The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(<span style="font-variant: small-caps">l</span>-Cys-<span style="font-variant: small-caps">d</span>-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from <i>cis</i> to <i>trans</i>)...

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Bibliographic Details
Main Authors: Marcin Witkowski, Damian Trzybiński, Sylwia Pawlędzio, Krzysztof Woźniak, Wojciech Dzwolak, Agata Królikowska
Format: Article
Language:English
Published: MDPI AG 2023-08-01
Series:Molecules
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Online Access:https://www.mdpi.com/1420-3049/28/15/5902
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Summary:Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from <i>cis</i> to <i>trans</i>) can lead to significant structural differences. This work presents the results of a study of cyclo(<span style="font-variant: small-caps;">l</span>-Cys-<span style="font-variant: small-caps;">d</span>-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the <i>P</i>-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(<span style="font-variant: small-caps;">l</span>-Cys-<span style="font-variant: small-caps;">d</span>-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(<span style="font-variant: small-caps;">l</span>-Cys-<span style="font-variant: small-caps;">d</span>-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.
ISSN:1420-3049