1
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Wu T, Kessler J, Zhao H, Zhao Y. Phosphorylation site of L-alanyl-L-glutamine identified by Raman optical activity spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124587. [PMID: 38850816 DOI: 10.1016/j.saa.2024.124587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Phosphorylated peptides are instrumental in studying protein phosphorylation events. In the present study, Raman optical activity (ROA) is employed to elucidate the structure of a dipeptide, L-alanyl-L-glutamine (L-Ala-L-Gln) and its two differently alkylated N-phosphorylated derivatives. Theoretical simulations were conducted to aid the interpretation of peptide conformation variations upon phosphorylation, and of the measured Raman and ROA spectra. Induced circularly polarized luminescence (CPL) was also recorded in solution, in the presence of a simple europium aqua ion. As the spectra are peptide specific, this type of stereochemical analysis is expected to aid identification of the phosphorylation sites also in other peptides and possibly proteins.
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Affiliation(s)
- Tao Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic.
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Hua Zhao
- Institute of Drug Discovery Technology, Ningbo University, 315 211 Ningbo, Zhejiang, China; Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315 211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, 315 211 Ningbo, Zhejiang, China; Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315 211, China; Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361 005, China.
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2
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Spasovová M, Kapitán J, Jílek Š, Siddhique Para Kkadan M, Klener J, Scott Lynn N, Kopecký V, Baumruk V, Profant V. Probing solution conformations of l-DOPA: Integration of experiment and simulation via vibrational optical activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124119. [PMID: 38452461 DOI: 10.1016/j.saa.2024.124119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/24/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l-DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l-DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l-DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l-DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs.
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Affiliation(s)
- Monika Spasovová
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic; FZU - Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague 8, Czech Republic
| | - Josef Kapitán
- Department of Optics, Faculty of Sciences, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Štěpán Jílek
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Mohammed Siddhique Para Kkadan
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry AS CR v.v.i., Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Jakub Klener
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Nicolas Scott Lynn
- FZU - Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague 8, Czech Republic
| | - Vladimír Kopecký
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Vladimír Baumruk
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Václav Profant
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic.
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3
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Machalska E, Halat M, Tani T, Fujisawa T, Unno M, Kudelski A, Baranska M, Zając G. Why Does One Measure Resonance Raman Optical Activity? A Unique Case of Measurements under Strong Resonance versus Far-from-Resonance Conditions. J Phys Chem Lett 2024; 15:4913-4919. [PMID: 38684076 PMCID: PMC11089565 DOI: 10.1021/acs.jpclett.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Raman optical activity (ROA) spectroscopy exhibits significant potential in the study of (bio)molecules as it encodes information on their molecular structure, chirality, and conformations. Furthermore, the method reveals details on excited electronic states when applied under resonance conditions. Here, we present a combined study of the far from resonance (FFR)-ROA and resonance ROA (RROA) of a single relatively small molecular system. Notably, this study is the first to employ the density functional theory (DFT) analysis of both FFR-ROA and RROA spectra. This is illustrated for cobalamin derivatives using near-infrared and visible light excitation. Although the commonly observed monosignate RROA spectra lose additional information visible in bisignate nonresonance ROA spectra, the RROA technique acts as a complement to nonresonance ROA spectroscopy. In particular, the combination of these methods integrated with DFT calculations can reveal a complete spectral picture of the structural and conformational differences between tested compounds.
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Affiliation(s)
- Ewa Machalska
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
- Laboratory
for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Monika Halat
- Department
of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture, Al. Mickiewicza 21, 31-120 Krakow, Poland
| | - Takumi Tani
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tomotsumi Fujisawa
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Andrzej Kudelski
- Faculty of
Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093 Warsaw, Poland
| | - Malgorzata Baranska
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
- Faculty of
Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz Zając
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
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4
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Fujisawa T, Unno M. Near-Infrared Excited Raman Optical Activity as a Tool to Uncover Active Sites of Photoreceptor Proteins. J Phys Chem B 2024; 128:2228-2235. [PMID: 38441478 DOI: 10.1021/acs.jpcb.4c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024]
Abstract
Raman optical activity (ROA) is a chiral sensitive technique to measure the difference in Raman scattering intensity between right and left circularly polarized light. The method has been applied to the study of biological molecules such as proteins, and it is now recognized as a powerful tool for investigating biomolecular structures. We have expanded the capability of this chiroptical technique to colored molecules, such as photoreceptor proteins, by using a near-infrared excitation. A photoreceptor protein contains a light-absorbing chromophore as an active site, and the precise determination of its structure is vital for comprehending the protein's function at the atomic level. In a photoreceptor protein, the protein environment can distort an achiral chromophore into a chiral conformation. ROA spectroscopy offers detailed structural information about the chromophore under physiological conditions. Here we explore recent progress in near-infrared ROA spectroscopy and its application to biological systems.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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5
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Fusè M, Mazzeo G, Abbate S, Ruzziconi R, Bloino J, Longhi G. Mid-IR and CH stretching vibrational circular dichroism spectroscopy to distinguish various sources of chirality: The case of quinophaneoxazoline based ruthenium(II) complexes. Chirality 2024; 36:e23649. [PMID: 38409881 DOI: 10.1002/chir.23649] [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: 12/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
