Journal of Computational Chemistry

Cover image for Vol. 37 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: 3.589

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. Software News and Updates

    1. sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections

      Md Tamjidul Hoque, Yuedong Yang, Avdesh Mishra and Yaoqi Zhou

      Article first published online: 5 FEB 2016 | DOI: 10.1002/jcc.24298

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      Accurate energy function is needed for predicting protein structure from its sequence. Instead of the sole statistical information, extracted from protein structure database to build an energy-function, a sequence-specific statistical energy function, if formulated, can be more accurate. Thus the statistical potentials with sequence specific matching scores of predicted and model structural properties including predicted main-chain torsion angles and accessible surface area are optimally combined to develop better energy function.

  2. Full Papers

    1. Additive CHARMM force field for naturally occurring modified ribonucleotides

      You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. MacKerell Jr. and Lennart Nilsson

      Article first published online: 3 FEB 2016 | DOI: 10.1002/jcc.24307

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      All naturally occurring modified ribonucleotides were systematically parametrized in this additive CHARMM force field. This will allow for computational investigation of how specific modifications influence RNA structures, providing insight on structural stability and binding affinity of RNA complexes, such as transfer RNA participating in decoding interactions on the ribosome.

  3. Software News and Updates

    1. Cuby: An integrative framework for computational chemistry

      Jan Řezáč

      Article first published online: 3 FEB 2016 | DOI: 10.1002/jcc.24312

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      Cuby is a software framework that provides unified access to a wide range of computational methods by interfacing external software and implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows.

  4. Full Papers

    1. Focused grid-based resampling for protein docking and mapping

      Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda and Dima Kozakov

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24273

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      The fast Fourier transform (FFT) algorithm enables extremely fast evaluation of energy functions, and hence has been used with great success for protein-protein docking and for the characterization of the binding properties of proteins by docking small probe molecules. While both applications of FFT involve global systematic sampling, the same algorithm can also be used to refine the results by focused resampling on the regions of interest using finer grids or by retaining more structures.

    2. Structures and energetics of complexation of metal ions with ammonia, water, and benzene: A computational study

      Bhaskar Sharma, Y. Indra Neela and G. Narahari Sastry

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24288

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      Understanding metal ions with amines, water and aromatic systems is of outstanding importance in biology. An exhaustive computational study has been carried out up to CCSD(T)/def2-TZVP level on a number of main group and transition metal ion interaction with benzene, water and ammonia. Density functional theory based symmetry adapted perturbation theory(DFT-SAPT) analysis has been performed to estimate the contribution of various energy components for the binding energy.

    3. The catalytic effect of the NH3 base on the chemical events in the caryolene-forming carbocation cascade

      Daniela E. Ortega, Quynh Nhu N. Nguyen, Dean J. Tantillo and Alejandro Toro-Labbé

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24294

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      Caryolene formation occurs asynchronously in a concerted way through carbocationic rearrangements involving the generation of a secondary or a tertiary carbocation, depending on the absence or in the presence of NH3. Both mechanisms are analyzed within the general framework of the reaction force. The reaction force constant is used to gain insights into the synchronicity of the mechanisms and the reaction electronic flux aids characterization of the electronic activity taking place during reaction.

    4. Fast search algorithms for computational protein design

      Seydou Traoré, Kyle E. Roberts, David Allouche, Bruce R. Donald, Isabelle André, Thomas Schiex and Sophie Barbe

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24290

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      Computational protein design (CPD) through Cost Function Networks (CFN) provides important speedups to explore large sequence-conformation spaces and provably identifies the sequence with the conformation of optimal stability (Global Minimum Energy Conformation, GMEC). In addition to quickly finding the GMEC of highly complex protein design problems, CFN-based methods also enable the efficient enumeration of suboptimal solutions. These approaches offer an attractive alternative to the usual CPD methods and were implemented in the well-established CPD package Osprey.

    5. A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides

      Xiao Ru, Ce Song and Zijing Lin

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24311

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      The structural information of amino acids and dipeptides is carefully analyzed. An improved GA algorithm with a new encoding strategy utilizing the structural information is proposed. Technical improvements are also made to minimize the possibility of premature convergence of the GA search. Applications to representative amino acids, dipeptides and tripeptide with complicated side chains confirm that the new GA scheme is both efficient and reliable for providing the most complete conformational coverage of the molecules.

