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Solid-state structure of cyclic dipeptides : an X-ray and computational study of cis- and trans-diketo-piperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines

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Abstract
Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the beta, gamma or delta position) or thia-proline (with sulfur in the beta or gamma position) and N-methyl phenylalanine [(NMe) Phe]: cyclo[(beta-S) Pip-(NMe) Phe], cyclo[(gamma-S) Pip-(NMe) Phe], cyclo[(delta-S) Pip-(NMe) Phe], cyclo[(beta-S) Pro-(NMe) Phe] and cyclo[(beta-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 center dot center dot center dot center dot 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.
Keywords
HYDROGEN-BONDED TAPES, SULFOXIDE CONFIGURATION, SOLUTION CONFORMATION, NMR-SPECTROSCOPY, DFT CALCULATIONS, RINGS, DIKETOPIPERAZINES, DIOXOPIPERAZINES, REFINEMENT, PEPTIDE, sulfur-containing cyclic dipeptides, X-ray crystal structures, DFT, calculations, molecular flexibility

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Chicago
Budesinsky, Milos, Ivana Cisarova, Frans Borremans, José Martins, and Ewald Pauwels. 2017. “Solid-state Structure of Cyclic Dipeptides : an X-ray and Computational Study of Cis- and Trans-diketo-piperazines of N-methyl-phenylalanine with the Thia-pipecolic Acids and Thia-prolines.” Acta Crystallographica Section B-structural Science Crystal Engineering and Materials 73 (6): 1179–1193.
APA
Budesinsky, M., Cisarova, I., Borremans, F., Martins, J., & Pauwels, E. (2017). Solid-state structure of cyclic dipeptides : an X-ray and computational study of cis- and trans-diketo-piperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS, 73(6), 1179–1193.
Vancouver
1.
Budesinsky M, Cisarova I, Borremans F, Martins J, Pauwels E. Solid-state structure of cyclic dipeptides : an X-ray and computational study of cis- and trans-diketo-piperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS. 2017;73(6):1179–93.
MLA
Budesinsky, Milos et al. “Solid-state Structure of Cyclic Dipeptides : an X-ray and Computational Study of Cis- and Trans-diketo-piperazines of N-methyl-phenylalanine with the Thia-pipecolic Acids and Thia-prolines.” ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 73.6 (2017): 1179–1193. Print.
@article{8543997,
  abstract     = {Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the beta, gamma or delta position) or thia-proline (with sulfur in the beta or gamma position) and N-methyl phenylalanine [(NMe) Phe]: cyclo[(beta-S) Pip-(NMe) Phe], cyclo[(gamma-S) Pip-(NMe) Phe], cyclo[(delta-S) Pip-(NMe) Phe], cyclo[(beta-S) Pro-(NMe) Phe] and cyclo[(beta-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 center dot center dot center dot center dot 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.},
  author       = {Budesinsky, Milos and Cisarova, Ivana and Borremans, Frans and Martins, José and Pauwels, Ewald},
  issn         = {2052-5206},
  journal      = {ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS},
  keywords     = {HYDROGEN-BONDED TAPES,SULFOXIDE CONFIGURATION,SOLUTION CONFORMATION,NMR-SPECTROSCOPY,DFT CALCULATIONS,RINGS,DIKETOPIPERAZINES,DIOXOPIPERAZINES,REFINEMENT,PEPTIDE,sulfur-containing cyclic dipeptides,X-ray crystal structures,DFT,calculations,molecular flexibility},
  language     = {eng},
  number       = {6},
  pages        = {1179--1193},
  title        = {Solid-state structure of cyclic dipeptides : an X-ray and computational study of cis- and trans-diketo-piperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines},
  url          = {http://dx.doi.org/10.1107/S2052520617014731},
  volume       = {73},
  year         = {2017},
}

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