1
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Taniguchi T, Agbo DO, Yang Q, Kapitán J, Wu T, Oyama S, Akai S, Sawama Y, Bouř P. Raman optical activity study of deuterated sugars: deuterium labelling as a tool for structural analysis. Phys Chem Chem Phys 2024; 26:21568-21574. [PMID: 39082369 DOI: 10.1039/d4cp02406k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Structural analyses using Raman optical activity (ROA) spectroscopy conventionally rely on vibrational signals in the fingerprint region ranging from 100 to 1800 cm-1. Use of deuterium labelling to observe ROA signals in the C-D stretching region provides additional information about a local structure of large molecular systems. So far, the potential of C-D stretching ROA signals for structural analysis has rarely been explored. In the present work, we synthesized model deuterated glucose monosaccharides and studied their ROA properties by employing molecular dynamics and density functional theory to interpret the spectra. A good agreement between the simulated and experimental spectra is achieved when the proper conformer ratios are considered. This shows the usefulness of ROA spectroscopy assisted by deuterium labelling for stereochemical and conformational analysis.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Tao Wu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Shuki Oyama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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Berešová M, Bufka J, Šafařík M, Bouř P, Šebestík J. Conformations and hydration of halopropionic acids studied by molecular dynamics and Raman optical activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123852. [PMID: 38217987 DOI: 10.1016/j.saa.2024.123852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Chiral 2-halopropionic acids and their derivatives were synthesized and their properties studied computationally using Raman and Raman optical activity (ROA) spectroscopy. For neat acids present as liquids small amount of water led to significant changes in the spectra, resulting even to flipping of some ROA band signs. We find this interesting for the role water plays in interpretation of vibrational optical activity spectra of biomolecules. Analysis of the results shows that when the water is present, it can change ROA band signs due to the changes in acidobasic equilibrium. Corresponding esters without acidic hydrogens do not exhibit such effects.
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Affiliation(s)
- Marie Berešová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Jiří Bufka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic; Department of Pediatrics, Faculty of Medicine in Pilsen, Faculty Hospital, Charles University in Prague, Alej Svobody 80, 323 00 Pilsen, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.
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3
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D'haese LCG, Daugey N, Pitrat D, Brotin T, Kapitán J, Liégeois V. Understanding the surrounding effects on Raman optical activity signatures of a chiral cage system: Cryptophane-PP-111. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123484. [PMID: 37898056 DOI: 10.1016/j.saa.2023.123484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/18/2023] [Accepted: 10/01/2023] [Indexed: 10/30/2023]
Abstract
Cryptophane molecules are cage-like structures consisting in two hemispheres, each made of three benzene rings. These hemispheres are bound together with three O(CH2)nOlinkers of various lengths giving rise to a plethora of cryptophane derivatives. Moreover, they are able to encapsulate neutral guests: CH2Cl2, CHCl3, …; and charged species: Cs+, Tl+, …. Finally, they exhibit chiroptical properties thanks to the anti arrangement of the linkers between the hemispheres. This work focuses on the Raman optical activity (ROA) signatures of Cryptophane-111 (n=1 for each linker). More specifically, we aim at simulating accurately its ROA spectra with and without a xenon atom inside its cavity. Experimental data (Buffeteau et al., 2017) have already demonstrated the effect of the encapsulation in the low-wavenumbers region. To generate the initial structures, we rely on the novel Conformer-Rotamer Ensemble Sampling Tool (CREST) program, developed by S. Grimme and co-workers. This is required due to the flexibility provided by the linkers. The CREST algorithm seems promising and has already been used to sample the potential energy surface (PES) of target systems before the simulation of their vibrational spectroscopies (Eikås et al., 2022). We observe large similarities between the two sets of conformers (one with and one without Xe encapsulated), demonstrating the robustness of the CREST algorithm. For corresponding structures, the presence of xenon pushed the two hemispheres slightly further apart. After optimization at the DFT level, only one unique conformer has a Boltzmann population ratio greater than 1%, pointing out the relative rigidity of the cage. Based on this unique conformer, our simulations are in good agreement with the experimental data. Regarding xenon encapsulation, the (experimental and theoretical) ROA signatures at low wavenumbers are impacted: slight shifts in wavenumbers are observed as well as a decrease in relative ROA intensity for bands around 150 cm-1. The wavenumber shifts were very well reproduced by our simulations, but the experimental decrease in the ROA intensity was unfortunately not reproduced.