Five diastereomers of ruthenium(II) complexes based on quinolinophaneoxazoline ligands were investigated by vibrational circular dichroism (VCD) in the mid-IR and CH stretching regions. Diastereomers differ in three sources of chirality: the planar chirality of the quinolinophane moiety, the central chirality of an asymmetric carbon atom of the oxazoline ring, and the chirality of the ruthenium atom. VCD, allied to DFT calculations, has been found to be effective in disentangling the various forms of chirality. In particular, a VCD band is identified in the CH stretching region directly connected to the chirality of the metal. The analysis of the calculated VCD spectra is carried out by partitioning the complexes into fragments. The anharmonic analysis is also performed with a recently proposed reduced-dimensionality approach: such treatment is particularly important when examining spectroscopic regions highly perturbed by resonances, like the CH stretching region.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
| | - Renzo Ruzziconi
- Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
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6
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Rode JE, Łyczko K, Kaczorek D, Kawęcki R, Dobrowolski JC. VCD spectra of chiral naphthalene-1-carboxamides in the solid-state. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123939. [PMID: 38301569 DOI: 10.1016/j.saa.2024.123939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The VCD spectra of chiral 2,3-dihydro-1H-benzo[de]isoquinolin-1-one (8-substituted naphthalene-1-carboxamide, BIQ) were studied in KBr pellets. The X-ray diffractometry revealed that the Me, Ph, and pClPh BIQs crystalize in the monoclinic P21, while nBu, pMePh, and oMeOPh BIQs in the orthorhombic P212121 space group. Only the Me-BIQ crystal exhibits the presence of cyclic amide dimers, while the others contain chains of the amid group hydrogen bonds. For all BIQs, except pMePh, the most intense IR band in the 1750-1550 cm-1 region is located at ca. 1680 cm-1 and is accompanied by two weak ones at ca. 1618 and 1590 cm-1. For the pMePh derivative, four almost equally intense IR bands at 1662, 1639, 1614, and 1588 cm-1 are observed. This region of the IR spectra of BIQs, but pMePh, is well reproduced by calculations based on BIQ monomers. On the other hand, the complex IR pattern of pMePh is computationally reproduced when larger crystal fragments, like octamers, are considered. Registration of the VCD spectra enabled recognizing the complexity of IR contours at ca. 1680 cm-1 by the corresponding VCD motives. For (i) Me, Ph and pClPh (R)-enantiomers, two (+)(-) bands were distinguished and for (ii) nBu and pMePh ones, one VCD band with right-side asymmetry was found. For (iii) oMeOPh the VCD pattern cannot be unambiguously assigned. Thus, the VCD spectra in the ν(C=O) range diverse the studied compounds. Among the set of molecules, pMePh has exceptional crystal geometry. Therefore, its most intense ν(C=O) band position and shape can be connected with the geometry of the hydrogen bonds, interactions, and crystal packing. Interpretation of the VCD spectra is based on linear and packed BIQ octamers. This cluster model can reproduce the main features of the solid-state VCD of BIQs.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland.
| | - Krzysztof Łyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
| | - Dorota Kaczorek
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Robert Kawęcki
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
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7
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Wu T, Bouř P, Fujisawa T, Unno M. Molecular Vibrations in Chiral Europium Complexes Revealed by Near-Infrared Raman Optical Activity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305521. [PMID: 37985561 PMCID: PMC10767399 DOI: 10.1002/advs.202305521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/05/2023] [Indexed: 11/22/2023]
Abstract
Raman optical activity (ROA) is commonly measured with green light (532 nm) excitation. At this wavelength, however, Raman scattering of europium complexes is masked by circularly polarized luminescence (CPL). This can be avoided using near-infrared (near-IR, 785 nm) laser excitation, as demonstrated here by Raman and ROA spectra of three chiral europium complexes derived from camphor. Since luminescence is strongly suppressed, many vibrational bands can be detected. They carry a wealth of structural information about the ligand and the metal core, and can be interpreted based on density functional theory (DFT) simulations of the spectra. For example, jointly with ROA experimental data, the simulations make it possible to determine absolute configuration of chiral lanthanide compounds in solution.
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Affiliation(s)
- Tao Wu
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo náměstí 2Prague166 10Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo náměstí 2Prague166 10Czech Republic
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied ChemistryFaculty of Science and EngineeringSaga UniversitySaga840‐8502Japan
| | - Masashi Unno
- Department of Chemistry and Applied ChemistryFaculty of Science and EngineeringSaga UniversitySaga840‐8502Japan
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8
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Hermann DR, Ramer G, Riedlsperger L, Lendl B. Chiral Monitoring Across Both Enantiomeric Excess and Concentration Space: Leveraging Quantum Cascade Lasers for Sensitive Vibrational Circular Dichroism Spectroscopy. APPLIED SPECTROSCOPY 2023; 77:1362-1370. [PMID: 37847076 DOI: 10.1177/00037028231206186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Recently, high-throughput quantum cascade laser-based vibrational circular dichroism (QCL-VCD) technology has reduced the measurement time for high-quality vibrational circular dichroism spectra from hours to a few minutes. This study evaluates QCL-VCD for chiral monitoring using flow-through measurement of a changing sample in a circulating loop. A balanced detection QCL-VCD system was applied to the enantiomeric pair R/S-1,1'-bi-2-naphthol in solution. Different mixtures of the two components were used to simulate a racemization process, collecting spectral data at a time resolution of 6 min, and over three concentration levels. The goal of this experimental setup was to evaluate QCL-VCD in terms of both molar and enantiomeric excess (EE) sensitivity at a time resolution relevant to chiral monitoring in chemical processes. Subsequent chemometric evaluation by partial least squares regression revealed a cross-validated prediction accuracy of 2.8% EE with a robust prediction also for the test data set (error = 3.5% EE). In addition, the data set was also treated with the least absolute shrinkage and selection operator (LASSO), which also achieved a robust prediction. Due to the operating principle of LASSO, the obtained coefficients constituted a few discrete spectral frequencies, which represent the most variance. This information can be used in the future for dedicated QCL-based instrument design, gaining a higher time resolution without sacrificing predictive capabilities.
