSS software packages are tethered together. Improved agreement with experiment is found with MP2/CM5 QM/MM calculations compared with previously reported investigations using semiempirical methods.

    2. Computational assessment of electron density in metallo-organic nickel pincer complexes for formation of P[BOND]C bonds

      Joshua J. Eller and Karen Downey

      Article first published online: 25 AUG 2015 | DOI: 10.1002/jcc.24034

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      Nickel-based POCOP complexes are modeled with semi-empirical, Hartree-Fock, and density functional theory methods. DFT-B3LYP/6-31G* results suggest HOMO/LUMO electron densities anticipated to be suitable for catalytic hydrophosphination. These electron distributions are remarkably consistent across electron-donating, electron-neutral, and electron-withdrawing monodentate ligands, as well as with respect to alkyl vs aryl substituents on the diphosphinito ligand.

    3. d-AO spherical aromaticity in Ce6O8

      Xiaohu Yu, Artem R. Oganov, Ivan A. Popov and Alexander I. Boldyrev

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24049

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      A highly stable bare Ce6O8 cluster of a spherical shape is predicted using evolutionary algorithm and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that the bare Ce6O8 cluster exhibits a unique 6c[BOND]2e chemical bonding, thus, explaining its exotic geometry and stability.

    4. Aromaticity, quantum multimolecular polyhedra, and quantum QSPR fundamental equation

      Ramon Carbó-Dorca

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24021

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      A concise description of the Kekulé's historical origin of aromaticity and the current state of the field is given. Still, space is left for a discussion about the existence of aromaticity's quantum mechanical foundation. Quantum multimolecular polyhedra (QMP), based on density functions sets attached to QMP vertices, collective QMP distances, QSPR fundamental equation, and aromaticity descriptors are proposed as a way to construct an equation, able to estimate aromaticity via expectation values of Hermitian operators. Image created by Pep Camps, Girona.

    5. pKA in proteins solving the Poisson–Boltzmann equation with finite elements

      Ilkay Sakalli and Ernst-Walter Knapp

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24053

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      pKA computation of titratable residues in proteins by an electrostatic continuum approach relies on the precise construction of molecular surfaces separating solvent and protein volume. Traditional approaches use simple cubic grids for solving the Poisson–Boltzmann equation (PBE) by finite differences. Here, finite elements of triangles and tetrahedrons are used covering surface and volume, respectively. Thus, high precision is obtained with less grid points, reducing the CPU time for solving the PBE considerably.

    6. New density functional parameterizations to accurate calculations of electric field gradient variations among compounds

      Régis Tadeu Santiago and Roberto Luiz Andrade Haiduke

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24052

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      Standard exchange-correlation functionals are compared for the calculation of electric field gradient (EFG) changes at nuclear positions among compounds. Hybrid and long-range corrected versions are more accurate for this case. Thus, a reparameterization of PBE0 is proposed and evaluated by means of linear regressions between experimental nuclear quadrupole coupling constants and calculated EFGs. This modified functional, PBE0q, improves the description of transition metals, provides larger correlation coefficients, and decreases systematic EFG errors.

    7. Effects of the Ionization in the Tautomerism of Uracil: A Reaction Electronic Flux Perspective

      Al Mokhtar Lamsabhi, Soledad Gutiérrez-Oliva, Otilia Mó, Alejandro Toro-Labbé and Manuel Yáñez

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24054

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      The tautomerism of the ionized uracil compared with its neutral counterpart is monitored along the reaction coordinate through the reaction electronic flux that obeys a delicate balance between the acid and basic character of the atoms involved in the hydrogen transfer.

    8. SCC-DFTB parameters for simulating hybrid gold-thiolates compounds

      Arnaud Fihey, Christian Hettich, Jérémy Touzeau, François Maurel, Aurélie Perrier, Christof Köhler, Bálint Aradi and Thomas Frauenheim

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24046

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      We present a novel parametrization of the self-consistent charge density functional-based tight-binding scheme method to describe organic–inorganic materials where the metallic part is a gold aggregate. With an emphasis of the Au-S binding situation, we describe the electronic and energetic parameters of model Au3SCH3 and Au25SCH3 systems. The potential energy surface describing the adsorption of the molecule on the gold cluster is in very well agreement with reference density functional theory data.