  5. Software News and Updates

    1. SIMPRE1.2: Considering the hyperfine and quadrupolar couplings and the nuclear spin bath decoherence

      Salvador Cardona-Serra, Luis Escalera-Moreno, José J. Baldoví, Alejandro Gaita-Ariño, Juan M. Clemente-Juan and Eugenio Coronado

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24313

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      SIMPRE1.2 goes beyond Single Ion Magnet Magnetic Prediction. By considering the coupling between the electronic and the nuclear spins of the lanthanoid ion, it now provides a better description of the low-energy levels. By calculating dipolar interactions, it estimates the quantum decoherence created by the environmental nuclear spins in the crystal. In sum, it is now useful as a tool to provide a first inexpensive description of lanthanoid complexes as molecular spin qubits.

  6. Corrigendum

    1. You have free access to this content
      Corrigendum: Ion strength limit of computed excess functions based on the linearized poisson–boltzmann equation

      Dan Fraenkel

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24302

      This article corrects:

      Ion strength limit of computed excess functions based on the linearized Poisson–Boltzmann equation

      Vol. 36, Issue 31, 2302–2316, Article first published online: 23 OCT 2015

  7. Full Papers

    1. Sequence-based prediction of protein–peptide binding sites using support vector machine

      Ghazaleh Taherzadeh, Yuedong Yang, Tuo Zhang, Alan Wee-Chung Liew and Yaoqi Zhou

      Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24314

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      Protein–peptide interactions play vital roles in cellular processes. Experimental determination of protein–peptide interaction, however, is difficult and costly due to peptide flexibility and low binding affinity. Thus, making “educated” computational prediction prior to experimental studies is necessary. All existing computational techniques infer peptide binding sites from protein structures although the structures for the majority of proteins are unknown. Here the first sequence-based method is developed and its accuracy is shown comparable to or better than existing structure-based techniques.

    2. Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR

      Tiziana Ginex, Jordi Muñoz-Muriedas, Enric Herrero, Enric Gibert, Pietro Cozzini and F. J. Luque

      Article first published online: 26 JAN 2016 | DOI: 10.1002/jcc.24305

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      A novel set of hydrophobic descriptors derived from quantum mechanical-self consistent reaction field IEF/PCM-MST calculations is described within the framework of the hydrophobic pharmacophore (HyPhar) method. The combination of electrostatic and nonelectrostatic components of the octanol/water partition coefficient yields pharmacophoric models fully comparable with the predictive potential of standard 3D-QSAR techniques. HyPhar descriptors provide a novel approach to structure–activity relationships.

    3. Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD)

      Xin Zhang, Yuan Zhao, Honggao Yan, Zexing Cao and Yirong Mo

      Article first published online: 26 JAN 2016 | DOI: 10.1002/jcc.24306

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      Yeast cytosine deaminase (yCD) is an enzyme responsible for the activation process of anticancer drugs, and efforts have been put to understand its structure and functions. Computational simulations were performed in order to elucidate how yCD catalyzes the hydrolytic deamination of cytosine to uracil. While the computations show that Glu64 serves as the proton shuttle in various reaction steps, the decisive step was identified as the release of uracil from its trapped state.

    4. Structure and electrochemical properties for complexes of nitrocompounds with inorganic ions: A theoretical approach

      Liudmyla K. Sviatenko, Leonid Gorb, Frances C. Hill, Danuta Leszczynska and Jerzy Leszczynski

      Article first published online: 26 JAN 2016 | DOI: 10.1002/jcc.24310

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      Redox properties of nitrocompounds, such as 2,4,6-trinitrotoluene, 2,4-dinitrotoluene, 2,4-dinitroanisole, and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one, are of considerable interest because these compounds may be encountered as groundwater and soil contaminants and redox reactions play a central role in their environmental fate or cleanup under biotic and abiotic conditions. The influence of complexation with common inorganic ions, which can be found in soil and water, on the ability of the nitrocompounds to undergo redox transformations was investigated.

    5. Density functional theory of the CuA-like Cu2S2 diamond core in Cu 2II(NGuaS)2Cl2

      M. Witte, U. Gerstmann, A. Neuba, G. Henkel and W. G. Schmidt

      Article first published online: 24 JAN 2016 | DOI: 10.1002/jcc.24289

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      Density functional theory calculations for the recently reported dicopper thiolate species Cu2(NGuaS)2Cl2 are performed to analyze the magnetic coupling and electronic structure of the CuA-like Cu2S2 diamond core. For both hybrid and semilocal functionals, the neutral complex provides an electronic structure with broken symmetry character. Within the antiferromagnetically coupled [Cu2+…Cu2+] Cu-site, the coupling is mainly driven by super exchange interaction within the Cu2S2 diamond core (figure).