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Affiliation(s)
- Daniel-Ralph Hermann
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Georg Ramer
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Lisa Riedlsperger
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Bernhard Lendl
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
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9
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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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10
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Jähnigen S. Vibrational Circular Dichroism Spectroscopy of Chiral Molecular Crystals: Insights from Theory. Angew Chem Int Ed Engl 2023; 62:e202303595. [PMID: 37071543 DOI: 10.1002/anie.202303595] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/19/2023]
Abstract
Chirality is a curious phenomenon that appears in various forms. While the concept of molecular (RS-)chirality is ubiquitous in chemistry, there are also more intricate forms of structural chirality. One of them is the enantiomorphism of crystals, especially molecular crystals, that describes the lack of mirror symmetry in the unit cell. Its relation to molecular chirality is not obvious, but still an open question, which can be addressed with chiroptical tools. Vibrational circular dichroism (VCD) denotes chiral infrared (IR) spectroscopy that is susceptible to both, the molecular as well as the intermolecular space by means of vibrational transitions. When carried out in the solid state, VCD delivers a very rich set of non-local contributions that are determined by crystal packing and collective motion. Since its discovery in the 1970s, VCD has become the method of choice for the determination of absolute configurations, but its applicability reaches beyond towards the study of different crystal forms and polymorphism. This brief review summarises the theoretical concepts of crystal chirality and how computations of solid-state VCD can shed light into the intimate connection of chiral structure and vibrational optical activity.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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11
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Blasius J, Kirchner B. Selective Chirality Transfer to the Bis(trifluoromethylsulfonyl)imide Anion of an Ionic Liquid. Chemistry 2023; 29:e202301239. [PMID: 37341169 DOI: 10.1002/chem.202301239] [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: 04/19/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/22/2023]
Abstract
Chirality transfer from the chiral molecule (R)-1,2-propylene oxide to the achiral anion of the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid is observed. The chiral probe selectively affects one part of the binary ionic liquid, i. e., it has previously been shown experimentally and theoretically that this particular imidazolium cation can be affected by chirality transfer, but in the present system chirality is almost exclusively transferred to the anion and not to both parts of the solvent (anion and cation). This observation is of high relevance because of its selectivity and because anion effects are usually much more important in ionic liquid research than cation effects. From ab initio molecular dynamics simulations, a conformational analysis and dissected vibrational circular dichroism spectra are obtained to study the chirality transfer. While in the neat ionic liquid two mirror imaged trans conformers of the anion occur almost equally, we observe an excess of one of these conformers in the presence of the chiral solute, causing optical activity of the anion. Although the cis conformers are not tremendously affected by the chirality transfer, they gain in total population when (R)-1,2-propylene oxide is dissolved in the ionic liquid.
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Affiliation(s)
- Jan Blasius
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115, Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115, Bonn, Germany
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12
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Osadchuk I, Luts HE, Norvaiša K, Borovkov V, Senge MO. Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis. Chemistry 2023; 29:e202301408. [PMID: 37227167 DOI: 10.1002/chem.202301408] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/26/2023]
Abstract
The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Karolis Norvaiša
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Mathias O Senge
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
- Institute for Advanced Study (TUM-IAS), Technical University of Munich, Lichtenberg Str. 2a, 85748, Garching, Germany
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13
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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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14
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Li D, Xu C, Xie J, Lee C. Research Progress in Surface-Enhanced Infrared Absorption Spectroscopy: From Performance Optimization, Sensing Applications, to System Integration. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2377. [PMID: 37630962 PMCID: PMC10458771 DOI: 10.3390/nano13162377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Infrared absorption spectroscopy is an effective tool for the detection and identification of molecules. However, its application is limited by the low infrared absorption cross-section of the molecule, resulting in low sensitivity and a poor signal-to-noise ratio. Surface-Enhanced Infrared Absorption (SEIRA) spectroscopy is a breakthrough technique that exploits the field-enhancing properties of periodic nanostructures to amplify the vibrational signals of trace molecules. The fascinating properties of SEIRA technology have aroused great interest, driving diverse sensing applications. In this review, we first discuss three ways for SEIRA performance optimization, including material selection, sensitivity enhancement, and bandwidth improvement. Subsequently, we discuss the potential applications of SEIRA technology in fields such as biomedicine and environmental monitoring. In recent years, we have ushered in a new era characterized by the Internet of Things, sensor networks, and wearable devices. These new demands spurred the pursuit of miniaturized and consolidated infrared spectroscopy systems and chips. In addition, the rise of machine learning has injected new vitality into SEIRA, bringing smart device design and data analysis to the foreground. The final section of this review explores the anticipated trajectory that SEIRA technology might take, highlighting future trends and possibilities.
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Affiliation(s)
- Dongxiao Li
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore; (D.L.); (C.X.); (J.X.)
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Cheng Xu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore; (D.L.); (C.X.); (J.X.)
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Junsheng Xie
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore; (D.L.); (C.X.); (J.X.)
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore; (D.L.); (C.X.); (J.X.)
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
- NUS Suzhou Research Institute (NUSRI), Suzhou 215123, China
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15
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Přáda Brichtová E, Krupová M, Bouř P, Lindo V, Gomes Dos Santos A, Jackson SE. Glucagon-like peptide 1 aggregates into low-molecular-weight oligomers off-pathway to fibrillation. Biophys J 2023; 122:2475-2488. [PMID: 37138517 PMCID: PMC10323027 DOI: 10.1016/j.bpj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/04/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation.