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Affiliation(s)
- Lou C G D'haese
- Theoretical Chemistry Laboratory (LCT), Namur Institute of Structured Matter (NISM), University of Namur, 5000 Namur, Belgium.
| | - Nicolas Daugey
- Groupe Spectroscopie Moléculaire (GSM), Institut des Sciences Moléculaires (ISM), UMR-5255 CNRS, University of Bordeaux, 33405 Talence, France
| | - Delphine Pitrat
- Laboratoire de Chimie de l'ENSL, UMR-5182 CNRS, University of Lyon, 69342 Lyon, France
| | - Thierry Brotin
- Laboratoire de Chimie de l'ENSL, UMR-5182 CNRS, University of Lyon, 69342 Lyon, France
| | - Josef Kapitán
- Department of Optics, Palacký University of Olomouc, 77146 Olomouc, Czech Republic
| | - Vincent Liégeois
- Theoretical Chemistry Laboratory (LCT), Namur Institute of Structured Matter (NISM), University of Namur, 5000 Namur, Belgium
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Yang Q, Bloino J, Šestáková H, Šebestík J, Kessler J, Hudecová J, Kapitán J, Bouř P. Combination of Resonance and Non-Resonance Chiral Raman Scattering in a Cobalt(III) Complex. Angew Chem Int Ed Engl 2023; 62:e202312521. [PMID: 37728178 DOI: 10.1002/anie.202312521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
Resonance Raman optical activity (RROA) spectra with high sensitivity reveal details on molecular structure, chirality, and excited electronic properties. Despite the difficulty of the measurements, the recorded data for the Co(III) complex with S,S-N,N-ethylenediaminedisuccinic acid are of exceptional quality and, coupled with the theory, spectacularly document the molecular behavior in resonance. This includes a huge enhancement of the chiral scattering, contribution of the antisymmetric polarizabilities to the signal, and the Herzberg-Teller effect significantly shaping the spectra. The chiral component is by about one order of magnitude bigger than for an analogous aluminum complex. The band assignment and intensity profile were confirmed by simulations based on density functional and vibronic theories. The resonance was attributed to the S0 →S3 transition, with the strongest signal enhancement of Raman and ROA spectral bands below about 800 cm-1 . For higher wavenumbers, other excited electronic states contribute to the scattering in a less resonant way. RROA spectroscopy thus appears as a unique tool to study the structure and electronic states of absorbing molecules in analytical chemistry, biology, and material science.
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Affiliation(s)
- Qin Yang
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Hana Šestáková
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
- University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Jana Hudecová
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
- University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
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Taniguchi T, Agbo DO. Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region. Phys Chem Chem Phys 2023; 25:28567-28575. [PMID: 37861094 DOI: 10.1039/d3cp04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
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Das M, Gangopadhyay D, Hudecová J, Kessler J, Kapitán J, Bouř P. Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics. Chempluschem 2023; 88:e202300219. [PMID: 37283530 DOI: 10.1002/cplu.202300219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/08/2023]
Abstract
Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.