    6. A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices

      Yasushige Yonezawa

      Article first published online: 24 JAN 2016 | DOI: 10.1002/jcc.24296

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      A simple and efficient method that predicts natural transition pathways between two endpoint states of an allosteric protein is proposed. Multiple iterative molecular dynamics simulations guided by different distance matrices provide an approach for identifying states involving concerted slow motion.

    7. Reduced-cost sparsity-exploiting algorithm for solving coupled-cluster equations

      Jiri Brabec, Chao Yang, Evgeny Epifanovsky, Anna I. Krylov and Esmond Ng

      Article first published online: 24 JAN 2016 | DOI: 10.1002/jcc.24293

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      By sparsifying the amplitude correction to approximate solutions to the coupled-cluster amplitude equations, the number of operations in the tensor contraction performed in the inexact Newton algorithm can be significantly reduced. Nearly, the same convergence rate is maintained even when roughly 90% of nonzero elements in the amplitude correction are set to zero (i.e., z = 10%).

    8. Wave-function frozen-density embedding: Approximate analytical nuclear ground-state gradients

      Johannes Heuser and Sebastian Höfener

      Article first published online: 24 JAN 2016 | DOI: 10.1002/jcc.24301

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      We report analytical nuclear subsystem gradients for wave-function-based frozen-density embedding (FDE), using density fitting and resolution of the identity methods. The new method allows for efficient geometry optimizations of single molecules surrounded by explicit atomistic surroundings, outperforming conventional RICC2 schemes already for small numbers of environment molecules.

    9. Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

      Bachir Aoun

      Article first published online: 22 JAN 2016 | DOI: 10.1002/jcc.24304

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      fullrmc is a Reverse Monte Carlo package designed with artificial intelligence to create atomic and molecular models from a set of experimental data and constraints. fullrmc class hierarchy and implementation are quite innovative, allowing easy setup for almost any kind of reverse modeling engine for all sorts of applications. Concepts such as Group, GroupSelector, and MoveGenerator and RMC modeling modes (recurring, refining, and exploring) stand out from all other existing RMC software and packages.

    10. Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

      Evan J. Arthur and Charles L. Brooks III

      Article first published online: 20 JAN 2016 | DOI: 10.1002/jcc.24280

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      A new algorithm for the Generalized Born model with a Simple sWitching function (GBSW) uses an efficient approximation of the Poisson–Boltzmann theory to accelerate mapping on GPU platforms. Depending on the system size and nonbonded force cutoffs, the new algorithm offers speed increases of 1–2 orders of magnitude over previous implementations while maintaining similar levels of accuracy. The speed enhancements make accessible folding studies of peptides and potentially small proteins.

    11. Recasting wave functions into valence bond structures: A simple projection method to describe excited states

      Julien Racine, Denis Hagebaum-Reignier, Yannick Carissan and Stéphane Humbel

      Article first published online: 20 JAN 2016 | DOI: 10.1002/jcc.24267

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      A bridge was formulated between molecular orbitals and valence bonds wave functions, for both ground and excited states. The approach is shown on calculations that embed multi references and the configuration interaction of singles and double excitations. The overlap is used to assess that the VB description corresponds indeed to the MO's. The cases of allyl (cation or radical) and of the V state of ethene are used.

    12. Proton solvation in protic and aprotic solvents

      Emanuele Rossini and Ernst-Walter Knapp

      Article first published online: 19 JAN 2016 | DOI: 10.1002/jcc.24297

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      Proton affinities, electrostatic energies of salvation, and pKA values of a reference set of organic molecules are computed combining quantum chemical and electrostatic approaches. Proportional to the free energy of proton dissociation, the pKA calculation is strongly dependent on the free energy of proton solvation. Such energy is here determined with high accuracy in order to obtain the best match between measured and computed pKA values in acetonitrile, methanol, water, and dimethyl sulfoxide.

