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Merten C. Modelling solute-solvent interactions in VCD spectra analysis with the micro-solvation approach. Phys Chem Chem Phys 2023; 25:29404-29414. [PMID: 37881890 DOI: 10.1039/d3cp03408a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy has become an important part of the (stereo-)chemists' toolbox as a reliable method for the determination of absolute configurations. Being the chiroptical version of infrared spectroscopy, it has also been recognized as being very sensitive to conformational changes and intermolecular interactions. This sensitivity originates from the fact that the VCD spectra of individual conformers are often more different than their IR spectra, so that changes in conformational distributions or band positions and intensities become more pronounced. What is an advantage for studies focussing on intermolecular interactions can, however, quickly turn into a major obstacle during AC determinations: solute-solvent interactions can have a strong influence on spectral signatures and they must be accurately treated when simulating VCD and IR spectra. In this perspective, we showcase selected examples which exhibit particularly pronounced solvent effects. It is demonstrated that it is typically sufficient to model solute-solvent interactions by placing single solvent molecules near hydrogen bonding sites of the solute and subsequently use the optimized structures for spectra simulations. This micro-solvation approach works reasonably well for medium-sized, not too conformationally flexible molecules. We thus also discuss its limitations and outline the next steps that method development needs to take in order to further improve the workflows for VCD spectra predictions.
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Affiliation(s)
- Christian Merten
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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2
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Batista JM, Nicu VP. Simplified and enhanced VCD analysis of cyclic peptides guided by artificial intelligence. Phys Chem Chem Phys 2023; 25:22111-22116. [PMID: 37560904 DOI: 10.1039/d3cp01986a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Cyclic peptides are privileged structures in medicinal chemistry; however, their solution-state structure characterization is difficult. Vibrational circular dichroism (VCD) spectroscopy is a powerful alternative to NMR, but requires challenging calculations. We present a VCD approach guided by a genetic algorithm, which is simple, more effective, and has a higher conformer resolution.
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Affiliation(s)
- João M Batista
- Federal University of São Paulo, Institute of Science and Technology, R. Talim 330, 12231-280, São José dos Campos-SP, Brazil.
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3
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Golub TP, Feßner M, Engelage E, Merten C. Dynamic Stereochemistry of a Biphenyl‐Bisprolineamide Model Catalyst and its Imidazolidinone Intermediates. Chemistry 2022; 28:e202201317. [PMID: 35611719 PMCID: PMC9545261 DOI: 10.1002/chem.202201317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 12/15/2022]
Abstract
In this study, we characterize the dynamic stereochemistry of a biphenyl‐2,2’‐bis(proline amide) catalyst in chloroform and DMSO as representative weakly and strongly hydrogen bonding solvents. Using vibrational circular dichroism (VCD) spectroscopy and density functional theory (DFT) based spectra calculations, we show that the preferred axial stereochemistry of the catalyst is determined by solute‐solvent interactions. Explicitly considering solvation with DMSO molecules is found to be essential to correctly predict the conformational preferences of the catalyst. Furthermore, we investigate the stereochemistry of the corresponding enamines and imidazolidinones that are formed upon reaction with isovaleraldehyde. The enamines are found to rapidly convert to endo‐imidazolidinones and the thermodynamically favored exo‐imidazolidinones are formed only slowly. The present study demonstrates that the stereochemistry of these imidazolidinones can be deduced directly from the VCD spectra analysis without any further detailed analysis of NMR spectra. Hence, we herein exemplify the use of VCD spectroscopy for an in situ characterization of intermediates relevant in asymmetric catalysts.
