An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems
- PMID: 12759906
- DOI: 10.1002/jcc.10171
An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems
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.
Similar articles
-
A new force field (ECEPP-05) for peptides, proteins, and organic molecules.J Phys Chem B. 2006 Mar 16;110(10):5025-44. doi: 10.1021/jp054994x. J Phys Chem B. 2006. PMID: 16526746
-
Development of polyphosphate parameters for use with the AMBER force field.J Comput Chem. 2003 Jul 15;24(9):1016-25. doi: 10.1002/jcc.10262. J Comput Chem. 2003. PMID: 12759902
-
Development of the force field parameters for phosphoimidazole and phosphohistidine.J Comput Chem. 2004 Aug;25(11):1313-21. doi: 10.1002/jcc.20055. J Comput Chem. 2004. PMID: 15185324
-
Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field.Langmuir. 2013 Feb 12;29(6):1754-65. doi: 10.1021/la3038846. Epub 2013 Jan 16. Langmuir. 2013. PMID: 23276161 Review.
-
Empirical force fields for biological macromolecules: overview and issues.J Comput Chem. 2004 Oct;25(13):1584-604. doi: 10.1002/jcc.20082. J Comput Chem. 2004. PMID: 15264253 Review.
Cited by
-
Ion Mobility Mass Spectrometry for Large Synthetic Molecules: Expanding the Analytical Toolbox.J Am Chem Soc. 2024 Apr 3;146(13):8800-8819. doi: 10.1021/jacs.4c00354. Epub 2024 Mar 18. J Am Chem Soc. 2024. PMID: 38498971 Free PMC article. Review.
-
Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics.J Biol Inorg Chem. 2012 Aug;17(6):927-38. doi: 10.1007/s00775-012-0909-9. Epub 2012 Jun 7. J Biol Inorg Chem. 2012. PMID: 22674434 Free PMC article.
-
Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.J Phys Chem B. 2012 Jun 21;116(24):7088-101. doi: 10.1021/jp3019759. Epub 2012 Jun 6. J Phys Chem B. 2012. PMID: 22612331 Free PMC article.
-
Modeling Cu(II) binding to peptides using the extensible systematic force field.Bioinorg Chem Appl. 2010;2010:724210. doi: 10.1155/2010/724210. Epub 2010 Mar 11. Bioinorg Chem Appl. 2010. PMID: 20300581 Free PMC article.
-
Identification of arsenic-binding proteins in human breast cancer cells.Cancer Lett. 2007 Sep 18;255(1):95-106. doi: 10.1016/j.canlet.2007.03.025. Epub 2007 May 17. Cancer Lett. 2007. PMID: 17499915 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources