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Bond‐Optimized ring closure for proline: Comparison of conformations and semiempirical energies with small molecule X‐ray structures
Author(s) -
Thomasson Kathryn A.,
Applequist Jon
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360300321
Subject(s) - torsion (gastropod) , bond length , chemistry , maxima and minima , crystallography , ring (chemistry) , molecular geometry , molecule , dihedral angle , molecular physics , closure (psychology) , mathematics , hydrogen bond , crystal structure , mathematical analysis , medicine , surgery , organic chemistry , economics , market economy
A method is described for generating proline ring structures by successive addition of atoms, wherein ring closure is achieved by optimizing the fit to known ring bond‐angles and one closing bond‐length (“bond‐optimized ring closure”). Two ring torsion angles are fixed independently within broad, allowed ranges, and the remaining torsion angles are determined uniquely in most cases. The independent torsion angles are chosen as ϕ and χ 2 , and ring closure is achieved without prohibitive strain through most of the ranges −130° < ϕ < −20° and −60° < χ 2 < 60°. Comparisons of predicted ring structures to 191 X‐ray diffraction structures from the literature, starting with the known values of ϕ and χ 2 , yielded root‐mean‐square deviations of 4.8° in χ 1 , 4.7° in χ 3 , 8.3° in χ 4 , and 0.3–2% in the ring bond angles and the N‐C δ distance. Semiempirical energies were calculated for the optimized structures using three sets of energy parameters from the literature. The energy surfaces show broad minima coinciding with the torsion angle regions in which the highest concentrations of observed structures are found. Two of the sets of energy parameters produce double minima corresponding to the “up” and “down” puckered conformations.