Literature DB >> 12759906

An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems.

Shenghua Shi1, Lisa Yan, Yang Yang, Jodi Fisher-Shaulsky, Tom Thacher.   

Abstract

ESFF is a rule-based force field designed for modeling organic, inorganic, and organometallic systems. To cover this broad range of molecular systems, ESFF was developed in an extensible and systematic manner. Several unique features were introduced including pseudoangle and a dot product function representing torsion energy terms. The partial atomic charges that are topology-dependent are determined from ab initio (DFT) calculated electronegativity and hardness for valence orbitals. The van der Waals parameters are charge-dependent, and correlated with the ionization potential for atoms in various valence states. To obtain a set of well-defined and physically meaningful parameters, ESFF employs semiempirical rules to translate atomic-based parameters to parameters typically associated with a covalent valence force field. The atomic parameters depend not only on atom type, but also on internal type, thus resulting in a more accurate force field. This article presents the theory and the method used to develop the force field. The force field has been applied to molecular simulations of a wide variety of systems including nucleic acids, peptides, hydrocarbons, porphyrins, transition metal complexes, zeolites, and organometallic compounds. Agreement with the experimental results indicates that ESFF is a valuable tool in molecular simulations for understanding and predicting both crystal and gas phase molecular structures. Copyright 2003 Wiley Periodicals, Inc.

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Year:  2003        PMID: 12759906     DOI: 10.1002/jcc.10171

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  7 in total

1.  Structures of metallosupramolecular coordination assemblies can be obtained by ion mobility spectrometry-mass spectrometry.

Authors:  Erin R Brocker; Stanley E Anderson; Brian H Northrop; Peter J Stang; Michael T Bowers
Journal:  J Am Chem Soc       Date:  2010-09-29       Impact factor: 15.419

2.  Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.

Authors:  Junmei Wang; Piotr Cieplak; Jie Li; Qin Cai; Meng-Juei Hsieh; Ray Luo; Yong Duan
Journal:  J Phys Chem B       Date:  2012-06-06       Impact factor: 2.991

3.  Carbohydrate force fields.

Authors:  B Lachele Foley; Matthew B Tessier; Robert J Woods
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2012-07

4.  Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics.

Authors:  Olivia Wise-Scira; Liang Xu; George Perry; Orkid Coskuner
Journal:  J Biol Inorg Chem       Date:  2012-06-07       Impact factor: 3.358

5.  Modeling Cu(II) binding to peptides using the extensible systematic force field.

Authors:  Faina Ryvkin; Frederick T Greenaway
Journal:  Bioinorg Chem Appl       Date:  2010-03-11       Impact factor: 7.778

6.  Identification of arsenic-binding proteins in human breast cancer cells.

Authors:  Xinyan Zhang; Fan Yang; Joong-Youn Shim; Kenneth L Kirk; D Eric Anderson; Xiaoxin Chen
Journal:  Cancer Lett       Date:  2007-05-17       Impact factor: 8.679

7.  EzCatDB: the Enzyme Catalytic-mechanism Database.

Authors:  Nozomi Nagano
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

  7 in total

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