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Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo (Pip-Phe), cyclo (Pro-Phe) and their N-methyl derivatives

Milos Budesinsky, Ivana Cisarova, Jaroslav Podlaha, Frans Borremans UGent, José Martins UGent, Michel Waroquier UGent and Ewald Pauwels UGent (2010) ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE. 66(6). p.662-677
abstract
The crystal structures of eight cyclodipeptides are determined, incorporating pipecolic acid or proline and phenylalanine or N-methyl phenylalanine. This set of structures allows the evaluation of the effects on molecular conformation and crystal packing of imino acid ring-size, relative configuration of the two amino acids, and N-methylation. In the nonmethylated compounds, hydrogen-bonding interactions form one-dimensional motifs that dominate the packing arrangement. Three compounds have more than one symmetryindependent molecule in the asymmetric unit (Z0 > 1), indicative of a broad and shallow molecular energy minimum. Density functional theory calculations reveal the interplay between inter- and intramolecular factors in the crystals. Only for the N-methylated compounds do simulations of the molecules in the isolated state succeed to reproduce the observed crystallographic conformations. Puckering of the diketopiperazine ring and the deviation from planarity of the amide bonds are not reproduced in the remaining compounds. Cluster in vacuo calculations with a central cyclodipeptide molecule surrounded by hydrogen-bound molecules establish that hydrogen bonding is of major importance but that other intermolecular interactions must also contribute substantially to the crystal structure. More advanced periodic calculations, incorporating the crystallographic environment to the full extent, are necessary to correctly describe all the conformational features of these cyclodipeptide crystals.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
cluster in vacuo, cyclic dipeptides, periodic approach, HYDROGEN-BONDED TAPES, DENSITY-FUNCTIONAL THERMOCHEMISTRY, CRYSTAL-STRUCTURE, INTERMOLECULAR INTERACTIONS, MAGNETIC-RESONANCE, CONFORMATION, PROLINE, DIKETOPIPERAZINES, DIOXOPIPERAZINES, PEPTIDE
journal title
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE
Acta Crystallogr. Sect. B-Struct. Sci.
volume
66
issue
6
pages
662 - 677
Web of Science type
Article
Web of Science id
000284549900009
JCR category
CRYSTALLOGRAPHY
JCR impact factor
1.829 (2010)
JCR rank
10/25 (2010)
JCR quartile
2 (2010)
ISSN
0108-7681
DOI
10.1107/S0108768110040243
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1076083
handle
http://hdl.handle.net/1854/LU-1076083
date created
2010-11-18 08:41:00
date last changed
2013-09-17 10:50:08
@article{1076083,
  abstract     = {The crystal structures of eight cyclodipeptides are determined, incorporating pipecolic acid or proline and phenylalanine or N-methyl phenylalanine. This set of structures allows the evaluation of the effects on molecular conformation and crystal packing of imino acid ring-size, relative configuration of the two amino acids, and N-methylation. In the nonmethylated compounds, hydrogen-bonding interactions form one-dimensional motifs that dominate the packing arrangement. Three compounds have more than one symmetryindependent molecule in the asymmetric unit (Z0 {\textrangle} 1), indicative of a broad and shallow molecular energy minimum. Density functional theory calculations reveal the interplay between inter- and intramolecular factors in the crystals. Only for the N-methylated compounds do simulations of the molecules in the isolated state succeed to reproduce the observed crystallographic conformations. Puckering of the diketopiperazine ring and the deviation from planarity of the amide bonds are not reproduced in the remaining compounds. Cluster in vacuo calculations with a central cyclodipeptide molecule surrounded by hydrogen-bound molecules establish that hydrogen bonding is of major importance but that other intermolecular interactions must also contribute substantially to the crystal structure. More advanced periodic calculations, incorporating the crystallographic environment to the full extent, are necessary to correctly describe all the conformational features of these cyclodipeptide crystals.},
  author       = {Budesinsky, Milos and Cisarova, Ivana and Podlaha, Jaroslav and Borremans, Frans and Martins, Jos{\'e} and Waroquier, Michel and Pauwels, Ewald},
  issn         = {0108-7681},
  journal      = {ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE},
  keyword      = {cluster in vacuo,cyclic dipeptides,periodic approach,HYDROGEN-BONDED TAPES,DENSITY-FUNCTIONAL THERMOCHEMISTRY,CRYSTAL-STRUCTURE,INTERMOLECULAR INTERACTIONS,MAGNETIC-RESONANCE,CONFORMATION,PROLINE,DIKETOPIPERAZINES,DIOXOPIPERAZINES,PEPTIDE},
  language     = {eng},
  number       = {6},
  pages        = {662--677},
  title        = {Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo (Pip-Phe), cyclo (Pro-Phe) and their N-methyl derivatives},
  url          = {http://dx.doi.org/10.1107/S0108768110040243},
  volume       = {66},
  year         = {2010},
}

Chicago
Budesinsky, Milos, Ivana Cisarova, Jaroslav Podlaha, Frans Borremans, José Martins, Michel Waroquier, and Ewald Pauwels. 2010. “Structures of Cyclic Dipeptides: An X-ray and Computational Study of Cis- and Trans-cyclo (Pip-Phe), Cyclo (Pro-Phe) and Their N-methyl Derivatives.” Acta Crystallographica Section B-structural Science 66 (6): 662–677.
APA
Budesinsky, M., Cisarova, I., Podlaha, J., Borremans, F., Martins, J., Waroquier, M., & Pauwels, E. (2010). Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo (Pip-Phe), cyclo (Pro-Phe) and their N-methyl derivatives. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 66(6), 662–677.
Vancouver
1.
Budesinsky M, Cisarova I, Podlaha J, Borremans F, Martins J, Waroquier M, et al. Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo (Pip-Phe), cyclo (Pro-Phe) and their N-methyl derivatives. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE. 2010;66(6):662–77.
MLA
Budesinsky, Milos, Ivana Cisarova, Jaroslav Podlaha, et al. “Structures of Cyclic Dipeptides: An X-ray and Computational Study of Cis- and Trans-cyclo (Pip-Phe), Cyclo (Pro-Phe) and Their N-methyl Derivatives.” ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE 66.6 (2010): 662–677. Print.