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Affiliation(s)
- Moumita Das
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
- Department of Analytical Chemistry Faculty of Chemical Engineering, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Debraj Gangopadhyay
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Jana Hudecová
- Department of Optics, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
- Department of Analytical Chemistry Faculty of Chemical Engineering, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
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Wu T, Pelc R, Bouř P. Molecular Properties of 3d and 4f Coordination Compounds Deciphered by Raman Optical Activity Spectroscopy. Chempluschem 2023; 88:e202300385. [PMID: 37665573 DOI: 10.1002/cplu.202300385] [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: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/05/2023]
Abstract
Molecular properties of coordination compounds can be efficiently studied by vibrational spectroscopy. The scope of Raman spectroscopy has been greatly enhanced by the introduction of Raman optical activity (ROA) sensitive to chirality. The present review describes some of its recent applications to study the coordination compounds. 3d and 4f metal complexes often absorb the excitation light, or exhibit luminescence. Therefore, effects caused in ROA spectra by electronic circular dichroism (ECD) and circularly polarized luminescence (CPL) must be taken into consideration.In 3d metal complexes ECD and circularly-polarized Raman scattering compete with the resonance ROA (RROA) signal. Pure RROA spectrum can thus be obtained by subtracting the so-called ECD-Raman component. CPL is frequently encountered in 4f systems. While it can mask the ROA spectra, it is useful to study molecular structure. These electronic effects can be reduced by using near-infrared excitation although vibrational ROA signal is much weaker compared to the usual green laser excitation scenario. The ROA methodology is thus complex, but capable of providing unique information about the molecules of interests and their interaction with light.
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Affiliation(s)
- Tao Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Radek Pelc
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
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Schrenková V, Para Kkadan MS, Kessler J, Kapitán J, Bouř P. Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution. Phys Chem Chem Phys 2023; 25:8198-8208. [PMID: 36880812 DOI: 10.1039/d2cp05756e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3' hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.
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Affiliation(s)
- Věra Schrenková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Mohammed Siddhique Para Kkadan
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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Dobšíková K, Michal P, Spálovská D, Kuchař M, Paškanová N, Jurok R, Kapitán J, Setnička V. Conformational analysis of amphetamine and methamphetamine: a comprehensive approach by vibrational and chiroptical spectroscopy. Analyst 2023; 148:1337-1348. [PMID: 36857656 DOI: 10.1039/d2an02014a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
After cannabis, the most commonly used illicit substance worldwide is amphetamine and its derivatives, such as methamphetamine, with an ever-increasing number of synthetic modifications. Thus, fast and reliable methods are needed to identify them according to their spectral patterns and structures. Here, we have investigated the use of molecular spectroscopy methods to describe the 3D structures of these substances in a solution that models the physiological environment. The substances were analyzed by Raman and infrared (IR) absorption spectroscopy and by chiroptical methods, vibrational circular dichroism (VCD) and Raman optical activity (ROA). The obtained experimental data were supported by three different computational approaches based on density functional theory (DFT) and molecular dynamics (MD). Successful interpretation relies on good agreement between experimental and predicted spectra. The determination of the conformer populations of the studied molecules was based on maximizing the similarity overlap of weighted conformer spectra by a global minimization algorithm. Very good agreement was obtained between the experimental spectra and optimized-population weighted spectra from MD, providing a detailed insight into the structure of the molecules and their interaction with the solvent. The relative population of three amphetamine and six methamphetamine conformers was determined and is consistent with a previous NMR study. However, this work shows that only a few isolated conformers are not sufficient for the successful interpretation of the spectra, but the entire conformational space needs to be sampled appropriately and explicit interaction with the solvent needs to be included.
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Affiliation(s)
- Kristýna Dobšíková
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.
| | - Pavel Michal
- Department of Optics, Palacký University Olomouc, Olomouc, 771 46, Czech Republic.
| | - Dita Spálovská
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.
| | - Martin Kuchař
- Forensic Laboratory of Biologically Active Substances, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.,National Institute of Mental Health, Klecany 250 67, Czech Republic
| | - Natalie Paškanová
- Forensic Laboratory of Biologically Active Substances, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic
| | - Radek Jurok
- Forensic Laboratory of Biologically Active Substances, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.,Department of Organic Chemistry, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, Olomouc, 771 46, Czech Republic.
| | - Vladimír Setnička
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague 6, 166 28, Czech Republic.