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Affiliation(s)
- Tino P. Golub
- Ruhr Universität Bochum Fakultät für Chemie und Biochemie Organische Chemie II Universitätsstraße 150 44801 Bochum Germany
| | - Malte Feßner
- Ruhr Universität Bochum Fakultät für Chemie und Biochemie Organische Chemie II Universitätsstraße 150 44801 Bochum Germany
| | - Elric Engelage
- Ruhr Universität Bochum Fakultät für Chemie und Biochemie Organische Chemie II Universitätsstraße 150 44801 Bochum Germany
| | - Christian Merten
- Ruhr Universität Bochum Fakultät für Chemie und Biochemie Organische Chemie II Universitätsstraße 150 44801 Bochum Germany
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4
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Scholten K, Merten C. Solvation of the Boc-Val-Phe- nPr peptide characterized by VCD spectroscopy and DFT calculations. Phys Chem Chem Phys 2022; 24:3611-3617. [PMID: 35103263 DOI: 10.1039/d1cp05457k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The conformational preferences of peptides are strongly determined by hydrogen bonding interactions. Intermolecular solute-solvent interactions compete with intramolecular interactions, which typically stabilize the secondary structure of the peptide. The analysis of vibrational circular dichroism (VCD) spectra can give insights into solvation-induced changes in the conformational distribution of small peptides. Here we describe the VCD spectroscopic characterization of the model peptide Boc-Val-Phe-nPr in chloroform as representative for a weakly interacting solvent and dimethyl sulfoxide (DMSO-d6) as a strongly hydrogen bonding solvent. We show that the conformational preferences of the peptide in chloroform are well-described by the computationally predicted distribution of the isolated molecule assuming only implicit solvation effects through a continuum solvation model. In order to simulate the spectra recorded in DMSO-d6, solvation was accounted for explicitly by computed microsolvated structures containing one to three solvent molecules. A good match of the computed spectra with the experimental data is obtained by this method. Comparing the conformational distributions in deuterated chloroform-d1 and DMSO-d6, structures with intramolecular hydrogen bonds such as the (δ,δ)-conformer family contribute to the conformational distribution only when there is no strong interaction with the solvent. This is in contrast to the results for the related Boc-Pro-Phe-nPr studied before, for which the intramolecular interaction was found to persist in DMSO-d6. Furthermore, we discuss the influence of hydrogen bonding to different numbers of solvent molecules on the spectral signatures and show that the structure of the peptide in DMSO-d6 is best described as a mixture of twofold-solvated (δ,β)- and threefold-solvated (β,β)-conformers.
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Affiliation(s)
- Kevin Scholten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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5
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Saemi Yokomichi MA, Leite Silva HR, Eivazian Vianna Nogueira Brandao L, Festozo Vicente E, Batista Junior JM. Conformational preferences induced by cyclization in orbitides: a vibrational CD study. Org Biomol Chem 2022; 20:1306-1314. [DOI: 10.1039/d1ob02170b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orbitides are bioactive head-to-tail natural cyclic peptides from plant species. Their bioactivity is intrinsically related to the main conformations adopted in solution, whose correct characterization represents an important bottleneck for...
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6
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Vermeyen T, Merten C. Solvation and the secondary structure of a proline-containing dipeptide: insights from VCD spectroscopy. Phys Chem Chem Phys 2020; 22:15640-15648. [PMID: 32617548 DOI: 10.1039/d0cp02283g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study we investigate the IR and VCD spectra of the diastereomeric dipeptide Boc-Pro-Phe-(n-propyl) 1 in chloroform-d1 (CDCl3) and the strongly hydrogen bonding solvent dimethylsulfoxide-d6 (DMSO-d6). From comparison of the experimental spectra, the amide II spectral region is identified as marker signature for the stereochemistry of the dipeptide: the homochiral LL-1 features a (+/-)-pattern in the amide II region of the VCD spectrum, while the amide II signature of the diastereomer LD-1 is inverted. Computational analysis of the IR and VCD spectra of LL-1 reveals that the experimentally observed amide II signature is characteristic for a βI-turn structure of the peptide. Likewise, the inverted pattern found for LD-1 arises from a βII-turn structure of the dipeptide. Following a micro-solvation approach, the experimental spectra recorded in DMSO-d6 are computationally well reproduced by considering only a single solvent molecule in a hydrogen bond with N-H groups. Considering a second solvent molecule, which would lead to a cleavage of intramolecular hydrogen bonds in 1, is found to give a significantly worse match with the experiment. Hence, the detailed computational analysis of the spectra of LL- and LD-1 recorded in DMSO-d6 confirms that the intramolecular hydrogen bonding pattern, that stabilizes the β-turns and other conformations of LL- and LD-1 in apolar solvents, remains intact. Our findings also show that it is essential to consider solvation explicitly in the analysis of the IR and VCD spectra of dipeptides in strongly hydrogen bonding solvents. As the solute-solvent interactions affect both conformational preferences and spectral signatures, it is also demonstrated that this inclusion of solvent molecules cannot be circumvented by applying fitting procedures to non-solvated structures.
