Journal of Computational Chemistry

Cover image for Vol. 35 Issue 27

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

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

Impact Factor: 3.601

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

Online ISSN: 1096-987X

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

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  1. Full Papers

    1. Distinguishing between keto–enol and acid–base forms of firefly oxyluciferin through calculation of excited-state equilibrium constants

      Olle Falklöf and Bo Durbeej

      Article first published online: 16 SEP 2014 | DOI: 10.1002/jcc.23735

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      Aqueous keto–enol and acid–base excited-state equilibrium constants between six neutral, monoanionic, and dianionic forms of oxyluciferin—the cofactor responsible for the bioluminescence of firefly luciferase—are for the first time calculated from free energies of a Born–Haber cycle, rather than using the Förster equation. Thereby, it is found that the phenolate-keto-OxyLH monoanion is the preferred excited-state form of oxyluciferin in aqueous solution, attributing a potential key role to this species in the bioluminescence of fireflies.

    2. Using chiral molecules as an approach to address low-druggability recognition sites

      Xavier Lucas and Stefan Günther

      Article first published online: 16 SEP 2014 | DOI: 10.1002/jcc.23726

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      Using chiral molecules as an approach to address low-druggability recognition sites The reported theoretical study on the DrugBank database shows that the content of chiral atoms or structural complexity correlates well with relevant physicochemical properties of drugs and their target's recognition site, including its hydrophobic character and druggability. The reported results set the basis for a better understanding of protein–drug recognition and for the inclusion of target information in the filtering of large ligand libraries for drug discovery.

    3. Efficiency of perturbation-selection and its orbital dependence in the SAC-CI calculations for valence excitations of medium-size molecules

      Ryoichi Fukuda and Masahiro Ehara

      Article first published online: 15 SEP 2014 | DOI: 10.1002/jcc.23729

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      The efficiency and accuracy of the perturbation-selection for the SAC-CI calculations are investigated for excited states of 21 medium-size molecules. Benchmark SAC-CI calculations with up to 110 million operators are performed. The efficiency of the selection using the canonical and localized MO (LMO) is also examined. Except for highly symmetric molecules, using LMOs improves the efficiency and accuracy. The perturbation-selection with LMOs is a promising method for excited states in larger molecules.

    4. The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ3-iodanes): Facing the limit of the stationary quantum chemical approach

      Oliver Sala, Hans Peter Lüthi and Antonio Togni

      Article first published online: 15 SEP 2014 | DOI: 10.1002/jcc.23727

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      Hypervalent iodine compounds, in particular λ3-iodanes, have gained considerable attention in synthesis. However, little is known about the mechanistic details. Exploring the reaction mechanism of an iodane reagent with a nucleophile (acetonitrile), we show that the same products may be obtained via two different reaction mechanisms. These show a very distinct response to the effect of the solvent; the correct prediction of the mechanism will call for an explicit treatment of the solvent.

    5. You have full text access to this OnlineOpen article
      A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

      Junya Yamagishi, Noriaki Okimoto, Gentaro Morimoto and Makoto Taiji

      Article first published online: 15 SEP 2014 | DOI: 10.1002/jcc.23728

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      A collection of atomic radii, which determines the distribution of dielectric constants around the solute, is an important parameter for the Poisson–Boltzmann implicit solvent. For accurate estimation of the salvation free energy of proteins, a new parameter was developed based on results from explicit solvent simulations. New radii showed good agreement with the explicit solvent simulations for large peptides at the level of the small molecular fragment.

    6. Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction

      Huiying Zhao, Yuedong Yang, Mark von Itzstein and Yaoqi Zhou

      Article first published online: 15 SEP 2014 | DOI: 10.1002/jcc.23730

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      Discovering new carbohydrate-binding proteins (CBPs) is important as they are potential biomarkers and drug targets. A template-based technique is developed to predict CBPs by structural alignment and binding affinity scoring. Its application to structural genome targets yields several novel CBPs.

    7. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network

      James Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip Paliwal, Abdul Sattar, Yaoqi Zhou and Yuedong Yang

      Article first published online: 12 SEP 2014 | DOI: 10.1002/jcc.23718

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      Local structures (15-residue fragment) derived from predicted Cα-based angles are more accurate than and complementary to the local structures derived from predicted backbone torsion angles, providing a new coarse-grained restraint for tertiary structure prediction.