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Affiliation(s)
- Eva Přáda Brichtová
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Monika Krupová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic; Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic
| | - Viv Lindo
- AstraZeneca, Cambridge, United Kingdom
| | | | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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16
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Ohya M, Kikukawa T, Matsuo J, Tsukamoto T, Nagaura R, Fujisawa T, Unno M. Structure and Heterogeneity of Retinal Chromophore in Chloride Pump Rhodopsins Revealed by Raman Optical Activity. J Phys Chem B 2023. [PMID: 37201188 DOI: 10.1021/acs.jpcb.3c01801] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chloride transport by microbial rhodopsins is actively being researched to understand how light energy is converted to drive ion pumping across cell membranes. Chloride pumps have been identified in archaea and eubacteria, and there are similarities and differences in the active site structures between these groups. Thus, it has not been clarified whether a common mechanism underlies the ion pump processes for all chloride-pumping rhodopsins. Here, we applied Raman optical activity (ROA) spectroscopy to two chloride pumps, Nonlabens marinus rhodopsin-3 (NM-R3) and halorhodopsin from the cyanobacterium Mastigocladopsis repens (MrHR). ROA is a vibrational spectroscopy that provides chiral sensitivity, and the sign of ROA signals can reveal twisting of cofactor molecules within proteins. Our ROA analysis revealed that the retinal Schiff base NH group orients toward the C helix and forms a direct hydrogen bond with a nearby chloride ion in NM-R3. In contrast, MrHR is suggested to contain two retinal conformations twisted in opposite directions; one conformation has a hydrogen bond with a chloride ion like NM-R3, while the other forms a hydrogen bond with a water molecule anchored by a G helix residue. These results suggest a general pump mechanism in which the chloride ion is "dragged" by the flipping Schiff base NH group upon photoisomerization.
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Affiliation(s)
- Masaiku Ohya
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Junpei Matsuo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ryota Nagaura
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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17
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Eikås KDR, Krupová M, Kristoffersen T, Beerepoot MTP, Ruud K. Can the absolute configuration of cyclic peptides be determined with vibrational circular dichroism? Phys Chem Chem Phys 2023; 25:14520-14529. [PMID: 37190985 DOI: 10.1039/d2cp04942b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cyclic peptides show a wide range of biological activities, among others as antibacterial agents. These peptides are often large and flexible with multiple chiral centers. The determination of the stereochemistry of molecules with multiple chiral centers is a challenging and important task in drug development. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) can distinguish between different stereoisomers. The absolute configuration (AC) of a stereoisomer can be determined by comparing its experimental spectra to computed spectra of stereoisomers with known AC. In this way, the AC of rigid molecules with up to seven chiral centers has been assigned (Bogaerts et al., Phys. Chem. Chem. Phys., 2020, 22, 18014). The question arises whether this is possible with more conformationally flexible molecules such as cyclic peptides. We here investigate to what extent the AC of cyclic peptides can be determined with VCD. More specifically, we investigate the maximum number of chiral centers a cyclic peptide can have in order to be able to unambiguously assign the AC with VCD. We present experimental and computed IR and VCD spectra for a series of eight tetrapeptides and hexapeptides with two, three and four chiral centers. We use our recently developed computational protocol with a conformational search based on sampling with meta-dynamics. We use visual inspection to compare the computed spectra of different stereoisomers with an experimental spectrum of the corresponding cyclic peptide with known AC. We find that the AC of the investigated cyclic peptides with two chiral centers can be unambiguously assigned with VCD. This is however not possible for all of the cyclic peptides with three chiral centers and for none of those with four chiral centers. At best, one can limit the number of possible stereoisomers in those cases. Our work shows that other techniques are needed to assign the AC of cyclic peptides with three or more chiral centers. Our study also constitutes a warning that the spectra of all stereoisomers should be computed before attempting to match to an experimental spectrum, to avoid an accidental erroneous match.
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Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Monika Krupová
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Tone Kristoffersen
- Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.
- Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
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18
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Ditler E, Kumar C, Luber S. Vibrational circular dichroism spectra of natural products by means of the nuclear velocity perturbation theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 298:122769. [PMID: 37163900 DOI: 10.1016/j.saa.2023.122769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
We present the application of the recently implemented nuclear velocity perturbation theory, using the combined Gaussian and plane waves approach in CP2K, to the vibrational circular dichroism (VCD) spectra of a set of natural products. Even though the calculations were carried out for isolated molecules in the gas-phase limit, neglecting inter-molecular interactions and anharmonic effects, the match between simulated and experimental spectra is reasonable. We also study the influence of different density functionals on the conformational search and the resulting VCD spectra via group coupling matrices (GCMs). The GCM analysis reveals that the VCD signal can in some cases arise from moieties which are close to each other and in other cases from moieties far from each other. Differences in spectra obtained using different exchange-correlation density functionals can be attributed to interaction terms between different moieties in the molecules changing their sign.
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Affiliation(s)
- Edward Ditler
- University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Chandan Kumar
- University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Sandra Luber
- University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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19
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Guselnikova O, Elashnikov R, Svorcik V, Kartau M, Gilroy C, Gadegaard N, Kadodwala M, Karimullah AS, Lyutakov O. Coupling of plasmonic hot spots with shurikens for superchiral SERS-based enantiomer recognition. NANOSCALE HORIZONS 2023; 8:499-508. [PMID: 36752733 DOI: 10.1039/d3nh00008g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Detection of enantiomers is a challenging problem in drug development as well as environmental and food quality monitoring where traditional optical detection methods suffer from low signals and sensitivity. Application of surface enhanced Raman scattering (SERS) for enantiomeric discrimination is a powerful approach for the analysis of optically active small organic or large biomolecules. In this work, we proposed the coupling of disposable chiral plasmonic shurikens supporting the chiral near-field distribution with SERS active silver nanoclusters for enantio-selective sensing. As a result of the plasmonic coupling, significant difference in SERS response of optically active analytes is observed. The observations are studied by numerical simulations and it is hypothesized that the silver particles are being excited by superchiral fields generated at the surface inducing additional polarizations in the probe molecules. The plasmon coupling phenomena was found to be extremely sensitive to slight variations in shuriken geometry, silver nanostructured layer parameters, and SERS excitation wavelength(s). Designed structures were able to discriminate cysteine enantiomers at concentrations in the nanomolar range and probe biomolecular chirality, using a common Raman spectrometer within several minutes. The combination of disposable plasmonic substrates with specific near-field polarization can make the SERS enantiomer discrimination a commonly available technique using standard Raman spectrometers.
