Journal of Computational Chemistry

Cover image for Vol. 35 Issue 29

November 5, 2014

Volume 35, Issue 29

Pages i–iv, 2087–2161

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      Cover Image, Volume 35, Issue 29 (pages i–ii)

      Article first published online: 26 SEP 2014 | DOI: 10.1002/jcc.23754

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      Oxidative addition of aryl halides to gold(I) complexes are known to be kinetically sluggish. The reasons have so far not been understood. On page 2140 (DOI: 10.1002/jcc.23734), Israel Fernández, Lando P. Wolters, and F. Matthias Bickelhaupt provide the missing insight using the Activation Strain Model (ASM) of chemical reactivity. The relatively high rigidity of gold(I) complexes plays a key role. This rigidity, in combination with the fact that oxidative addition requires bending of the complex, leads to a high catalyst activation strain and thus a high activation energy. Based on this new insight, strategies are developed to achieve lower, more feasible reaction barriers.

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      Cover Image, Volume 35, Issue 29 (pages iii–iv)

      Article first published online: 26 SEP 2014 | DOI: 10.1002/jcc.23755

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      On page 2146 (DOI: 10.1002/jcc.23740), ground- and excited-state properties of copper(II) charge-transfer systems are investigated by Alexander Hoffmann, Martin Rohrmüller, Anton Jesser, Ines dos Santos Vieira, Wolf Gero Schmidt, and Sonja Herres-Pawlis starting from density-functional calculations with particular emphasis on the role of the exchange and correlation functional, the basis set, solvent effects, and the treatment of dispersive interactions. Furthermore, the applicability of TD-DFT to excitations of copper(II) bis(chelate) charge-transfer systems is explored by performing many-body perturbation theory (GW+BSE), independent-particle approximation (IPA) and ΔSCF calculations for a small model system containing simple guanidine and imine groups.

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    1. Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins (pages 2087–2095)

      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, and glycosidic linkage geometries, as well as the effects of glycosylation over protein structure and dynamics.

    2. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters (pages 2096–2106)

      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 computations. Six representative geometries are selected from short-duration molecular dynamics and energy-minimized. The ranking of their relative stabilities is identical to the quantum mechanical one. The impact of polarization and charge-transfer contributions is analyzed.

    3. Electronic spectra and intersystem spin-orbit coupling in 1,2- and 1,3-squaraines (pages 2107–2113)

      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. Using chiral molecules as an approach to address low-druggability recognition sites (pages 2114–2121)

      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.

    5. The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ3-iodanes): Facing the limit of the stationary quantum chemical approach (pages 2122–2131)

      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. By exploring the reaction mechanism of an iodane reagent with a nucleophile (acetonitrile), it is shown 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.

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      A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model (pages 2132–2139)

      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 solvation 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.

    7. Controlling the oxidative addition of aryl halides to Au(I) (pages 2140–2145)

      Israel Fernández, Lando P. Wolters and F. Matthias Bickelhaupt

      Article first published online: 26 SEP 2014 | DOI: 10.1002/jcc.23734

      Thumbnail image of graphical abstract

      The oxidative addition of aryl halides to Au(I) complexes is considered a kinetically sluggish reaction. By combining the Activation Strain Model and Energy Decomposition Analysis methods, the factors causing this reaction to be slow are been identified. Based on this new insight, we suggest the best combination of gold(I) complex and aryl halide to turn this process into a feasible, low-barrier transformation.

    8. Geometrical and optical benchmarking of copper(II) guanidine–quinoline complexes: Insights from TD-DFT and many-body perturbation theory (part II) (pages 2146–2161)

      Alexander Hoffmann, Martin Rohrmüller, Anton Jesser, Ines dos Santos Vieira, Wolf Gero Schmidt and Sonja Herres-Pawlis

      Article first published online: 25 SEP 2014 | DOI: 10.1002/jcc.23740

      Thumbnail image of graphical abstract

      Ground- and excited-state properties of copper(II) charge-transfer systems have been investigated starting from density-functional calculations with particular emphasis on the role of the exchange and correlation functional, the basis set, solvent effects, and the treatment of dispersive interactions. Furthermore, the applicability of TD-DFT to excitations of copper(II) bis(chelate) charge-transfer systems was explored by performing many-body perturbation theory (GW + BSE), independent-particle approximation (IPA) and ΔSCF calculations for a small model system that contains simple guanidine and imine groups.

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