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Rouquet E, Dupont J, Lepere V, Garcia GA, Nahon L, Zehnacker A. Conformer-Selective Photoelectron Circular Dichroism. Angew Chem Int Ed Engl 2024; 63:e202401423. [PMID: 38442011 DOI: 10.1002/anie.202401423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/07/2024]
Abstract
Conformational flexibility and chirality both play a key role in molecular recognition. It is therefore very useful to develop spectroscopic methods that simultaneously probe both properties. It has been theoretically predicted that photoelectron circular dichroism (PECD) should be very sensitive to conformational isomerism. However, experimental proof has been less forthcoming and only exists for a very few favorable cases. Here, we present a new PECD scheme based on resonance-enhanced two-photon ionization (RE2PI) using UV/Vis nanosecond laser excitations. The spectral resolution obtained thereby guarantees conformer-selectivity by inducing resonant conformer-specific ππ* S1←S0 transitions. We apply this experimental scheme to the study of chiral 1-indanol, which exists in two conformers linked by a ring inversion and defined by the position of the hydroxyl group, namely axial and equatorial. We show that the PECD of the equatorial and axial forms considerably differ in sign, magnitude and shape. We also discuss the influence of the total ionization energy, vibronic excitation of intermediate and final states, and relative polarization of the excitation and ionization lasers. Conformer-specificity adds a new dimension to the applications of PECD in analytical chemistry addressing now the general case of floppy systems.
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Affiliation(s)
- Etienne Rouquet
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192, Gif sur Yvette, France
| | - Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192, Gif sur Yvette, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192, Gif sur Yvette, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
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2
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Dupont J, Hartwig B, Le Barbu-Debus K, Lepere V, Guillot R, Suhm MA, Zehnacker A. Homochiral vs. heterochiral preference in chiral self-recognition of cyclic diols. Phys Chem Chem Phys 2024; 26:10610-10621. [PMID: 38506638 DOI: 10.1039/d4cp00351a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The structure and clustering propensity of a chiral derivative of cis-1,2-cyclohexanediol, namely, 1-phenyl-cis-1,2-cyclohexanediol (cis-PCD), has been studied under supersonic expansion conditions by combining laser spectroscopy with quantum chemistry calculations. The presence of the phenyl substituent induces conformational locking relative to cis-1,2-cyclohexanediol (cis-CD), and only one conformer of the bare molecule is observed by both Raman and IR-UV double resonance spectroscopy. The homochiral preference inferred for the dimer formation at low enough temperature is in line with the formation of a conglomerate in the solid state. The change in clustering propensity in cis-PCD relative to trans-1,2-cyclohexanediol (trans-CD), which shows heterochiral preference, is explained by the presence of the phenyl substituent rather than the effect of cis-trans isomerism. Indeed the transiently chiral cis-CD also forms preferentially heterodimers, whose structure is very close to that of the corresponding trans-CD dimer.
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Affiliation(s)
- Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
| | - Beppo Hartwig
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
| | - Regis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 17 Av. des Sciences Université Paris-Saclay, F-91405 Orsay, France
| | - Martin A Suhm
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, rue André Rivière, Université Paris-Saclay, F-91405 Orsay, France.
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3
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Rouquet E, Roy Chowdhury M, Garcia GA, Nahon L, Dupont J, Lepère V, Le Barbu-Debus K, Zehnacker A. Induced photoelectron circular dichroism onto an achiral chromophore. Nat Commun 2023; 14:6290. [PMID: 37813848 PMCID: PMC10562374 DOI: 10.1038/s41467-023-42002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023] Open
Abstract
An achiral chromophore can acquire a chiral spectroscopic signature when interacting with a chiral environment. This so-called induced chirality is documented in electronic or vibrational circular dichroism, which arises from the coupling between electric and magnetic transition dipoles. Here, we demonstrate that a chiroptical response is also induced within the electric dipole approximation by observing the asymmetric scattering of a photoelectron ejected from an achiral chromophore in interaction with a chiral host. In a phenol-methyloxirane complex, removing an electron from an achiral aromatic π orbital localised on the phenol moiety results in an intense and opposite photoelectron circular dichroism (PECD) for the two enantiomeric complexes with (R) and (S) methyloxirane, evidencing the long-range effect (~5 Å) of the scattering chiral potential. This induced chirality has important structural and analytical implications, discussed here in the context of growing interest in laser-based PECD, for in situ, real time enantiomer determination.
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Affiliation(s)
- Etienne Rouquet
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, F-91190, St Aubin, France
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | | | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, F-91190, St Aubin, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, F-91190, St Aubin, France.
| | - Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France.
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4
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Yoshizawa K, Hirata K, Ishiuchi SI, Fujii M, Zehnacker A. Does Chiral Sensitivity of a Structure Depend on the Metal Core? Alkali Ion Complexes of Cyclo(Tyr-Tyr). Chemphyschem 2023; 24:e202300172. [PMID: 37435753 DOI: 10.1002/cphc.202300172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Alkali metal complexes of cyclic dipeptide cyclo Tyr-Tyr have been studied under cryogenic ion trap conditions. Their structure was obtained by combining Infra-Red Photo-Dissociation (IRPD) and quantum chemical calculations. The structural motif strongly depends on the relative chirality of the tyrosine residues. For residues of identical chirality, the cation interacts with one amide oxygen and one of the aromatic rings only; the distance between the aromatic rings does not change with the nature of the metal. In contrast, for residues of opposite chirality, the metal cation is located in between the two aromatic rings and interacts with both of them. The distance between the two aromatic rings strongly depends on the metal. Electronic spectra obtained by Ultra Violet Photodissociation (UVPD) spectroscopy and analysis of the UV photo-fragments shed light on the excited state deactivation processes, which depend on both the chirality of the residue and that of the metal ion core. Na+ stands out by the presence of low-lying charge transfer states resulting in the broadening of the electronic spectrum.