    13. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields

      Eric G. Kratz, Alice R. Walker, Louis Lagardère, Filippo Lipparini, Jean-Philip Piquemal and G. Andrés Cisneros

      Article first published online: 18 JAN 2016 | DOI: 10.1002/jcc.24295

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      Hybrid QM/MM simulations have become a popular technique in computational chemistry and biology. However, many QM/MM software packages are limited to point-charge based MM potentials. We present a new software package, LICHEM, which performs multipolar and polarizable QM/MM simulations via unmodified QM and MM packages. Our calculations highlight the key features of LICHEM, the importance of including polarization in the MM region, and the polarizable pseudo-bond method.

  8. Rapid Communication

    1. Temperature dependence of the transport of single-file water molecules through a hydrophobic channel

      Jiaye Su and Keda Yang

      Article first published online: 17 JAN 2016 | DOI: 10.1002/jcc.24303

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      Molecular dynamics simulations were used to study the temperature effect on the transport of single-file water molecules through a hydrophobic channel. Of particular interest is that the water flow and average translocation time both exhibit exponential relations with temperature.

  9. Full Papers

    1. Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

      Simon W.L. Hogan and Tanja van Mourik

      Article first published online: 15 JAN 2016 | DOI: 10.1002/jcc.24264

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      Density functional theory calculations reveal competition between halogen- and hydrogen-bonding interactions in complexes of halogenated methyluracil and water.

    2. Possible mechanism of BN fullerene formation from a boron cluster: Density-functional tight-binding molecular dynamics simulations

      Y. Ohta

      Article first published online: 8 JAN 2016 | DOI: 10.1002/jcc.24287

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      Rapid formation of BN fullerene from a B36 cluster at 2000 K is simulated using the quantum mechanical molecular dynamics based on the density-functional tight-binding method. During the 200 ps simulations, N atoms are periodically supplied around the amorphous B cluster. The supplied N atoms are promptly incorporated into the B cluster. Continual atomic rearrangement of constituent B and N atoms and sporadic N2 dissociation lead to the formation of an sp2 single-shelled BN cluster.

    3. Combining classical molecular dynamics and quantum mechanical methods for the description of electronic excitations: The case of carotenoids

      Ingrid G. Prandi, Lucas Viani, Oliviero Andreussi and Benedetta Mennucci

      Article first published online: 8 JAN 2016 | DOI: 10.1002/jcc.24286

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      An effective strategy is presented to describe the structural effects on electronic excitations of carotenoids by combining specifically parameterized force field and TDDFT calculations. The important structural properties described by the new force field are in very good agreement with quantum mechanical reference values. This increased accuracy in the simulation of the structural fluctuations is also reflected in the description of excited states.

    4. Modeling emission features of salicylidene aniline molecular crystals: A QM/QM’ approach

      Davide Presti, Frédéric Labat, Alfonso Pedone, Michael J. Frisch, Hrant P. Hratchian, Ilaria Ciofini, Maria Cristina Menziani and Carlo Adamo

      Article first published online: 5 JAN 2016 | DOI: 10.1002/jcc.24282

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      This study applies a new computational protocol, relying on the use of electrostatic embedding derived from QM/QM’ ONIOM calculations, to simulate the effect of the crystalline environment on the emission spectra of molecular crystals to the β-form of salicylidene aniline.

    5. Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes

      Christine-Andrea Roth, Tom Dreyfus, Charles H. Robert and Frédéric Cazals

      Article first published online: 29 DEC 2015 | DOI: 10.1002/jcc.24256

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      Hybrid is an exploration algorithm combining the abilities of (1) basin-hopping to locate local minima via energy minimization and (2) rapidly growing random trees to explore yet unexplored regions.

    6. A mixed DFT-MD methodology for the in silico development of drug releasing macrocycles. Calix and thia-calix[N]arenes as carriers for Bosutinib and Sorafenib

      Rodrigo Galindo-Murillo, Luis Enrique Aguilar-Suárez and Joaquín Barroso-Flores

      Article first published online: 29 DEC 2015 | DOI: 10.1002/jcc.24281

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      Suitable calixarene-based drug delivery agents for Bosutinib and Sorafenib -both used in the treatment of chronic myeloid leukemia- were computationally designed through a mixed QM/DM methodology. The hydrophobic cavity of these macrocycles protect these drugs against non-target binding sites while allowing their release. Interaction energies at the B97D/6-31G(d,p) level of theory were calculated and +100 ns molecular dynamics simulations were run in order to assess the drug insertion and release processes.

