Literature DB >> 16592221

A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters.

L L Shipman1, A W Burgess, H A Scheraga.   

Abstract

An empirical potential energy function based on the interactions of the electrons and nuclei in molecules has been developed and tested. The potential energy of interaction is approximated by the sum of the coulombic interactions between all point charge centers (electrons and nuclei), an exponential repulsion to represent electron-electron overlap repulsion, and an R(-6) (R = distance) attraction to simulate dispersion and other attractive energies between the heavy atom fragments of the molecules. The parameters of the potential energy function have been determined from experimental gas-phase and crystal data.The results indicate that both intramolecular and intermolecular interaction energies can be treated with the same set of parameters. In comparison to other empirical interaction potentials now in use, there are fewer independent parameters, there is no need for intrinsic torsional potentials to obtain the correct rotational barriers, and there is no need for special hydrogen bonding functions to account for the directionality and energetics of hydrogen bonding.

Entities:  

Year:  1975        PMID: 16592221      PMCID: PMC432349          DOI: 10.1073/pnas.72.2.543

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


  5 in total

Review 1.  Theoretical and experimental studies of conformations of polypeptides.

Authors:  H A Scheraga
Journal:  Chem Rev       Date:  1971-04       Impact factor: 60.622

Review 2.  Conformation of polypeptides and proteins.

Authors:  G N Ramachandran; V Sasisekharan
Journal:  Adv Protein Chem       Date:  1968

3.  Energy parameters in polypeptides. V. An empirical hydrogen bond potential function based on molecular orbital calculations.

Authors:  R F McGuire; F A Momany; H A Scheraga
Journal:  J Phys Chem       Date:  1972-02-03

4.  Potential functions for hydrogen bond interactions. II. Formulation of an empirical potential function.

Authors:  R Balasubramanian; R Chidambaram; G N Ramachandran
Journal:  Biochim Biophys Acta       Date:  1970-11-17

5.  Conformation of analysis of macromolecules. IV. Helical structures of poly-L-alanine, poly-L-valine, poly-beta-methyl-L-aspartate, poly-gamma-methyl-L-glutamate, and poly-L-tyrosine.

Authors:  T Ooi; R A Scott; G Vanderkooi; H A Scheraga
Journal:  J Chem Phys       Date:  1967-06-01       Impact factor: 3.488

  5 in total
  2 in total

1.  A new approach to empirical intermolecular and conformational potential energy functions. II. Applications to crystal packing, rotational barriers, and conformational analysis.

Authors:  A W Burgess; L L Shipman; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1975-03       Impact factor: 11.205

Review 2.  The Last Secret of Protein Folding: The Real Relationship Between Long-Range Interactions and Local Structures.

Authors:  Aoneng Cao
Journal:  Protein J       Date:  2020-10-10       Impact factor: 2.371

  2 in total

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