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Affiliation(s)
- Olga Guselnikova
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, 634050, Russian Federation.
| | - Roman Elashnikov
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
| | - Vaclav Svorcik
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
| | - Martin Kartau
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Cameron Gilroy
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Nikolaj Gadegaard
- James Watt School of Engineering, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
| | - Malcolm Kadodwala
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Affar S Karimullah
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Oleksiy Lyutakov
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
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20
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Lam J, Lewis RJ, Goodman JM. Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence. J Cheminform 2023; 15:36. [PMID: 36945031 PMCID: PMC10031863 DOI: 10.1186/s13321-023-00706-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/26/2023] [Indexed: 03/23/2023] Open
Abstract
Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and we use this database to validate a method for the automated analysis of VCD spectra and the assignment of absolute configuration: the Cai•factor (Configuration: absolute information). The analysis of the data demonstrates that the procedure is a reliable and time-efficient method for determination of absolute configuration, which gives both the assignment and a measure of confidence in the outcome, even when the spectra are imperfect. The majority of molecules tested have a high confidence score and all of these have the correct assignment.
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Affiliation(s)
- Jonathan Lam
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Richard J Lewis
- Department of Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Jonathan M Goodman
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK.
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21
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Jähnigen S, Le Barbu-Debus K, Guillot R, Vuilleumier R, Zehnacker A. How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202215599. [PMID: 36441537 PMCID: PMC10107176 DOI: 10.1002/anie.202215599] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 11/29/2022]
Abstract
Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P21 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
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22
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Maniappan S, Reddy KL, Kumar J. Transmitting biomolecular chirality into carbon nanodots: a facile approach to acquire chiral light emission at the nanoscale. Chem Sci 2023; 14:491-498. [PMID: 36741532 PMCID: PMC9847681 DOI: 10.1039/d2sc05794h] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022] Open
Abstract
Since the observation of chirality at the nanoscale, research focused towards the design and synthesis of optically active nanomaterials has been at a brisk pace. In this regard, carbon based zero dimensional nanomaterials have attracted vast attention due to their rich optical properties, abundance of raw materials, minimal environmental hazardousness, good solubility, and ease of surface modification. However, efforts focused towards the synthesis of chiral carbon nanodots exhibiting optical activity both in their ground and excited states are rather scarce. Herein, we report a facile synthetic approach for the preparation of three sets of intrinsically chiral carbon nanodots that exhibit intense circularly polarized luminescence. Synthesis under optimized conditions using l- and d-isomers of the chiral precursors led to the formation of carbon nanodots that displayed mirror image circular dichroism and circularly polarized luminescence signals revealing their ground and excited state chirality. The experimental results are supportive of the reported core-shell model comprising an achiral carbon core that is enclosed within an amorphous shell contributing to the chiral luminescence. The luminescence anisotropy and wavelength could be tuned by varying the experimental conditions such as temperature and pH. The chiral emissive properties of the nanoparticles could be demonstrated in free-standing polymeric films revealing their potential to be used as chiral light emitting agents in optical devices, data storage and security tags. Being the first observation of intrinsic circularly polarized luminescence from a range of carbon nanodots, both in the solution and solid state, we envisage that the work will open new avenues for the investigation of excited stated chirality at the nanoscale.
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Affiliation(s)
- Sonia Maniappan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) TirupatiTirupati – 517507India
| | - Kumbam Lingeshwar Reddy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) TirupatiTirupati – 517507India
| | - Jatish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) TirupatiTirupati – 517507India
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23
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Yang Q, Bloino J. An Effective and Automated Processing of Resonances in Vibrational Perturbation Theory Applied to Spectroscopy. J Phys Chem A 2022; 126:9276-9302. [DOI: 10.1021/acs.jpca.2c06460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Qin Yang
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610Prague, Czech Republic
| | - Julien Bloino
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
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24
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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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25
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Krupová M, Leszczenko P, Sierka E, Emma Hamplová S, Pelc R, Andrushchenko V. Vibrational Circular Dichroism Unravels Supramolecular Chirality and Hydration Polymorphism of Nucleoside Crystals. Chemistry 2022; 28:e202201922. [DOI: 10.1002/chem.202201922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Hylleraas Centre for Quantum Molecular Sciences Department of Chemistry UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Patrycja Leszczenko
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
| | - Ewa Sierka
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
| | - Sára Emma Hamplová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Department of Biology and Biochemistry University of Bath Claverton Down Bath BA2 7AY United Kingdom
| | - Radek Pelc
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Third Faculty of Medicine Charles University Ruská 87 10000 Prague Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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26
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Eikås KDR, Beerepoot MTP, Ruud K. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides. J Phys Chem A 2022; 126:5458-5471. [PMID: 35930395 PMCID: PMC9393892 DOI: 10.1021/acs.jpca.2c02953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
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Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.,Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
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27
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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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28
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Wu T. A Raman optical activity spectrometer can sensitively detect lanthanide circularly polarized luminescence. Phys Chem Chem Phys 2022; 24:15672-15686. [PMID: 35735101 DOI: 10.1039/d2cp01641a] [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
Recently, many studies have appeared in which the Raman optical activity (ROA) instrument was found to be convenient for measuring circularly polarized luminescence (CPL). Typically, weak lanthanide luminescence including circular polarization could be detected. The new detection scheme is referred to as ROA-CPL spectroscopy. It is particularly useful when also the vibrational (ROA) itself is detectable as the molecule structure can be examined more reliably. In this review, development of this chiroptical approach and its applications in structural studies of biomolecules are summarized.
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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.