    9. Parametrization of macrolide antibiotics using the force field toolkit

      Anna Pavlova and James C Gumbart

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24043

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      Force field parameters for macrolides a type of antibiotics that target the ribosome are optimized from first principles using Force Field Toolkit. Multiple approaches to parametrization are tested and evaluated by molecular dynamics simulations. It is shown that the final parameters improve the conservation of key interactions with the ribosome.

    10. Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost

      Arkajyoti Sengupta, Raghunath O. Ramabhadran and Krishnan Raghavachari

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24050

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      Highly accurate extrapolated coupled-cluster with single and double and perturbative triple (CCSD(T)) energies were obtained using the Connectivity-Based Hierarchy method for medium to large sized radicals. A careful assessment was performed with a robust test set comprised of 49 diverse radicals including challenging systems with high ring strain and spin contamination. The most expensive calculation is MP2 on the entire radical, thereby breaking the existing bottleneck for calculating CCSD(T) energies of large open-shell organic molecules.

    11. Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

      Samuel Genheden, Ulf Ryde and Pär Söderhjelm

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24048

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      The binding of two ligands to galectin-3 is used as a test case for exploring methods that combine alchemical perturbation with quantum-mechanical energy evaluations.

    12. Continuum in the X-Z---Y weak bonds: Z= main group elements

      Jyothish Joy, Anex Jose and Eluvathingal D. Jemmis

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24036

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      Red- and blue- shift in the X-Z bonds during the X-Z---Y complex formation has been analyzed. A continuum in the X-Z bond length is observed for various classes of weak bonds such as H-bonds, halogen-bonds, chalcogen-bonds, and pnicogen-bonds. The balance between negative hyperconjugation within the X-Z molecule and charge transfer from Y-group provides a working model to explain the observations. The definition of the continuum in the weak (X-Z---Y) interactions is profitably extended to include strong (Z-Y) chemical bonds as well.

    13. Relativistic state-specific multireference perturbation theory incorporating improved virtual orbitals: Application to the ground state single-bond dissociation

      Anirban Ghosh, Rajat K. Chaudhuri, Sudip Chattopadhyay and Uttam Sinha Mahapatra

      Article first published online: 13 AUG 2015 | DOI: 10.1002/jcc.24037

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      The relativistic second order state-specific multireference perturbation (SSMRPT) method with improved virtual orbitals is used to describe the full ground state energy surfaces of homonuclear alkali and halogen dimmers. This work widens the range of illustrated utility of the SSMRPT method.

    14. Electron transfer pathways in mixed-valence paracyclophane-bridged bis-triarylamine radical cations

      Martin Kaupp, Simon Gückel, Manuel Renz, Sascha Klawohn, Kolja Theilacker, Matthias Parthey and Christoph Lambert

      Article first published online: 12 AUG 2015 | DOI: 10.1002/jcc.24038

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      Electron transfer through the π-stacked faces of paracyclophane bridge units in bis-triarylamine mixed-valence systems has been studied using a previously established quantum-chemical protocol. Pseudo-meta and pseudo-para connected systems exhibit very similar electronic couplings and thermal electron-transfer barriers, explained by resonant hole transfer. Through-space electron transfer through the π-stack dominates over through-bond transfer through the linkers.

    15. Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning

      Juan M. Bello-Rivas and Ron Elber

      Article first published online: 12 AUG 2015 | DOI: 10.1002/jcc.24039

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      We compute, using the Milestoning method, the stationary flux (shown), the mean first passage time of Brownian trajectories, and the free energy (not shown) on a large ensemble of random energy landscapes with varying degrees of roughness and at a wide range of temperatures. We find two different behaviors: a diffusive regime for high temperatures and an Arrhenius-like regime for low temperatures.

