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Solid‐state structure of cyclic dipeptides: an X‐ray and computational study of cis‐ and trans ‐diketopiperazines of N ‐methyl‐phenylalanine with the thia‐pipecolic acids and thia‐prolines
Author(s) -
Budesinsky Milos,
Cisarova Ivana,
Borremans Frans,
Martins Jose C.,
Pauwels Ewald
Publication year - 2017
Publication title -
acta crystallographica section b
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.604
H-Index - 33
ISSN - 2052-5206
DOI - 10.1107/s2052520617014731
Subject(s) - chemistry , pipecolic acid , diketopiperazines , hydrogen bond , planarity testing , molecule , ring (chemistry) , crystal structure , crystallography , stereochemistry , imino acid , dipeptide , intermolecular force , bicyclic molecule , amide , amino acid , proline , organic chemistry , biochemistry
Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia‐pipecolic acid (with sulfur in the β, γ or δ position) or thia‐proline (with sulfur in the β or γ position) and N ‐methyl phenylalanine [(NMe)Phe]: cyclo [(β‐S)Pip‐(NMe)Phe], cyclo [(γ‐S)Pip‐(NMe)Phe], cyclo [(δ‐S)Pip‐(NMe)Phe], cyclo [(β‐S)Pro‐(NMe)Phe] and cyclo [(γ‐S)Pro‐(NMe)Phe] were determined with X‐ray crystallography. Density functional theory calculations of these molecules in the gas phase succeed in reproducing the observed molecular conformations in the crystal remarkably well. This illustrates the weak to moderate impact of intermolecular packing forces in the absence of classical N—H…O hydrogen bonds. The effect of sulfur on the geometry of the DKP ring and details of amide bond non‐planarity are discussed. Molecular flexibility of the DKP ring, as estimated from the calculated deformation energies of its endocyclic ring torsion angles, is not in general the decisive factor for the occurrence of multiple symmetry independent molecules in the unit cell ( Z ′ > 1), though in some cases a correlation is observed.