Journal of Computational Chemistry

Cover image for Vol. 35 Issue 25

September 30, 2014

Volume 35, Issue 25

Pages i–iv, 1809–1881

  1. Cover Image

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    1. You have free access to this content
      Cover Image, Volume 35, Issue 25 (pages i–ii)

      Article first published online: 21 AUG 2014 | DOI: 10.1002/jcc.23722

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      On page 1835 (DOI: 10.1002/jcc.23693), Tatsuki Negami, Kentaro Shimizu, and Tohru Terada report the use of coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field reproduce the protein-ligand binding processes. Arrows in the image depict fluxes of the ligand averaged over the periods when the ligand approaches the ligand-binding site in the CGMD simulations of the levansucrase-sucrose system. The image demonstrates that the CG ligand molecules tend to enter the ligand-binding pocket through grooves on the protein surface.

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      Cover Image, Volume 35, Issue 25 (pages iii–iv)

      Article first published online: 21 AUG 2014 | DOI: 10.1002/jcc.23723

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      Chiral discrimination by NMR spectroscopy can be achieved through the pseudo-scalar derived from the dipole shielding polarisability tensor, which describes the interaction of a magnetic and electric field with matter. Stefano Pelloni and Inmaculada García Cuesta report on page 1815 (DOI: 10.1002/jcc.23689) that this tensor changes sign when passing from one system to its mirror image. It is therefore possible to, in principle, recognize two enantiomers of a molecule. Predictions of the chiral NMR effects are carried out by CCSD-CTOCD calculations and some nuclei in oxaziridine derivatives are proposed as good candidates for a chiral nuclear magnetic resonance experiment.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Basis set error estimation for DFT calculations of electronic g-tensors for transition metal complexes (pages 1809–1814)

      Morten N. Pedersen, Erik D. Hedegård and Jacob Kongsted

      Article first published online: 25 JUL 2014 | DOI: 10.1002/jcc.23688

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      The calculation of the electronic g-tensor for electron paramagnetic resonance (EPR) is a promising route to aid experimental investigations, especially within bio-inorganic chemistry. However, as the number of basis functions greatly increase for compounds containing d-block elements, it would be desirable if a smaller basis set could be used for the ligands in a so-called locally dense basis set approach. This article reports the accuracy of several locally dense basis set schemes and compares these to an extrapolated complete basis set value.

    2. CCSD-CTOCD static dipole shielding polarizability for quantification of the chiral NMR effects in oxaziridine derivatives (pages 1815–1823)

      Stefano Pelloni and Inmaculada García Cuesta

      Article first published online: 22 JUL 2014 | DOI: 10.1002/jcc.23689

      Thumbnail image of graphical abstract

      Chiral discrimination by NMR spectroscopy can be achieved through the pseudo-scalar derived from the dipole shielding polarizability tensor, which has an opposite sign in each enantiomer and is zero for achiral molecules. An accurate theoretical description of the magnitude is of fundamental importance to if it is to be unequivocally confirmed by experiment. CCSD calculations of the pseudo-scalar in oxaziridine derivatives show important effects caused by the chiral nuclei 19F and 31P.

    3. Shape-based virtual screening with volumetric aligned molecular shapes (pages 1824–1834)

      David Ryan Koes and Carlos J. Camacho

      Article first published online: 22 JUL 2014 | DOI: 10.1002/jcc.23690

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      Volumetric aligned molecular shapes provide a way to screen libraries of molecular shapes that approaches the speed of the fastest shape-based methods and the accuracy of the most successful shape-based methods which are orders of magnitude slower. Volumetric aligned molecular shapes also offer a novel minimum/maximum shape constraint search that allows the user to precisely specify the desired shape and search millions of shapes in a fraction of a second.

    4. Coarse-grained molecular dynamics simulations of protein–ligand binding (pages 1835–1845)

      Tatsuki Negami, Kentaro Shimizu and Tohru Terada

      Article first published online: 20 JUL 2014 | DOI: 10.1002/jcc.23693

      Thumbnail image of graphical abstract

      Coarse-grained molecular dynamics simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. Spatial distributions of the CG ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. Analysis of the ligand fluxes demonstrated that the CG ligand molecules tended to enter the ligand-binding pockets through grooves on the protein surfaces.

    5. To be or not to be butterfly: New mechanistic insights in the Aza-Michael asymmetric addition of lithium (R)-N-benzyl-N-(α-methylbenzyl)amide (pages 1846–1853)

      Carlos T. Nieto, David Díez and Narciso M. Garrido

      Article first published online: 22 JUL 2014 | DOI: 10.1002/jcc.23694

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      The asymmetric Aza-Michael addition of homochiral lithium benzylamides to α,β-unsaturated esters represents an extended protocol to obtain enantioenriched β-amino esters. A QM/MM transition state protocol is presented, revising the original proposed mechanism. Theoretical results, a Si/Re 99:1 diastereoselective ratio, in good agreement with experimental results, is reported. Two TS conformers in a “V-stacked” orientation of the amide's phenyl rings, differing in the THF molecule arrangement coordinated to lithium, are the most suitable TS geometries.

    6. Factors affecting the computation of the 13C shielding in disaccharides (pages 1854–1864)

      Pablo G. Garay, Osvaldo A. Martin, Harold A. Scheraga and Jorge A. Vila

      Article first published online: 28 JUL 2014 | DOI: 10.1002/jcc.23697

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      Knowledge of the three-dimensional structures of carbohydrate molecules, as for maltose shown in the figure, is indispensable for a full molecular understanding of the biological processes in which carbohydrates are involved. For this purpose, it is important to determine first, which carbons can be used as probes to sense conformational changes and second, all factors that affect the computation of the shielding, at the density functional theory (DFT) level of theory, of those carbons.

    7. Looking for some free energy? Call JEFREE (…) (pages 1865–1881)

      Mirco Zerbetto, Andrea Piserchia and Diego Frezzato

      Article first published online: 3 AUG 2014 | DOI: 10.1002/jcc.23701

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      The calculation of Helmholtz free energy profiles along relevant degrees of freedom of a system is the key to access its thermodynamic properties. This article presents a new computational strategy developed within the framework of nonequilibrium transformations, which proved to be outperforming with respect to standard routes. Also, such a protocol is implemented into a novel and easy-to-use C++ library.

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