  2. Full Paper

    1. Predicting hydration energies for multivalent ions

      Martin P. Andersson and Susan L. S. Stipp

      Article first published online: 11 SEP 2014 | DOI: 10.1002/jcc.23733

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      The free energy of hydration is predicated for some monovalent and multivalent cations and anions using density functional theory and the implicit solvent model COSMO-RS. Agreement with experimental data is good, particularly for monovalent and divalent ions for which there are no systematic errors. Results indicate that COSMO-RS is a reliable implicit solvent method to combine with quantum chemical calculations for screening-level studies of multivalent ions in solution. One important example is homogeneous catalysis with transition metal complexes and other ligand exchange reactions.

  3. Full Papers

    1. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters

      Nohad Gresh, Krystel El Hage, David Perahia, Jean-Philip Piquemal, Catherine Berthomieu and Dorothée Berthomieu

      Article first published online: 11 SEP 2014 | DOI: 10.1002/jcc.23724

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      The existence of a network of structured waters in the vicinity of the bimetallic site of Cu, Zn-SOD has been inferred from high-resolution X-ray crystallography. The accuracy of a polarizable force-field, SIBFA, is benchmarked by comparisons with quantum mechanics (QM) computations. Six representative geometries are selected from short-duration MD and energy-minimized. The ranking of their relative stabilities is identical to the QM one. The impact of polarization and charge-transfer contributions is analyzed.

    2. Resolutions of the Coulomb operator: VIII. Parallel implementation using the modern programming language X10

      Taweetham Limpanuparb, Josh Milthorpe and Alistair P. Rendell

      Article first published online: 11 SEP 2014 | DOI: 10.1002/jcc.23720

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      A key bottleneck in the Hartree–Fock method is exchange matrix calculation. Using the Ewald resolution, this step can be split as shown in the picture to multiple computing nodes. At each node, the standard linear algebra subroutines DGEMM and DSYRK perform the matrix–matrix multiplications necessary to compute exchange matrix elements.

    3. Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil

      Minhajul Arfeen, Dhilon S. Patel, Sheenu Abbat, Nikhil Taxak and Prasad V. Bharatam

      Article first published online: 5 SEP 2014 | DOI: 10.1002/jcc.23719

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      Electronic structure analysis was carried out on the model reaction of proguanil to cycloguanil to understand the role of cytochromes in cyclization reaction. The results showed that cyclization of proguanil involve loss of two hydrogen atoms in the form radical.

    4. Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins

      Laercio Pol-Fachin, Hugo Verli and Roberto D. Lins

      Article first published online: 5 SEP 2014 | DOI: 10.1002/jcc.23721

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      The GROMOS 53A6glyc parameter set is suitable for molecular simulations of carbohydrates and glycoproteins. It can properly describe monosaccharide ring pucker, relative abundance of the hydroxymethyl group, glycosidic linkage geometries, as well as the effects of glycosylation over protein structure and dynamics.

    5. Electronic spectra and intersystem spin-orbit coupling in 1,2- and 1,3-squaraines

      Marta E. Alberto, Gloria Mazzone, Angelo D. Quartarolo, Flavio Fortes Ramos Sousa, Emilia Sicilia and Nino Russo

      Article first published online: 1 SEP 2014 | DOI: 10.1002/jcc.23725

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      The main photophysical properties of a series of recently synthetized 1,2- and 1,3-squaraines have been investigated by means of density functional theory (DFT) and time-dependent DFT approaches. Two singlet-triplet intersystem crossings have been found, which could contribute to the excited singlet oxygen production.

  4. Software News and Updates

    1. The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

      Saleh Riahi and Christopher N. Rowley

      Article first published online: 1 SEP 2014 | DOI: 10.1002/jcc.23716

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      The interface between CHARMM and TURBOMOLE allows researchers to perform extensive QM/MM molecular dynamics simulations using accurate quantum mechanical methods. This code also makes it possible to use a molecular mechanical model that is capable of describing induced electronic polarization within a simulation. Time-averaged electronic absorption, circular dichroism, and emission spectra can also be calculated.

  5. Full Papers

    1. Kinetics of radical-molecule reactions in aqueous solution: A benchmark study of the performance of density functional methods

      Annia Galano and Juan Raúl Alvarez-Idaboy

      Article first published online: 21 AUG 2014 | DOI: 10.1002/jcc.23715

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      Six density functional approximations are recommended for kinetic calculations in aqueous solution: LC-ωPBE, M06-2X, BMK, B2PLYP, M05-2X, and MN12SX, in that order. This result was obtained using the SMD model, conventional transition state theory, zero-curvature tunneling correction, and experimental data as reference.

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