Journal of Computational Chemistry
© Wiley Periodicals, Inc.
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
Recently Published Articles
- You have full text access to this OnlineOpen articleRealistic sampling of amino acid geometries for a multipolar polarizable force field
Timothy J. Hughes, Salvatore Cardamone and Paul L. A. Popelier
Article first published online: 3 AUG 2015 | DOI: 10.1002/jcc.24006
The Quantum Chemical Topological Force Field uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms. Kriging must operate on relevant and realistic training sets. Conformational space by seeds from the Protein Data Bank and distorted by nonstationary point normal modes is discussed. More than 60% of external test geometries have their electrostatic energy predicted within 4 kJ mol−1 by all kriging models.
- Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds
Manuel Hitzenberger and Thomas S. Hofer
Article first published online: 3 AUG 2015 | DOI: 10.1002/jcc.24032
By identifying and applying the ideal parameter set for the representation of the CαCβ bond of amino acids via a QM/MM link atom approach, the behavior of a fully QM-derived description can be mimicked exactly. Furthermore, the applicability of global parameters for different amino acids and the influence of protonation states, QM-methods and the chemical environment is discussed in detail.
- A topological assessment of the electronic structure of mesoionic compounds
Italo Curvelo Anjos and Gerd Bruno Rocha
Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24027
Mesoionic compounds have been described as heterocyclic molecules with delocalized π-bonds and strong charge separation. Classical representations of these compounds place the positive and negative charges at well-defined regions. Topological calculations, however, show that neither the charge nor the π-delocalization are restricted to these specific regions. They both depend on the nature of the ring atoms and the substituent groups attached to them.
- An enhanced monte–carlo outlier detection method
Liangxiao Zhang, Peiwu Li, Jin Mao, Fei Ma, Xiaoxia Ding and Qi Zhang
Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24026
Based on Monte–Carlo outlier detection, an enhanced Monte–Carlo outlier detection method by establishing cross-prediction models using determinate normal samples and analyzing the distribution of prediction errors individually for dubious samples.
- Electron density analysis of large (molecular and periodic) systems: A parallel implementation
Silvia Casassa, Alessandro Erba, Jacopo Baima and Roberto Orlando
Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24033
A parallel implementation is presented of a series of algorithms for the analysis of the wave-function of large molecular and periodic systems. The speedup of the calculation as a function of the number of processors used is documented also for Bader's topological analysis of the electron charge density in the case of the crambin crystallized protein.