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Force field parameters for molecular mechanical simulation of dehydroamino acid residues
Author(s) -
Alagona Giuliano,
Ghio Caterina,
Pratesi Claudio
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120805
Subject(s) - force field (fiction) , chemistry , computational chemistry , tripeptide , molecular dynamics , energy minimization , potential energy , dehydroalanine , molecular model , atomic charge , nucleic acid , crystallography , stereochemistry , molecule , amino acid , physics , atomic physics , organic chemistry , quantum mechanics , biochemistry
Parameters suitable to describe the conformational behavior of α – β unsaturated aminoacids and peptides in the framework of an existing force field for nucleic acids and proteins (S.J. Weiner, P.A. Kollman, D.A. Case, U. Chandra Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner, J. Am. Chem. Soc. , 106 , 765 (1984)) are proposed and tested. Attention is primarily focused on dehydrophenylalanine and dehydroalanine containing peptides. The values of the parameters needed were obtained from experimental measurements available in the literature and from ad hoc quantum mechanical calculations. The selected values have subsequently been adapted and refined through molecular mechanical simulations on model compounds, such as Ac‐ΔPhe‐NMe, for which it was possible to carry out STO‐3G/SCF calculations to check selected points on the ϕ,ψ conformational map, and Ac‐ΔAla‐NMe, where the comparison was carried out at the 4‐31G level. The newly determined force field was then applied to Ac‐ΔPhe‐Ala‐ΔPhe‐NMe, whose minimal energy structures allowed us to explain the different circular dichroism behavior observed in CH 2 Cl 2 and in dioxane. Starting from two minimum energy geometries of this tripeptide, the full optimization with AM1 produced an independent guess to their structure and stability in good agreement with the molecular mechanical one.