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Yang Q, Kapitán J, Bouř P, Bloino J. Anharmonic Vibrational Raman Optical Activity of Methyloxirane: Theory and Experiment Pushed to the Limits. J Phys Chem Lett 2022; 13:8888-8892. [PMID: 36125432 PMCID: PMC9531246 DOI: 10.1021/acs.jpclett.2c02320] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Combining Raman scattering and Raman optical activity (ROA) with computer simulations reveals fine structural and physicochemical properties of chiral molecules. Traditionally, the region of interest comprised fundamental transitions within 200-1800 cm-1. Only recently, nonfundamental bands could be observed as well. However, theoretical tools able to match the observed spectral features and thus assist their assignment are rather scarce. In this work, we present an accurate and simple protocol based on a three-quanta anharmonic perturbative approach that is fully fit to interpret the observed signals of methyloxirane within 150-4500 cm-1. An unprecedented agreement even for the low-intensity combination and overtone transitions has been achieved, showing that anharmonic Raman and ROA spectroscopies can be valuable tools to understand vibrations of chiral molecules or to calibrate computational models.
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Affiliation(s)
- Qin Yang
- Scuola Normale
Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Josef Kapitán
- Department
of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí
2, 16610 Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale
Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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11
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Hudecová J, Kapitán J, Dračínský M, Michal P, Profant V, Bouř P. Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity. Chemistry 2022; 28:e202202045. [DOI: 10.1002/chem.202202045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Josef Kapitán
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
| | - Pavel Michal
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Václav Profant
- Faculty of Mathematics and Physics Charles University Ke Karlovu 5 121 16 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
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12
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Accurate Determination of Enantiomeric Excess Using Raman Optical Activity. Symmetry (Basel) 2022. [DOI: 10.3390/sym14050990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The optical purity of a chiral sample is of particular importance to the analytical chemistry and pharmaceutical industries. In recent years, the vibrational optical activity (VOA) has become established as a sensitive and nondestructive technique for the analysis of chiral molecules in solution. However, the relatively limited accuracy in the range of about 1–2% reported in published papers and the relatively small spread of experimental facilities to date have meant that vibrational spectroscopy has not been considered a common method for determining enantiomeric excess. In this paper, we attempt to describe, in detail, a methodology for the determination of enantiomeric excess using Raman optical activity (ROA). This method achieved an accuracy of 0.05% for neat α-pinene and 0.22% for alanine aqueous solution, after less than 6 h of signal accumulation for each enantiomeric mixture, which we believe is the best result achieved to date using vibrational optical activity techniques. An algorithm for the elimination of systematic errors (polarization artifacts) is proposed, and the importance of normalizing ROA spectra to correct for fluctuations in excitation power is established. Results comparable to those obtained with routinely used chemometric analysis by the partial least squares (PLS) method were obtained. These findings show the great potential of ROA spectroscopy for the quantitative analysis of enantiomeric mixtures.
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Michal P, Kapitan J, Kessler J, Bour P. Low-frequency Raman Optical Activity Provides Insight into Structure of Chiral Liquids. Phys Chem Chem Phys 2022; 24:19722-19733. [DOI: 10.1039/d2cp02290g] [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
Vibrational frequencies of modes involving intermolecular motions in liquids are relatively small, in the Raman scattering close to the excitation frequency, and the bands may merge into a diverging uninterpretable...
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Yamamoto S, Ishiro S, Kessler J, Bouř P. Intense chiral signal from α-helical poly-L-alanine observed in low-frequency Raman optical activity. Phys Chem Chem Phys 2021; 23:26501-26509. [PMID: 34806737 DOI: 10.1039/d1cp04401j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman optical activity (ROA) spectral features reliably indicate the structure of peptides and proteins, but the signal is often weak. However, we observed significantly enhanced low-frequency bands for α-helical poly-L-alanine (PLA) in solution. The biggest ROA signal at ∼100 cm-1 is about 10 times stronger than higher-frequency bands described previously, which facilitates the detection. The low-frequency bands of PLA were compared to those of α-helical proteins. For PLA, density functional simulations well reproduced the experimental spectra and revealed that about 12 alanine residues within two turns of the α-helix generate the strong ROA band. Averaging based on molecular dynamics (MD) provided an even more realistic spectrum compared to the static model. The low-frequency bands could be largely related to a collective motion of the α-helical backbone, partially modulated by the solvent. Helical and intermolecular vibrational coordinates have been introduced and the helical unwinding modes were assigned to the strongest ROA signal at 101-128 cm-1. Further analysis indicated that the helically arranged amide and methyl groups are important for the strong chiral signal of PLA, while the local chiral centers CαH contribute in a minor way only. The strong low-frequency ROA can thus provide precious information about the motions of the peptide backbone and facilitate future protein studies.