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29
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Morgante P, Ludowieg HD, Autschbach J. Comparative Study of Vibrational Raman Optical Activity with Different Time-Dependent Density Functional Approximations: The VROA36 Database. J Phys Chem A 2022; 126:2909-2927. [PMID: 35512708 DOI: 10.1021/acs.jpca.2c00951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new database, VROA36, is introduced to investigate the performance of computational approaches for vibrational Raman optical activity (VROA) calculations. The database is composed of 36 molecules with known experimental VROA spectra. It includes 93 conformers. Normal modes calculated with B3LYP-D3(BJ)/def2-TZVP are used to compute the VROA spectra with four functionals, B3LYP-D3(BJ), ωB97X-D, M11, and optimally tuned LC-PBE, as well as several basis sets. SimROA indices and frequency scaling factors are used to compare calculated spectra with each other and with experimental data. The four functionals perform equally well independently of the basis set and usually achieve good agreement with the experimental data. For molecules in near- or at-resonance conditions, the inclusion of a complex (damped) linear response approach is important to obtain physically meaningful VROA intensities. The use of any of the tested functional approximations with the def2-SVPD Gaussian-type basis set, or a basis of similar flexibility, can be recommended for efficient and reliable theoretical VROA studies.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Herbert D Ludowieg
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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30
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Wu T, Kapitán J, Bouř P. Resolving Resonant Electronic States in Chiral Metal Complexes by Raman Optical Activity Spectroscopy. J Phys Chem Lett 2022; 13:3873-3877. [PMID: 35467874 DOI: 10.1021/acs.jpclett.2c00653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chiral metal complexes exhibit rich photophysical properties and are important for applications ranging from biosensing to photocatalysis. We present a combined experimental and computational approach leading to information about energies and transition moments of excited electronic states, documented on two chiral metal complexes. The experimental protocol for measurement of the resonance Raman optical activity comprises multiple techniques, i.e., absorption, circular dichroism, and polarized and differential Raman scattering. An accurate formula for subtraction of the interfering circular dichroism/polarized Raman scattering effect is given. An analysis of the spectra based on density functional theory calculations unveils the geometric and electronic structures of the molecules. Such insight into molecular electronic states of chromophores may be useful for understanding and tuning photochemical properties of metal-containing complexes, biomolecules, and supramolecules.
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Affiliation(s)
- Tao Wu
- 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
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31
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Ditler E, Zimmermann T, Kumar C, Luber S. Implementation of Nuclear Velocity Perturbation and Magnetic Field Perturbation Theory in CP2K and Their Application to Vibrational Circular Dichroism. J Chem Theory Comput 2022; 18:2448-2461. [PMID: 35363490 DOI: 10.1021/acs.jctc.2c00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of nuclear velocity perturbation theory (NVPT), using a pioneering combination of atom-centered (velocity-dependent) Gaussian basis functions and plane waves in the CP2K package. The atomic polar tensors (APTs) and atomic axial tensors (AATs) are evaluated in the velocity representation using efficient density functional perturbation theory. The presence of nonlocal pseudopotentials, the representation of potentials on numerical integration grids, and effects arising from the basis functions being centered on the atoms have been considered in the implementation. The Magnetic Field Perturbation Theory (MFPT) using gauge-including atomic orbitals is implemented in the same code and compared to the NVPT. Our implementation is the first to compare both approaches (MFPT and NVPT) in the same code. The implementation has been verified via sum rules and by investigating the gauge origin dependence of the AATs for a set of small molecules, oxirane, and fluoro-oxirane. We also present vibrational circular dichroism spectra that are related to the APTs and AATs, applying both theories.
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Affiliation(s)
- Edward Ditler
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Tomáš Zimmermann
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chandan Kumar
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
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32
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Machalska E, Zając G, Baranska M, Bouř P, Kaczorek D, Kawęcki R, Rode JE, Lyczko K, Dobrowolski JC. New chiral ECD-Raman spectroscopy of atropisomeric naphthalenediimides. Chem Commun (Camb) 2022; 58:4524-4527. [PMID: 35302568 DOI: 10.1039/d1cc06974h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, we found that a recently discovered ECD-Raman effect dominated over the natural Raman optical activity in a series of atropisomeric naphthalenediimides, and we investigated the kind of information about the molecular structure that could be obtained from the spectra. The ECD-Raman effect is polarised Raman scattering modulated by electronic circular dichroism. We showed that the spectra significantly depended on the substitution of the solute and/or the change of the solvent. Moreover, the spectra could be well-predicted by the theory, thus providing an interesting tool to monitor the chirality of the binaphthyl compounds.
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Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Cracow, Poland.
| | - Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Cracow, Poland. .,Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic.
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Cracow, Poland.
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic.
| | - Dorota Kaczorek
- Faculty of Science, Siedlce University, 3 Maja Street No. 54, 08-110 Siedlce, Poland.
| | - Robert Kawęcki
- Faculty of Science, Siedlce University, 3 Maja Street No. 54, 08-110 Siedlce, Poland.
| | - Joanna E Rode
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland.
| | - Krzysztof Lyczko
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland.
| | - Jan Cz Dobrowolski
- Laboratory for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, 16 Dorodna-Street, 03-195 Warsaw, Poland.
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33
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Yamamoto S, Kimura F. Probing the solvation of the α-helix with extended amide III bands in Raman optical activity. Phys Chem Chem Phys 2022; 24:3191-3199. [PMID: 35043805 DOI: 10.1039/d1cp04480j] [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
Experimental and theoretical Raman optical activity (ROA) study of α-helical peptides and proteins has suggested that the relative intensity of two extended amide III ROA bands at ∼1340 cm-1 (I band) and ∼1300 cm-1 (II band) can be used to monitor the permittivity of the surrounding medium of the α-helix. So far, the ROA intensity ratio, II/III, has been interpreted from two different viewpoints. The first one is in terms of a direct effect of permittivity around the α-helix. The second one is based on a structural equilibrium of two types of α-helical structures, "hydrated" and "unhydrated" ones. In the present study, temperature- and solvent-dependences of II/III are measured for highly-α-helical peptides and compared to the theoretical spectra while varying the permittivity or the type of α-helical structure. A fragment method with partial optimization in the normal modes is adopted in density functional theory calculations. The main features of the experimental spectra and a trend of the observed II/III are well reproduced by the simulations, which leads us to a conclusion that the II/III is dominantly governed by a direct influence of the permittivity of the environment and just accessorily by the equilibrium of the two types of α-helices. The simulations also opposed the conventional assignments of the I and II bands to "hydrated" and "unhydrated" α-helical structures, respectively. In the case of α-helical proteins, solvent exposure of the α-helix may be monitored by the ROA ratio.
