Literature DB >> 16593959

Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces.

J R Maple1, U Dinur, A T Hagler.   

Abstract

We present a technique for addressing the problem of deriving potential energy functions for the simulation of organic, polymeric, and biopolymeric systems, as well as for modeling vibrational spectroscopic properties. This method is designed to address three major objectives: deriving and comparing optimal functional forms for describing the energies of molecular deformations and interactions, developing a technique to rapidly and objectively determine reasonable force constants for intermolecular and intramolecular interactions, and determining the transferability of these potential forms and constants. The first two of these objectives are addressed in this paper, while the latter problem will be treated elsewhere. The technique uses ab initio molecular energy surfaces, which are described by the energy and its first and second derivatives with respect to coordinates. As an example, application to a small model compound (i.e., the formate anion) is given. A variety of analytical forms for the potential are tested against the data, to find which forms are best. The importance of anharmonicity and cross terms in accounting for structure and energy, as well as for dynamics, is demonstrated and a more accurate representation of the out-of-plane deformation for a trigonal center is derived from the energy surfaces.

Entities:  

Year:  1988        PMID: 16593959      PMCID: PMC281753          DOI: 10.1073/pnas.85.15.5350

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  3 in total

1.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals.

Authors:  A T Hagler; E Huler; S Lifson
Journal:  J Am Chem Soc       Date:  1974-08-21       Impact factor: 15.419

Review 2.  Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

Authors:  S Krimm; J Bandekar
Journal:  Adv Protein Chem       Date:  1986

3.  Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers.

Authors:  P A Kollman; P K Weiner; A Dearing
Journal:  Biopolymers       Date:  1981-12       Impact factor: 2.505

  3 in total
  40 in total

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2.  Nucleic acid duplexes incorporating a dissociable covalent base pair.

Authors:  K Gao; L E Orgel
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-21       Impact factor: 11.205

3.  On the suitability of semiempirical calculations as sources of force field parameters.

Authors:  C Alemán; M Orozco
Journal:  J Comput Aided Mol Des       Date:  1992-08       Impact factor: 3.686

4.  Molecular modelling prediction of ligand binding site flexibility.

Authors:  Ami Yi-Ching Yang; Per Källblad; Ricardo L Mancera
Journal:  J Comput Aided Mol Des       Date:  2004-04       Impact factor: 3.686

5.  PAPQMD parametrization of molecular systems with cyclopropyl rings: conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid.

Authors:  C Alemán; J Casanovas; S E Galembeck
Journal:  J Comput Aided Mol Des       Date:  1998-05       Impact factor: 3.686

6.  Fluorescence lifetime probe of biomolecular conformations.

Authors:  Xiangguo Shi; Joel H Parks
Journal:  J Am Soc Mass Spectrom       Date:  2010-01-25       Impact factor: 3.109

7.  Conformational study on cyclic melanocortin ligands and new insight into their binding mode at the MC4 receptor.

Authors:  Paolo Grieco; Diego Brancaccio; Ettore Novellino; Victor J Hruby; Alfonso Carotenuto
Journal:  Eur J Med Chem       Date:  2011-05-23       Impact factor: 6.514

8.  Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB.

Authors:  P R Gerber
Journal:  J Comput Aided Mol Des       Date:  1998-01       Impact factor: 3.686

9.  CD and DNA binding studies of a proline repeat-containing segment of the replication arrest protein Tus.

Authors:  M L Nedved; P A Gottlieb; G R Moe
Journal:  Nucleic Acids Res       Date:  1994-11-25       Impact factor: 16.971

10.  Polyamines and Pectins (I. Ion Exchange and Selectivity).

Authors:  J. Messiaen; P. Cambier; P. Van Cutsem
Journal:  Plant Physiol       Date:  1997-02       Impact factor: 8.340

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