    16. Modeling exact exchange potential in spherically confined atoms

      Sergei F. Vyboishchikov

      Article first published online: 10 AUG 2015 | DOI: 10.1002/jcc.24040

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      Local exchange potentials corresponding to the Hartree–Fock electron density have been obtained for a number of closed-shell confined atoms and ions. The potentials obtained and the resulting density was compared with those given by the Becke–Johnson (BJ) model potential. Introducing a scaling factor to the BJ potential allows improving the quality of the resulting density. The optimum scaling factor increases with decreasing confinement radius.

    17. Enhanced stability of the model mini-protein in amino acid ionic liquids and their aqueous solutions

      Guillaume Chevrot, Eudes Eterno Fileti and Vitaly V. Chaban

      Article first published online: 6 AUG 2015 | DOI: 10.1002/jcc.24042

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      The solvation of investigated mini-protein by amino acid ionic liquids is definitely favorable, as it better preserves its genuine structure than water. These liquids emerge as an interesting candidate solvent or cosolvent for a robust protein solvation, conservation, and storage.

    18. GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field

      Yun Ding, Ye Fang, Wei P. Feinstein, Jagannathan Ramanujam, David M. Koppelman, Juana Moreno, Michal Brylinski and Mark Jarrell

      Article first published online: 6 AUG 2015 | DOI: 10.1002/jcc.24031

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      Ligand molecular docking is routinely used to identify potential leads in modern drug discovery. GeauxDock, a new docking approach that builds on the ideas of ligand homology modeling, is described. GeauxDock features a descriptor-based scoring function and a mixed-resolution molecular representation. It also uses evolutionary constraints derived from related systems to improve docking accuracy; however, the scarcity of this information can be effectively compensated by increasing the contribution from physics-based energy components.

    19. Coupled folding and binding with 2D Window-Exchange Umbrella Sampling

      Alex Dickson, Logan S. Ahlstrom and Charles L. Brooks III

      Article first published online: 6 AUG 2015 | DOI: 10.1002/jcc.24004

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      Intrinsically disordered proteins often fold in conjunction with binding to their partner. Sampling configurations corresponding to the transition between unfolded and bound conformational ensembles presents a complex sampling problem. A two-dimensional sampling method, Window-Exchange Umbrella Sampling using contact fractions, is developed to address this issue.

  2. Software News and Updates

    1. New QM/MM implementation of the DFTB3 method in the gromacs package

      Tomáš Kubař, Kai Welke and Gerrit Groenhof

      Article first published online: 4 AUG 2015 | DOI: 10.1002/jcc.24029

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      Hybrid QM/MM computational methods are a valuable tool to study biomolecular systems. Several appealing methods and programs were combined: Gromacs as an efficient molecular dynamics package; PLUMED as a free energy and extended sampling engine; and DFTB3 as a fast and reliable quantum chemical method. The resulting framework is versatile and efficient, as illustrated in several applications.

    2. You have full text access to this OnlineOpen article
      Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

      Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot and Helmut Grubmüller

      Article first published online: 4 AUG 2015 | DOI: 10.1002/jcc.24030

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      Molecular dynamics (MD) simulation is a crucial tool for the study of (bio)molecules. MD simulations typically run for weeks or months even on modern compute clusters. Choosing the optimal hardware for carrying out these simulations can increase the trajectory output twofold or threefold. With GROMACS, the maximum amount of MD trajectory for a fixed budget is produced using nodes with a well-balanced ratio of CPU and consumer-class GPU resources.

  3. Full Papers

    1. Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds

      Manuel Hitzenberger and Thomas S. Hofer

      Article first published online: 3 AUG 2015 | DOI: 10.1002/jcc.24032

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      By identifying and applying the ideal parameter set for the representation of the Cα[BOND]Cβ bond of amino acids via a QM/MM link atom approach, the behavior of a fully QM-derived description can be mimicked exactly. Furthermore, the applicability of global parameters for different amino acids and the influence of protonation states, QM-methods and the chemical environment is discussed in detail.

    2. Electron density analysis of large (molecular and periodic) systems: A parallel implementation

      Silvia Casassa, Alessandro Erba, Jacopo Baima and Roberto Orlando

      Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24033

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      A parallel implementation is presented of a series of algorithms for the analysis of the wave-function of large molecular and periodic systems. The speedup of the calculation as a function of the number of processors used is documented also for Bader's topological analysis of the electron charge density in the case of the crambin crystallized protein.

  4. Erratum

    1. You have free access to this content
      Erratum: “A solvation-free-energy functional: A reference-modified density functional formulation” [J. Comput. Chem. 2015, 36, 1359–1369]

      Tomonari Sumi, Ayori Mitsutake and Yutaka Maruyama

      Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24035

      This article corrects:

      A solvation-free-energy functional: A reference-modified density functional formulation

      Vol. 36, Issue 18, 1359–1369, Article first published online: 31 MAY 2015

  5. Full Papers

    1. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

      Riccardo Petraglia, Adrien Nicolaï, Matthew D. Wodrich, Michele Ceriotti and Clemence Corminboeuf

      Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24025

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      Replica-exchange molecular dynamics (REMD) is combined with density functional tight binding (DFTB) and applied to organic chemical problems. REMD@DFTB permits thorough exploration of the potential energy surface and reveals new insights and chemistry that likely would be missed using static electronic structure computations.

    2. Bis(azulene) “submarine” metal dimer sandwich compounds (C10H8)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations

      Hongyan Wang, Hui Wang, R. Bruce King and Henry F. Schaefer III

      Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24013

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      The lowest energy (C10H8)2M2 submarine sandwich structures of the early transition metals Ti, V, Cr, and Mn have the azulene units functioning as bis(pentahapto) ligands to each metal atom. For the later transition metals Fe, Co, and Ni the lowest energy (C10H8)2M2 structures contain pentahapto-trihapto azulene ligands with an uncomplexed C[DOUBLE BOND]C double bond

    3. A deeper insight into strain for the sila-bi[6]prismane ( Si18H12) cluster with its endohedrally trapped silicon atom, Si19H12

      Holger Vach, Lena V. Ivanova, Qadir K. Timerghazin, Fatme Jardali and Ha-Linh Thi Le

      Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24009

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      Formation of overcoordinated silicon hydride nanoclusters with nontetrahedral atomic configurations is the result of a self-assembly process in a silane/hydrogen plasma reactor operated close to dusty plasma conditions as shown in our ab initio molecular dynamics simulations. Both symmetric and asymmetric Si19H12 isomers are ultrastable and exhibit aromatic-like behavior. Ultrastability results from extensive electron delocalization that is induced by electron-deficient bonds.

    4. Strain in nonclassical silicon hydrides: An insight into the “ultrastability” of sila-bi[6]prismane (Si18H12) cluster with the endohedrally trapped silicon atom, Si19H12

      Grygoriy A. Dolgonos and Koshka Mekalka

      Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24014

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      Formation of a tubular silicon hydride nanocluster bearing nontetrahedral atomic configurations requires significant amount of energy. As in the case of recently proposed tubular “ultrastable” sila-bi[6]prismane with one encaged silicon atom, Si19H12, the energy difference with respect to the tetrahedral reference molecules (called “strain energy”) is high enough to cause isomerization or fragmentation reactions. Consequently, this isomer cannot be considered as “ultrastable” nor as aromatic. Two new low-lying Si19H12 isomers have been proposed.