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Affiliation(s)
- Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Fumiya Kimura
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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34
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Sato H, Aisawa S, Ida H, Shimizu M, Watanabe K, Koshoubu J, Yoshida J, Kawamura I. Two-dimensional Imaging of a Model Pharmaceutical Dosage Tablet Using a Scanning Vibrational Circular Dichroism System. CHEM LETT 2021. [DOI: 10.1246/cl.210635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Sumio Aisawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, 020-8551, Japan
| | - Honoka Ida
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, 020-8551, Japan
| | | | | | - Jun Koshoubu
- JASCO Corporation, Hachioji, Tokyo, 192-8537, Japan
| | - Jun Yoshida
- Department of Chemistry, College of Humanities & Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
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35
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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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36
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Zając G, Bouř P. Measurement and Theory of Resonance Raman Optical Activity for Gases, Liquids, and Aggregates. What It Tells about Molecules. J Phys Chem B 2021; 126:355-367. [PMID: 34792364 DOI: 10.1021/acs.jpcb.1c08370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Resonance Raman Optical Activity (RROA) appeared as a natural extension of the nonresonance branch. It combines the structural sensitivity of chiroptical spectroscopy with the signal enhancement coming from the resonance of molecular electronic transitions with the excitation laser light. However, the idea has been hampered by many technical and theoretical problems that are being clarified only in recent years. We provide the theoretical basis and several examples documenting the problems, achievements, and potential of RROA, in particular in biomolecular studies.
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Affiliation(s)
- Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague, 16610, Czech Republic
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37
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Kaminský J, Horáčková F, Biačková N, Hubáčková T, Socha O, Kubelka J. Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity. J Phys Chem B 2021; 125:11350-11363. [PMID: 34612644 DOI: 10.1021/acs.jpcb.1c05480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lactic and malic acids are key substances in a number of biochemical processes in living cells and are also utilized in industry. Vibrational spectroscopy represents an efficient and sensitive way to study their structure and interactions. Since water is the natural environment, proper understanding of their molecular dynamics in aqueous solutions is of critical importance. To this end, we employed Raman spectroscopy and Raman optical activity (ROA) to study the conformation of l-lactic and l-malic acids in water (while varying pH, temperature, and concentration), with special emphasis on their double hydrogen bonding dimerization propensity. Raman and ROA experimental data were supported by extensive theoretical calculations of the vibrational properties and by additional experiments (IR absorption, vibrational circular dichroism, and NMR). Conformational behavior of the acids in water was described by molecular dynamics simulations. Reliability of the results was verified by calculating the vibrational properties of populated conformers and by comparing thus obtained spectral features with the experimental data. Calculations estimated the incidence of H-bonded dimers in water to be low in lactic acid and comparable to monomers in malic acid. The "hybrid" approach presented here reveals limitations of relying on the experimental spectra alone to study dimer formation.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Františka Horáčková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Nina Biačková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Tereza Hubáčková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jan Kubelka
- University of Wyoming, 651 N. 19th Street, Laramie, Wyoming 82072, United States
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38
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Li G, Alshalalfeh M, Yang Y, Cheeseman JR, Bouř P, Xu Y. Can One Measure Resonance Raman Optical Activity? Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guojie Li
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Mutasem Alshalalfeh
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Yanqing Yang
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - James R. Cheeseman
- Gaussian Inc. 340 Quinnipiac St., Bldg. 40 Wallingford CT 06492-4050 USA
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Yunjie Xu
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
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39
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Górecki M, Enamullah M, Islam MA, Islam MK, Höfert SP, Woschko D, Janiak C, Pescitelli G. Synthesis and Characterization of Bis[( R or S)- N-1-(X-C 6H 4)ethyl-2-oxo-1-naphthaldiminato-κ 2N, O]-Λ/Δ-cobalt(II) (X = H, p-CH 3O, p-Br) with Symmetry- and Distance-Dependent Vibrational Circular Dichroism Enhancement and Sign Inversion. Inorg Chem 2021; 60:14116-14131. [PMID: 34477372 PMCID: PMC8456410 DOI: 10.1021/acs.inorgchem.1c01503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The enantiopure Schiff
bases (R or S)-N-1-(X-C6H4)ethyl-2-hydroxy-1-naphthaldimine
{X = H [(R or S)-HL1], p-CH3O [(R or S)-HL2],
and p-Br [(R- or S)-HL3]} react with cobalt(II) acetate to give bis[(R or S)-N-1-(X-C6H4)ethyl-2-oxo-1-naphthaldiminato-κ2N,O]-Λ/Δ-cobalt(II) {X = H
[Λ/Δ-Co-(R or S)-L1], p-CH3O [Λ/Δ-Co-(R or S)-L2], and p-Br [Λ/Δ-Co-(R or S)-L3]} (1–3), respectively. Induced Λ and Δ chirality originates
at the metal center of the C2-symmetric
molecule in pseudotetrahedral geometry. Differential scanning calorimetry
analyses explored the thermal stability of the complexes, which undergo
reversible phase transformation from crystalline solid to isotropic
liquid phase for 1 and 3 but irreversible
phase transformation for 2. Like other cobalt(II) complexes,