    7. Toward the identification of molecular cogs

      Maciej Dziubiński and Bogdan Lesyng

      Article first published online: 23 DEC 2015 | DOI: 10.1002/jcc.24275

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      The potential of mean force (PMF) used in studying structural transformations of molecular systems typically does not convey the information which parts of the system propel these transformations. We propose a method of analyzing data from constrained molecular dynamics simulations (cMD) that identifies molecular cogs—groups of atoms which push the transformation forward/backward along a collective variable. Contributions of these molecular cogs are then incorporated into a PMF-like graph.

    8. Effective protein conformational sampling based on predicted torsion angles

      Yuedong Yang and Yaoqi Zhou

      Article first published online: 23 DEC 2015 | DOI: 10.1002/jcc.24285

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      The size dependence of sampling effectiveness is examined using the root-mean-squared distance from the target native structure. Using protein targets up to 460 residues from the critical assessment of structure prediction techniques, we show that the accuracy of the sampled near native structures is relatively independent of protein size but strongly depends on errors in the predicted torsion angles. © 2015 Wiley Periodicals, Inc.

    9. On the zeroth-order hamiltonian for CASPT2 calculations of spin crossover compounds

      Sergi Vela, Maria Fumanal, Jordi Ribas-Ariño and Vincent Robert

      Article first published online: 23 DEC 2015 | DOI: 10.1002/jcc.24283

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      The IPEA parameter used within CASPT2 is benchmarked for its use in the calculation of adiabatic energy gaps of Spin Crossover compounds. The importance of the recently discovered error in the ANO-RCC basis set contraction for carbon atoms is also unveiled.

    10. Effects of an electric field on interaction of aromatic systems

      Il Seung Youn, Woo Jong Cho and Kwang S. Kim

      Article first published online: 23 DEC 2015 | DOI: 10.1002/jcc.24284

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      The effect of uniform electric field on intermolecular interaction between aromatic molecules (benzene, hexafluorobenzene, and pyrene) and an argon atom are investigated by ab initio and DFT methods. We found that the direction of zero-field dipole moment by mutual polarization mainly determines the field effect. The post-HF and PBE0-based methods yield quantitatively correct result, while the vdW-DF2 functional sometimes shows artifacts due to its sensitivity to the quality of real space electron density.

    11. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM

      Jessica K. Gagnon, Sean M. Law and Charles L. Brooks III

      Article first published online: 21 DEC 2015 | DOI: 10.1002/jcc.24259

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      Proteins exist in an inter-converting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a challenge. Adding receptor flexibility improves protein-ligand docking within the CDOCKER approach. By integrating atomically detailed side chain flexibility with grid-based docking methods, efficiency is maintained while protein and ligand configurations explore conformational space simultaneously.

    12. The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone-receptor complex

      Roman Osman, Mihaly Mezei and Stanislav Engel

      Article first published online: 21 DEC 2015 | DOI: 10.1002/jcc.24276

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      Understanding the molecular mechanism of the formation of protein complexes may shed light on the organization and functioning of biological networks, and assist in the structure-based rational design of drugs targeting protein-protein interactions. Protein surfaces constituting the interfaces of protein-protein complexes are characterized by the presence of static areas—“stability patches.” The dynamic properties of protein surfaces are discussed, with particular attention to the presence of interfacial stability patches that may facilitate the formation of protein complexes.

    13. Real-time feedback from iterative electronic structure calculations

      Alain C. Vaucher, Moritz P. Haag and Markus Reiher

      Article first published online: 17 DEC 2015 | DOI: 10.1002/jcc.24268

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      Interactive reactivity exploration based on iterative electronic structure methods faces an unavoidable incompatibility of unpredictable execution times of such calculations and of the necessity for feedback to be delivered in fixed and short time intervals. This article proposes a mediator strategy involving surrogate potentials to provide real-time feedback that allows for an effective and reliable immersion of a user into the exploration process.

    14. Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH

      Leebyn Chong, Fikret Aydin and Meenakshi Dutt

      Article first published online: 17 DEC 2015 | DOI: 10.1002/jcc.24277

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      The implicit solvent Dry Martini coarse-grained model is applied to polyamidoamine (PAMAM) dendrimers. Through size and shape characterizations of generations 1–7 for various pH environments, good agreement is obtained from explicit solvent, and all-atom models, while expending significantly less computational resources. In addition, counter-ion distributions adequately describe the charge distributions of PAMAM caused by different pH environments.

