Journal of Computational Chemistry

Cover image for Vol. 34 Issue 18

5 July 2013

Volume 34, Issue 18

Pages i–iv, 1527–1609

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    5. Erratum
    1. You have free access to this content
      Cover Image, Volume 34, Issue 18 (pages i–ii)

      Article first published online: 11 JUN 2013 | DOI: 10.1002/jcc.23351

      Thumbnail image of graphical abstract

      The molecule illustrated on the cover is the tryptophanyl glutamic acid (Trp-Glu) dipeptide in the 1+ charge state, presented by Azaria Eisenberg and Laura Juszczak on page 1549. It represents a single conformation from a 30 ns molecular dynamics simulation. Three discrete values of the Chi 1 dihedral angle describe the motion of all Trp-Glu charge states: 60°, 180°, and 300°. For the Chi 1 angle of 60° shown here, the backbone curls over the indole ring, resulting in numerous backbone–ring noncovalent interactions. An electrostatic potential surface cuts through the indole plane, revealing the uneven charge distribution over the indole ring (red, −0.232 atomic units; blue, 0.207 atomic units).

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 18 (pages iii–iv)

      Article first published online: 11 JUN 2013 | DOI: 10.1002/jcc.23352

      Thumbnail image of graphical abstract

      Time-dependent density functional theory makes it possible to calculate excited electronic states. For the pyrrole molecule shown on the cover, for example, a sufficient number of molecules provide converged magnetic circular dichroism (MCD) and absorption spectra. This procedure by Petr Štěpánek and Petr Bourř on page 1531 can be faster than classical computations based on the response theory, thus enhancing MCD studies of electronic and molecular structure.

  2. Rapid Communication

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    5. Erratum
    1. Computational design of S-nitrosothiol “click” reactions (pages 1527–1530)

      Marat R. Talipov, Dmitry G. Khomyakov, Ming Xian and Qadir K. Timerghazin

      Article first published online: 3 APR 2013 | DOI: 10.1002/jcc.23279

      Thumbnail image of graphical abstract

      Making S-nitrosothiols click: CBS-QB3 calculations show that N-coordination of a Lewis acid (LA) is all that is necessary for S-nitrosothiols (RSNOs) to undergo efficient (3+2) cycloaddition reactions with activated alkynes or alkenes. LA-linked reagents may have great potential for labeling unstable protein-based RSNOs, as they are predicted to react with RSNOs with efficiency approaching click-chemistry based reactions.

  3. Full Papers

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    5. Erratum
    1. Computation of magnetic circular dichroism by sum-over-states summations (pages 1531–1539)

      Petr Štěpánek and Petr Bouř

      Article first published online: 23 MAR 2013 | DOI: 10.1002/jcc.23277

      Thumbnail image of graphical abstract

      The spectroscopy of magnetic circular dichroism has been benefited from accurate calculations of the spectra within density functional theory (DFT) and response theories. Surprisingly, the DFT sum-over-state path is a viable alternate approach, which under certain circumstances even significantly speeds up the spectral modeling.

    2. Parameters for molecular dynamics simulations of iron-sulfur proteins (pages 1540–1548)

      Alexandra T. P. Carvalho, Ana F. S. Teixeira, and Maria J. Ramos

      Article first published online: 23 APR 2013 | DOI: 10.1002/jcc.23287

      Thumbnail image of graphical abstract

      Iron-sulfur proteins have finely tuned redox potentials, which allow them to be highly efficient and specific. Bonded parameters compatible with the AMBER force field are derived for three metal centers, and molecular dynamics simulations are performed on three proteins. Results for the pattern of interactions with the metal centers are consistent with those obtained by nuclear magnetic resonance (NMR) experiments and density functional theory (DFT) calculations, allowing the application of molecular dynamics to the study of those proteins.