    5. Linear, planar, and tubular molecular structures constructed by double planar tetracoordinate carbon D2h C2(BeH)4 species via hydrogen-bridged [BOND]BeH2Be[BOND] bonds

      Xue-Feng Zhao, Haixia Li, Cai-Xia Yuan, Yan-Qin Li, Yan-Bo Wu and Zhi-Xiang Wang

      Article first published online: 22 JUL 2015 | DOI: 10.1002/jcc.24018

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      D2h C2(BeH)4 has been computationally characterized to be a species featuring double planar tetracoordinate carbons. Because of the electron deficiency nature of the BeH bonds, the species can serves as building blocks to construct nano-size structures via the intermolecular hydrogen-bridged -BeH2Be- bonds (HBB), as exemplified by our reported molecular chains, planar sheets, and tubes. Formation of a HBB is exothermic by more than 30.0 kcal/mol, implying a possibility to synthesize these nano-size molecules.

  6. Software News and Updates

    1. AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites

      Arina Afanasyeva, Sergey Izmailov, Michel Grigoriev and Michael Petukhov

      Article first published online: 22 JUL 2015 | DOI: 10.1002/jcc.24022

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      AquaBridge is a tool for seeking structural water molecules within protein binding pockets, developed as a module for the ICM-Pro software package for molecular modeling. This utility is based on Monte-Carlo energy minimization algorithms and selects the water molecule conformations that can form “water bridges” by calculating the values of the total energy of a modeled water molecule and of the number of hydrogen bonds that it can form between the target protein and the ligand.

  7. Full Papers

    1. Projected CAP/SAC-CI method with smooth Voronoi potential for calculating resonance states

      Masahiro Ehara, Ryoichi Fukuda and Thomas Sommerfeld

      Article first published online: 21 JUL 2015 | DOI: 10.1002/jcc.24010

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      The complex absorbing potential (CAP)/symmetry-adapted cluster-configuration interaction method with a smooth Voronoi potential (example shown in the inset of the figure) has been developed. The method is applied to the π* resonance states of small- to medium-size molecules with double-bond and heteroaromatic structures. The corrected η-trajectory provides a stable resonance energy and width for all the resonances studied. Generally, the stabilization of the trajectories is clearer for the CAPs with relatively large cavity size.

    2. Ab initio/GIAO-CCSD(T) 13C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6 H13+ and C7 H15+

      George A. Olah, G. K. Surya Prakash and Golam Rasul

      Article first published online: 20 JUL 2015 | DOI: 10.1002/jcc.24019

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      The rearrangement pathways of the equilibrating tertiary carbocations such as 2,3-dimethyl-2-butyl cation were calculated by the ab initio/GIAO-CCSD(T) method.

    3. Molybdatricarbaboranes as examples of isocloso metallaborane deltahedra with three carbon vertices

      Alexandru Lupan and R. Bruce King

      Article first published online: 16 JUL 2015 | DOI: 10.1002/jcc.23995

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      The lowest energy CpMoC3Bn−4Hn−1 (n = 8, 9, 10, 11) structures are based on isocloso or similar MoC3Bn−4 deltahedra with the molybdenum atom at the unique degree 6 vertex, the carbon atoms at the lowest degree vertices (typically degree 4 vertices), no pairs of adjacent carbon atoms (i.e., no C-C edges), and the maximum number of Mo-C edges.

    4. Self-guided Langevin dynamics via generalized Langevin equation

      Xiongwu Wu, Bernard R. Brooks and Eric Vanden-Eijnden

      Article first published online: 16 JUL 2015 | DOI: 10.1002/jcc.24015

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      Self-guided Langevin dynamics (SGLD) is a molecular simulation method that enhances conformational search and sampling via acceleration of the low frequency motions of the molecular system. To eliminate the need of reweighting, the SGLD-generalized Langevin equation (GLE) method is proposed, which samples exact ensemble distribution and has enhanced conformational sampling. Using an alanine dipeptide and liquid argon, SGLD-GLE can produce correct NVT and NPT ensemble distributions while achieving enhanced conformational sampling.