    15. A new algorithm for construction of coarse-grained sites of large biomolecules

      Min Li, John Z. H. Zhang and Fei Xia

      Article first published online: 15 DEC 2015 | DOI: 10.1002/jcc.24265

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      The multiscale simulation of biomolecules requires a rigorous definition of their coarse-grained (CG) representation. A stepwise optimization imposed with the boundary-constraint (SOBC) algorithm is developed to construct the CG sties of large biomolecules. The graph shows a four-site CG model of G-actin monomer derived from SOBC.

    16. Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range-separated density functional theory

      Haitao Sun, Shian Zhang, Cheng Zhong and Zhenrong Sun

      Article first published online: 15 DEC 2015 | DOI: 10.1002/jcc.24266

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      A fundamental understanding of the excited electronic states and photophysical properties of DNA bases and duplex has its great biological importance. In this work, excited states of various DNA base dimers and tetramers including Watson-Crick H-bonding and stacking interactions have been investigated by time-dependent density functional theory (TDDFT), using non-empirically tuned rangeseparated functionals. Their results are comparable to high-level coupled-cluster (CC) methods and significantly outperform their non-tuned version and widely-used B3LYP functional.

    17. How the substituents in corannulene and sumanene derivatives alter their molecular assemblings and charge transport properties?—A theoretical study with a dimer model

      Xi Chen, Fu-Quan Bai, Yongan Tang and Hong-Xing Zhang

      Article first published online: 15 DEC 2015 | DOI: 10.1002/jcc.24271

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      Substituent effects, intermolecular interactions, and charge transport properties of a series of corannulene and sumanene derivatives were investigated by DFT to provide a better understanding of the structure-property relationships for substituted corannulenes and sumanenes. The intermolecular interaction energies and potential energy surfaces of the dimers were also calculated, showing several local energy minimum values and demonstrating possible dimer structures.

    18. You have free access to this content
      4f fine-structure levels as the dominant error in the electronic structures of binary lanthanide oxides

      Bolong Huang

      Article first published online: 15 DEC 2015 | DOI: 10.1002/jcc.24272

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      The ground-state 4f fine-structure levels in the intrinsic optical transition gaps between the 2p and 5d orbitals of lanthanide sesquioxides (Ln2O3, Ln = La…Lu) were calculated by a two-way crossover search for the U parameters for DFT+U calculations. The diagram shows the influence of fully filled and partially filled localized orbitals through local-ranged and nonlocal-ranged perturbations. The difference of the two-way self-consistent output Hubbard U converges to zero for fully filled orbitals, while a rigid difference is found between the perturbations of partially filled orbitals due to the local screening of empty components of such orbitals.

    19. Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors

      Pin-Chih Su and Michael E. Johnson

      Article first published online: 15 DEC 2015 | DOI: 10.1002/jcc.24274

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      The article highlights the improved thermodynamic integration (TI) approach by using the new Amber molecular dynamics engine, pmemd, and the optimized MD simulation lengths, number of intermediate and transition states. The new TI approach is shown to be highly accurate and affordable in the tested system, the bacterial FabI enzyme with benzimidazole inhibitors. The results also provide structure-activity relationship insights and suggest that the para-halogen in benzimidazole compounds form a weak halogen bond with FabI.

    20. Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution

      Ryuhei Harada, Tomotake Nakamura and Yasuteru Shigeta

      Article first published online: 27 NOV 2015 | DOI: 10.1002/jcc.24255

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      Biologically rare events play important roles in understanding functions. To computationally reproduce them, Outlier FLOODing (OFLOOD) method is powerful, in which sparse distributions of biological states are detected as outliers and intensively resampled by MD simulations. As an extension, sparsity-weighted OFLOOD method is newly proposed, in which a hierarchical clustering defines ranks of outliers. Accordingly to the ranks, the confirmational resampling from outliers is performed, accerlarating the conformational sampling of bio-molecules.

    21. UV-photoexcitation and ultrafast dynamics of HCFC-132b (CF2ClCH2Cl)

      Gessenildo Pereira Rodrigues, Elizete Ventura, Silmar Andrade do Monte and Mario Barbatti

      Article first published online: 26 NOV 2015 | DOI: 10.1002/jcc.24260

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      HCFC-132b is an important industrial compound, with a strong impact on health and environment. Upon UV irradiation, it decomposes into dozens of different photoproducts. In this article, nonadiabatic dynamics simulation is used to explain how photo-decomposition takes place through the competition between diverse reaction pathways in the subpicosecond time scale.