    3. Relating Trp-Glu dipeptide fluorescence to molecular conformation: The role of the discrete chi 1 and chi 2 angles (pages 1549–1560)

      Azaria Solomon Eisenberg and Laura J. Juszczak

      Article first published online: 8 APR 2013 | DOI: 10.1002/jcc.23288

      Thumbnail image of graphical abstract

      Molecular dynamics simulation reveals the effect of the Trp-Glu charge state on dipeptide conformation preferences. Two general conformations are found, including one where the backbone stretches away from the indole ring, as shown here. The consequence of a “backbone-stretched” conformation is noncovalent interaction between the terminal amine cation and indole ring. Using this and other theoretical data, trends in tryptophan fluorescence maxima and lifetimes for different dipeptide species can be explained.

    4. Toward quantitative estimates of binding affinities for protein–ligand systems involving large inhibitor compounds: A steered molecular dynamics simulation route (pages 1561–1576)

      Paolo Nicolini, Diego Frezzato, Cristina Gellini, Marco Bizzarri and Riccardo Chelli

      Article first published online: 26 APR 2013 | DOI: 10.1002/jcc.23286

      Thumbnail image of graphical abstract

      Relative binding free energies of protein–ligand complexes formed by a focal adhesion kinase and various pyrrolopyrimidine-based compounds are calculated by means of steered molecular dynamics simulations. Nonequilibrium trajectories are analyzed using the Jarzynski equality for free energy calculations.

    5. Existence of dynamic tautomerism and divalent N(I) character in N-(pyridin-2-yl)thiazol-2-amine (pages 1577–1588)

      Sonam Bhatia, Yogesh J. Malkhede and Prasad V. Bharatam

      Article first published online: 22 APR 2013 | DOI: 10.1002/jcc.23293

      Thumbnail image of graphical abstract

      Quantum chemical calculations using density functional theory (DFT) (B3LYP), ab intio methods (MP2), and G2MP2 methods are carried out to understand the preferences of tautomerization in medicinal relevant N-(pyridin-2-yl)thiazol-2-amine (PTA) scaffolds. PTA-P1 is the most preferred isomer for this class of compounds. It shows high proton affinity (∼235 kcal/mol) and is converted into PTA-P1. Electronic structure analysis of PTA-P1 shows that this compound belongs to divalent N(I) of species, characterized by two lone pairs of electrons: π and σ type localized on the central nitrogen. Thus, the form PTA-P1 is labeled with the (L[RIGHTWARDS ARROW]N[LEFTWARDS ARROW]L) character.

    6. Dynamics and structural changes of small water clusters on ionization (pages 1589–1597)

      Han Myoung Lee and Kwang S. Kim

      Article first published online: 22 APR 2013 | DOI: 10.1002/jcc.23296

      Thumbnail image of graphical abstract

      Water cluster cations can have either Eigen-like forms or Zundel-like forms. Based on reliable molecular dynamics simulations, water clusters tend to have an Eigen-like form with the hydronium cation instead of a Zundel-like form in terms of energetics. For the vertically ionized water hexamer, the relatively stable (H2O)5+ (5sL4A) cluster tends to form with a detached water molecule (H2O).

    7. An efficient fluctuating charge model for transition metal complexes (pages 1598–1608)

      Peter Comba, Bodo Martin and Avik Sanyal

      Article first published online: 22 APR 2013 | DOI: 10.1002/jcc.23297

      Thumbnail image of graphical abstract

      An efficient fluctuating charge model for transition metal complexes, based on the Hirshfeld partitioning scheme, is developed and validated.

  4. Erratum

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    5. Erratum
    1. You have free access to this content
      Erratum: A convective replica-exchange method for sampling new energy basins (page 1609)

      Yannick G. Spill, Guillaume Bouvier and Michael Nilges

      Article first published online: 8 APR 2013 | DOI: 10.1002/jcc.23291

      This article corrects:

      A convective replica-exchange method for sampling new energy basins

      Vol. 34, Issue 2, 132–140, Article first published online: 7 SEP 2012

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