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Affiliation(s)
- Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Shota Ishiro
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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15
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Das M, Gangopadhyay D, Šebestík J, Habartová L, Michal P, Kapitán J, Bouř P. Chiral detection by induced surface-enhanced Raman optical activity. Chem Commun (Camb) 2021; 57:6388-6391. [PMID: 34085068 DOI: 10.1039/d1cc01504d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combination of optical activity with surface-enhanced Raman scattering has been a dream of physical chemists for a long time. We report a measurement protocol based on silver colloids and aromatic linkers where chiral acids could be detected in concentrations of about 10-5 M. We explain the mechanism by binding and self-assembly of the linkers into chiral aggregates on the silver surface. Following the "sergeants-and-soldiers" principle, the chirality is determined by the relatively minor acidic component. Such detection of biologically relevant molecules may be useful when other methods, such as electronic circular dichroism, are not sensitive enough. In the future, variations of the chemical structure of the linker or other conditions are needed to provide a more specific signal allowing one to better discriminate among the optically active molecules.
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Affiliation(s)
- Moumita Das
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic. and Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Debraj Gangopadhyay
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.
| | - Lucie Habartová
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Pavel Michal
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, Olomouc, 77146, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, Olomouc, 77146, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic. and Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
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16
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Kurochka A, Průša J, Kessler J, Kapitán J, Bouř P. α-Synuclein conformations followed by vibrational optical activity. Simulation and understanding of the spectra. Phys Chem Chem Phys 2021; 23:16635-16645. [DOI: 10.1039/d1cp02574k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For α-synuclein novel structural markers were identified in vibrational optical activity spectra and supported by theoretical modeling.
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Affiliation(s)
- Andrii Kurochka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
- Department of Analytical Chemistry
| | - Jiří Průša
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
- Department of Analytical Chemistry
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
| | - Josef Kapitán
- Department of Optics
- Palacký University Olomouc
- Olomouc
- Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
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17
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Palivec V, Michal P, Kapitán J, Martinez‐Seara H, Bouř P. Raman Optical Activity of Glucose and Sorbose in Extended Wavenumber Range. Chemphyschem 2020; 21:1272-1279. [DOI: 10.1002/cphc.202000261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Pavel Michal
- Department of OpticsPalacký University Olomouc 17. listopadu 12, 77146 Olomouc Czech Republic
| | - Josef Kapitán
- Department of OpticsPalacký University Olomouc 17. listopadu 12, 77146 Olomouc Czech Republic
| | - Hector Martinez‐Seara
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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18
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Krupová M, Kessler J, Bouř P. Recent Trends in Chiroptical Spectroscopy: Theory and Applications of Vibrational Circular Dichroism and Raman Optical Activity. Chempluschem 2020; 85:561-575. [DOI: 10.1002/cplu.202000014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and PhysicsCharles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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19
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Hope M, Šebestík J, Kapitán J, Bouř P. Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides. J Phys Chem A 2020; 124:674-683. [DOI: 10.1021/acs.jpca.9b10557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Hope
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Norwegian University of Science and Technology NO-7491 Trondheim, Norway
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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20
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Beć KB, Grabska J, Ozaki Y, Czarnecki MA, Huck CW. Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases. Sci Rep 2019; 9:17398. [PMID: 31758033 PMCID: PMC6874539 DOI: 10.1038/s41598-019-53827-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Mirosław A Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Christan W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
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