    22. A highly efficient hybrid method for calculating the hydration free energy of a protein

      Hiraku Oshima and Masahiro Kinoshita

      Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24253

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      Although the hydration free energy (HFE) is one of the most important factors in studies on the structural stability of a protein, its calculation is significantly difficult in computational cost and accuracy. We develop a new method for calculating the HFE by combining the generalized Born model and the morphometric approach. Our method gives almost the same result as that from the three-dimensional reference interaction site model (3D-RISM) theory with drastic reduction of computational cost.

    23. Revisiting the concept of the (a)synchronicity of diels-alder reactions based on the dynamics of quasiclassical trajectories

      Miguel A. F. de Souza, Elizete Ventura, Silmar A. do Monte, José M. Riveros and Ricardo L. Longo

      Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24245

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      Model Diels-Alder cycloaddition reactions were studied by static and dynamics approaches to establish the (a)synchronous character of the concerted mechanism. The use of static criteria, such as the asymmetry of the TS geometry, for classifying and quantifying the (a)synchronicity of the concerted reaction mechanism provides contradictory results and conclusions when compared to the dynamics approach.

    24. Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

      Alexander Cumberworth, Jennifer M. Bui and Jörg Gsponer

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24235

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      We compare changes in solvation free energy upon folding provided by several implicit solvent models and the TIP3P explicit solvent model. Inconsistencies of an unexpected magnitude were found across the models, which could only be corrected by using settings that were nonphysical or system-specific.

    25. Moment expansion of the linear density-density response function

      Arne Scherrer and Daniel Sebastiani

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24248

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      Intermolecular interactions lead to changes of the electronic charge density. We provide an efficient scheme to express these changes for an arbitrary interaction with an universal yet low-rank tensor. To that extend, we transform the linear density–density response function from its spectral decomposition to a more condensed representation, separating the contributions to the electronic response density from different multipole moments of the perturbation.

    26. Hierarchical atom type definitions and extensible all-atom force fields

      Zhao Jin, Chunwei Yang, Fenglei Cao, Feng Li, Zhifeng Jing, Long Chen, Zhe Shen, Liang Xin, Sijia Tong and Huai Sun

      Article first published online: 5 NOV 2015 | DOI: 10.1002/jcc.24244

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      A hierarchical definition of atom type is proposed to solve the problem of “missing parameters”. The extensible atom type definitions make the force field extensible. Two general force fields are parameterized for some common organic molecules. Parameters are derived from ab initial data and experimental liquid data. Calculation results show good accuracy of the parameters.

    27. The hydration properties of carboxybetaine zwitterion brushes

      Hongbo Du and Xianghong Qian

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24234

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      The average pair distribution functions (g(r)) correlates the C atoms on the hydrocarbon chains between the cationic and anionic groups and the O atoms in water as a function of the carbon spacer chain length (CSL) on a carboxybetaine trimer. The sudden decrease in the g(r) function correlates to the hydrophilic-to-hydrophobic transition when the CSL increases from 12 to 14.

    28. Application of zone-folding approach to the first-principles estimation of thermodynamic properties of carbon and ZrS2-based nanotubes

      Andrei V. Bandura, Vitaly V. Porsev and Robert A. Evarestov

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24243

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      In the case of nanotubes rolled up from the layers of layered compounds (such as graphite, ZrS2, or V2O5) the phonon contributions to the heat capacity and internal energy calculated directly and estimated with using the appropriate 2D layer supercell (within the zone-folding approach) remain very close to each other for temperatures up to 600 K.

    29. Surface chemistry of oxygen on aluminum—Performance of the density functionals: PBE, PBE0, M06, and M06-L

      Cláudio M. Lousada and Pavel A. Korzhavyi

      Article first published online: 29 OCT 2015 | DOI: 10.1002/jcc.24233

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      Within density functional theory (DFT), different functionals produce very large differences in the description of the molecular and dissociative adsorption of O2 at pure and doped aluminum surfaces. These differences are here reported and discussed in view of the type of physical descriptors of the electron density incorporated in each functional.

    30. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform

      Xiangda Peng, Yuebin Zhang, Huiying Chu and Guohui Li

      Article first published online: 23 OCT 2015 | DOI: 10.1002/jcc.24227

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      The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling molecular dynamics simulations using the AMOEBA polarizable force field on GPU platform. Two examples show that the implementation in the work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way

    31. 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.

    32. 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.

    33. 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.

  10. 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.

  11. 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. 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.

    3. 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.

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