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Affiliation(s)
- Tom Vermeyen
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany. and University of Antwerp, Department of Chemistry, MolSpec Group, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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7
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Tomassi S, Trotta AM, Ieranò C, Merlino F, Messere A, Rea G, Santoro F, Brancaccio D, Carotenuto A, D'Amore VM, Di Leva FS, Novellino E, Cosconati S, Marinelli L, Scala S, Di Maro S. Disulfide Bond Replacement with 1,4‐ and 1,5‐Disubstituted [1,2,3]‐Triazole on C‐X‐C Chemokine Receptor Type 4 (CXCR4) Peptide Ligands: Small Changes that Make Big Differences. Chemistry 2020; 26:10113-10125. [DOI: 10.1002/chem.202002468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/29/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Stefano Tomassi
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Anna Maria Trotta
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Caterina Ieranò
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Francesco Merlino
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Anna Messere
- DiSTABiF University of Campania “Luigi Vanvitelli” Via Vivaldi 43 81100 Caserta Italy
| | - Giuseppina Rea
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Federica Santoro
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Diego Brancaccio
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Alfonso Carotenuto
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Ettore Novellino
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Sandro Cosconati
- DiSTABiF University of Campania “Luigi Vanvitelli” Via Vivaldi 43 81100 Caserta Italy
| | - Luciana Marinelli
- Department of Pharmacy University of Naples “Federico II” Via Domenico Montesano 49 80131 Naples Italy
| | - Stefania Scala
- U.O.C. “Bersagli molecolari del microambiente” Istituto Nazionale Tumori—IRCCS—Fondazione “G. Pascale” Via M. Semmola 80131 Naples Italy
| | - Salvatore Di Maro
- DiSTABiF University of Campania “Luigi Vanvitelli” Via Vivaldi 43 81100 Caserta Italy
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8
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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9
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Berger N, Wollny LJB, Sokkar P, Mittal S, Mieres‐Perez J, Stoll R, Sander W, Sanchez‐Garcia E. Solvent‐Enhanced Conformational Flexibility of Cyclic Tetrapeptides. Chemphyschem 2019; 20:1664-1670. [DOI: 10.1002/cphc.201900345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Nadja Berger
- Organische Chemie IIRuhr-University of Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Laura J. B. Wollny
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Pandian Sokkar
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen Universitätsstr. 2 45141 Essen
| | - Sumit Mittal
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen Universitätsstr. 2 45141 Essen
| | - Joel Mieres‐Perez
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen Universitätsstr. 2 45141 Essen
| | - Raphael Stoll
- Biomolecular NMR SpectroscopyRuhr-University of Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Wolfram Sander
- Organische Chemie IIRuhr-University of Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Elsa Sanchez‐Garcia
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen Universitätsstr. 2 45141 Essen
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10
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Bayse CA, Pollard DB. Conformation dynamics of cyclic disulfides and selenosulfides in CXXC(U) (X = Gly, Ala) tetrapeptide redox motifs. J Pept Sci 2019; 25:e3160. [PMID: 30873692 DOI: 10.1002/psc.3160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 02/01/2023]
Abstract
Thioredoxin fold proteins often contain a Cys-(Xxx)n -Cys(Sec) or CXn C(U) motif, where the active cysteine (C) or selenocysteine (U) is bridged by X residues, which vary with protein function. The effect of the X residues on the conformation space of the oxidized disulfide and selenosulfide forms of the CXXC(U) motif has been investigated using molecular dynamics (MD) and density functional theory. Multi-microsecond-length MD simulations of the CGGC, CGAC, and CAGC cyclic peptides show that CGGC rings readily exchange between several conformations over the course of the simulation, but steric interactions with the methyl group of Ala limit the conformation space available to the cyclic peptide, especially for CGAC. The potential for the motif to be reduced, as measured by the energy of the lowest unoccupied molecular orbitals, is dependent upon the ring conformation. These results suggest that control of available conformations by the bridging residues and the protein tertiary structure may be important for defining the function of the CXXC motif. Theoretical 77 Se chemical shifts of the selenosulfide moiety are dependent upon the conformation and/or intramolecular Se···O interactions with the backbone carbonyl group of the C-terminal U residue.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
| | - Deanna B Pollard
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529
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11
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Rode JE, Dobrowolski JC, Lyczko K, Wasiewicz A, Kaczorek D, Kawęcki R, Zając G, Baranska M. Chiral Thiophene Sulfonamide—A Challenge for VOA Calculations. J Phys Chem A 2017; 121:6713-6726. [DOI: 10.1021/acs.jpca.6b11015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joanna E. Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Aleksandra Wasiewicz
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Dorota Kaczorek
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Grzegorz Zając
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
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12
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Merten C. Vibrational optical activity as probe for intermolecular interactions. Phys Chem Chem Phys 2017; 19:18803-18812. [DOI: 10.1039/c7cp02544k] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A detailed VCD spectroscopic analysis of well-selected chiral model systems can give valuable and unprecedented insights into intermolecular interactions such as solvation or reactant–substrate binding in catalysis.
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