The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Marcin Witkowski; Damian Trzybiński; Sylwia Pawlędzio; Krzysztof Woźniak; Wojciech Dzwolak; Agata Królikowska

doi:10.3390/molecules28155902

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Marcin Witkowski, Damian Trzybiński, Sylwia Pawlędzio, Krzysztof Woźniak, Wojciech Dzwolak, Agata Królikowska

Single Crystal Diffraction

Research output: Contribution to journal › Article › peer-review

Abstract

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 cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-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 P-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(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

Original language	English
Article number	5902
Journal	Molecules
Volume	28
Issue number	15
DOIs	https://doi.org/10.3390/molecules28155902
State	Published - Aug 2023

Funding

CCDC 2277461 contains the supplementary crystallographic data for this paper. These data can be obtained freely via http://www.ccdc.cam.ac.uk/data_request/cif (accessed on 4 August 2023), by emailing [email protected] , or by contacting directly the Cambridge Crystallographic Data Centre (12 Union Road, Cambridge CB2 1EZ, UK. Fax: +44-1223-336033). This study was carried out at the Biological and Chemical Research Centre, University of Warsaw, established within a project co-financed by the European Union with the European Regional Development Fund under the Operational Programme Innovative Economy, 2007\u20132013. The collection of X-ray diffraction data was accomplished at the Core Facility for Crystallographic and Biophysical Research to support the development of medicinal products. The \u201CCore Facility for Crystallographic and biophysical research to Support the Development of medicinal products\u201D project was carried out within the TEAM-TECH Core Facility Programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund. The computational part of the study was supported by the Wroclaw Centre for Networking and Supercomputing (M.W.), Grant No. 321. The experimental part of this work was financed with funds from the National Science Centre of Poland, Grant No. 2018/29/B/ST4/01310 (A.K.).

Keywords

DFT modeling
Raman spectroscopy
X-ray diffraction
cyclic dipeptides
structure determination
vibrational spectroscopy

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10.3390/molecules28155902

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abstract = "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 cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-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 P-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(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.",

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AU - Pawlędzio, Sylwia

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AU - Królikowska, Agata

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AB - 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 cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-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 P-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(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

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The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

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