    5. Noncatalytic bromination of benzene: A combined computational and experimental study

      Andrey V. Shernyukov, Alexander M. Genaev, George E. Salnikov, Henry S. Rzepa and Vyacheslav G. Shubin

      Article first published online: 14 JUL 2015 | DOI: 10.1002/jcc.23985

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      The noncatalytic bromination of benzene is shown experimentally to require high concentrations of bromine, proceeding at ambient temperatures to form predominantly bromobenzene and exhibiting a measured inverse deuterium isotope effect. Computed transition states models reveal an ionic concerted but asynchronous transition state involving a Br7 or Br9 cluster which acts as a Br+ donor, as a proton base and as a stabilizing arm forming weak dispersion interactions with benzene C[BOND]H hydrogens.

    6. Effect of methylation on relative energies of tautomers and on the intramolecular proton transfer barriers of protonated nitrosamine: A MR-CISD study

      Railton Barbosa de Andrade, Ezequiel Fragoso Vieira Leitão, Miguel Angelo Fonseca de Souza, Elizete Ventura and Silmar Andrade do Monte

      Article first published online: 14 JUL 2015 | DOI: 10.1002/jcc.24007

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      Nitrosamines have three protonation sites. The barrier heights associated with the proton transfer among these sites on protonated nitrosamine and N,N-dimethylnitrosamine were studied by highly correlated electronic structure calculations. Methylation of nitrosamine impacted significantly the relative energies of both the species protonated on the amine nitrogen atom and that of the transition state associate with proton transfer between the amine nitrogen and oxygen atoms.

    7. Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD

      Kęstutis Aidas, Kiril Lanevskij, Rytis Kubilius, Liutauras Juška, Daumantas Petkevičius and Pranas Japertas

      Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23998

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      Aqueous acidities of a family of primary benzenesulfonamides were computed using density functional theory and SMD model. The predicted inline image values compare to experimental data very well when a proton exchange thermodynamic cycle is used. It was found necessary to perform geometry optimization of neutral and deprotonated species in vacuum and solution separately as different conformations are stabilized in these two phases.

  8. Full PaperS

    1. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method

      Davide Branduardi, Fabrizio Marinelli and José D. Faraldo-Gómez

      Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23991

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      The mechanisms of isomerization of ATP-Mg2+ in solution are examined with three complementary enhanced-sampling simulation methods. The recently developed String Method with Optimal Molecular Alignment is used to identify and characterize the minimum free-energy paths for the major conformational transitions of the complex, in a 48-dimensional space. This analysis reveals the driving forces controlling these isomerization mechanisms at single-atom resolution.

  9. Full Papers

    1. Structure and stability of noble gas bound EX3+ compounds (E = C, Ge, Sn, Pb; X = H, F, Cl, Br)

      Sudip Pan, Diego Moreno, Sreyan Ghosh, Pratim K. Chattaraj and Gabriel Merino

      Article first published online: 1 JUL 2015 | DOI: 10.1002/jcc.23986

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      Making a bond: inline image (E = C-Pb; X = H, F-Br) could bind noble gas atoms, particularly Ar to Rn, quite effectively. The π back-bonding causing X [RIGHTWARDS ARROW] E electron transfer plays an important role in deciding their noble gas binding ability.

    2. On the inclusion of post-MP2 contributions to double-Hybrid density functionals

      Bun Chan, Lars Goerigk and Leo Radom

      Article first published online: 1 JUL 2015 | DOI: 10.1002/jcc.23972

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      Double-hybrid density functionals (DHDFs) use MP2-type correlation to significantly improve the accuracy of DFT approximations. The inclusion of higher-order MP3, MP4, CCSD, and CCSD(T) terms is explored. DHDFs are not as systematically improvable as their wave-function counterparts, and the use of MP2 represents a near-optimal balance of accuracy and efficiency. These findings provide valuable insights for future research in DHDF development.

    3. 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.

    4. 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.

    5. 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.

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    10. 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.

    11. 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.

    12. 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.

    13. 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.

    14. 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.

    15. 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.

    16. 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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