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Affiliation(s)
- Koki Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
- International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | - Anne Zehnacker
- International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, Japan
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
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5
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Witkowski M, Trzybiński D, Pawlędzio S, Woźniak K, Dzwolak W, Królikowska A. The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State. Molecules 2023; 28:5902. [PMID: 37570871 PMCID: PMC10421304 DOI: 10.3390/molecules28155902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
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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Affiliation(s)
- Marcin Witkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Agata Królikowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
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6
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Chotera‐Ouda A, Jeziorna A, Kaźmierski S, Dolot R, Dudek MK, Potrzebowski MJ. “Crystal memory” Affects the Properties of Peptide Hydrogels – The Case of the Cyclic Tyr‐Tyr dipeptide. Chemistry 2022; 28:e202202005. [DOI: 10.1002/chem.202202005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Agata Chotera‐Ouda
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Agata Jeziorna
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
- Lodz Institute of Technology Łukasiewicz Research Network M. Sklodowskiej-Curie 19/27 90-570 Lodz Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Marta K. Dudek
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences Sienkiewicza 112 90-363 Lodz Poland
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7
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Yoshizawa K, Hirata K, Ishiuchi SI, Fujii M, Zehnacker A. Do Stereochemical Effects Overcome a Charge-Induced Perturbation in Isolated Protonated Cyclo(Tyr-Tyr)? J Phys Chem A 2022; 126:6387-6394. [PMID: 36098637 DOI: 10.1021/acs.jpca.2c03789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr), namely, cyclo(LTyr-LTyr)H+ and cyclo(LTyr-DTyr)H+, are studied in a cryogenic ion trap by means of IR photodissociation spectroscopy combined with quantum chemical calculations. The two diastereomers have similar structures in which one of the rings is folded over the DKP ring and the other one is extended in a trans geometry, allowing a strong OH+···π interaction to take place. This contrasts to the observation of a stacked geometry for neutral cyclo(LTyr-LTyr) only under supersonic expansion conditions that do not exist for cyclo(LTyr-DTyr). In the protonated form, the strength of the OH+···π interaction is different for the two diastereomers, resulting in a ∼110 cm-1 difference in the ν(OH+) frequency and a smaller but clearly identifiable difference in the protonated amide ν(NH) frequency. Stereochemical effects are therefore still evidenced despite the strong perturbation due to the excess charge.
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Affiliation(s)
- Koki Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.,International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Anne Zehnacker
- International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, Orsay F-91405, France
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8
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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
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9
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Dupont J, Guillot R, Lepère V, Zehnacker A. Jet-cooled laser spectroscopy and solid-state vibrational circular dichroism of the cyclo-(Tyr-Phe) diketopiperazine dipeptide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Abstract
Protonated cyclic dipeptides undergo collision-induced dissociation, and this reaction mechanism strongly depends on the symmetry and the nature of the residues. We review the main dissociation mechanism for a series of cyclic dipeptides, obtained through chemical dynamics simulations. The systems range from the symmetrical cyclo-(glycyl-glycyl), with two possible symmetrical protonation sites located on the peptide ring, to cyclo-(tyrosyl-prolyl), where the symmetry of protonation sites on the peptide ring is broken by the dissimilar nature of the different residues. Finally, cyclo-(phenylalanyl-histidyl) shows a completely asymmetric situation, with the proton located on one of the dipeptide side chains, which explains the peculiar fragmentation mechanism induced by shuttling the proton, whose efficiency is strongly dependent on the relative chirality of the residues.
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11
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Segatta F, Rogers DM, Dyer NT, Guest EE, Li Z, Do H, Nenov A, Garavelli M, Hirst JD. Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides. Molecules 2021; 26:E396. [PMID: 33451152 PMCID: PMC7828623 DOI: 10.3390/molecules26020396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Naomi T. Dyer
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Ellen E. Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China;
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
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12
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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Pérez-Mellor A, Alata I, Lepère V, Zehnacker A. Conformational Study of the Jet-Cooled Diketopiperazine Peptide Cyclo Tyrosyl-Prolyl. J Phys Chem B 2019; 123:6023-6033. [PMID: 31268717 DOI: 10.1021/acs.jpcb.9b04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The conformational landscape of the diketopiperazine (DKP) dipeptide built on tyrosine and proline, namely, cyclo Tyr-Pro, is studied by combining resonance-enhanced multiphoton ionization, double resonance infrared ultraviolet (IR-UV) spectroscopy, and quantum chemical calculations. Despite the geometrical constraints due the two aliphatic rings, DKP and proline, cyclo Tyr-Pro is a flexible molecule. For both diastereoisomers, cyclo LTyr-LPro and cyclo LTyr-DPro, two structural families coexist under supersonic jet conditions. In the most stable conformation, the aromatic tyrosine substituent is folded over the DKP ring (g+ geometry of the aromatic ring) as it is in the solid state. The other structure is completely extended (g- geometry of the aromatic ring) and resembles that proposed for the vapor phase. IR-UV results are not sufficient for unambiguous assignment of the observed spectra to either folded or extended conformations and the simulation of the vibronic pattern of the S0-S1 transition is necessary. Still, the comparison between IR-UV results and anharmonic calculations allows explanation of the minor structural differences between cyclo LTyr-LPro and cyclo LTyr-DPro in terms of different NH···π and CH···π interactions.
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Affiliation(s)
- Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay , France
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