compounds 1–3 exhibit a continuous
ensemble of absorption and circular dichroism bands, which span from
the UV to IR region and can be collected into a superspectrum. Infrared
vibrational circular dichroism (IR-VCD) spectra witness the coupling
between Co2+-centered low-lying electronic states and ligand-centered
vibrations. The coupling produces enhanced and almost monosignate
VCD spectra, with both effects being mode-dependent in terms of the A or B symmetry (in the C2 point group) and distance from the Co2+ core. Chiroptical superspectra of naphthaldiminatocobalt(II)
complexes 1−3 exhibit a continuous
ensemble of absorption
and circular dichroism bands from the UV to IR region, including peculiar
and almost monosignate vibrational circular dichroism (VCD) spectra
dominated by the coupling between Co2+-centered low-lying
electronic states and ligand-centered vibrations, which depend on
the normal-mode symmetry and distance from the Co2+ core
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Affiliation(s)
- Marcin Górecki
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa 56126, Italy.,Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 01-224, Poland
| | - Mohammed Enamullah
- Department of Chemistry, Jahangirnagar University, Dhaka 1342, Bangladesh
| | | | | | - Simon-Patrick Höfert
- Institute of Inorganic Chemistry and Structural Chemistry, Heinrich-Heine-University of Düsseldorf, Düsseldorf 40225, Germany
| | - Dennis Woschko
- Institute of Inorganic Chemistry and Structural Chemistry, Heinrich-Heine-University of Düsseldorf, Düsseldorf 40225, Germany
| | - Christoph Janiak
- Institute of Inorganic Chemistry and Structural Chemistry, Heinrich-Heine-University of Düsseldorf, Düsseldorf 40225, Germany
| | - Gennaro Pescitelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa 56126, Italy
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40
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Machalska E, Zajac G, Wierzba AJ, Kapitán J, Andruniów T, Spiegel M, Gryko D, Bouř P, Baranska M. Recognition of the True and False Resonance Raman Optical Activity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Krakow Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET) Jagiellonian University Bobrzynskiego 14 30-348 Krakow Poland
| | - Grzegorz Zajac
- Jagiellonian Centre for Experimental Therapeutics (JCET) Jagiellonian University Bobrzynskiego 14 30-348 Krakow Poland
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Aleksandra J. Wierzba
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Josef Kapitán
- Department of Optics Palacký University Olomouc 17. listopadu 12 77146 Olomouc Czech Republic
| | - Tadeusz Andruniów
- Department of Chemistry Wroclaw University of Science and Technology Wyb. Wyspianskiego 27 50-370 Wroclaw Poland
| | - Maciej Spiegel
- Department of Pharmacognosy and Herbal Medicine Wroclaw Medical University Borowska 211A 50-556 Wroclaw Poland
| | - Dorota Gryko
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Malgorzata Baranska
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Krakow Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET) Jagiellonian University Bobrzynskiego 14 30-348 Krakow Poland
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41
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Machalska E, Zajac G, Wierzba AJ, Kapitán J, Andruniów T, Spiegel M, Gryko D, Bouř P, Baranska M. Recognition of the True and False Resonance Raman Optical Activity. Angew Chem Int Ed Engl 2021; 60:21205-21210. [PMID: 34216087 PMCID: PMC8519086 DOI: 10.1002/anie.202107600] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/01/2021] [Indexed: 12/16/2022]
Abstract
Resonance Raman optical activity (RROA) possesses all aspects of a sensitive tool for molecular detection, but its measurement remains challenging. We demonstrate that reliable recording of RROA of chiral colorful compounds is possible, but only after considering the effect of the electronic circular dichroism (ECD) on the ROA spectra induced by the dissolved chiral compound. We show RROA for a number of model vitamin B12 derivatives that are chemically similar but exhibit distinctively different spectroscopic behavior. The ECD/ROA effect is proportional to the concentration and dependent on the optical pathlength of the light propagating through the sample. It can severely alter relative band intensities and signs in the natural RROA spectra. The spectra analyses are supported by computational modeling based on density functional theory. Neglecting the ECD effect during ROA measurement can lead to misinterpretation of the recorded spectra and erroneous conclusions about the molecular structure.
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Affiliation(s)
- Ewa Machalska
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
- Jagiellonian Centre for Experimental Therapeutics (JCET)Jagiellonian UniversityBobrzynskiego 1430-348KrakowPoland
| | - Grzegorz Zajac
- Jagiellonian Centre for Experimental Therapeutics (JCET)Jagiellonian UniversityBobrzynskiego 1430-348KrakowPoland
- Institute of Organic Chemistry and BiochemistryAcademy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Aleksandra J. Wierzba
- Institute of Organic ChemistryPolish Academy of SciencesKasprzaka 44/5201-224WarsawPoland
| | - Josef Kapitán
- Department of OpticsPalacký University Olomouc17. listopadu 1277146OlomoucCzech Republic
| | - Tadeusz Andruniów
- Department of ChemistryWroclaw University of Science and TechnologyWyb. Wyspianskiego 2750-370WroclawPoland
| | - Maciej Spiegel
- Department of Pharmacognosy and Herbal MedicineWroclaw Medical UniversityBorowska 211A50-556WroclawPoland
| | - Dorota Gryko
- Institute of Organic ChemistryPolish Academy of SciencesKasprzaka 44/5201-224WarsawPoland
| | - Petr Bouř
- Institute of Organic Chemistry and BiochemistryAcademy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Malgorzata Baranska
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
- Jagiellonian Centre for Experimental Therapeutics (JCET)Jagiellonian UniversityBobrzynskiego 1430-348KrakowPoland
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42
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Jähnigen S, Zehnacker A, Vuilleumier R. Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge. J Phys Chem Lett 2021; 12:7213-7220. [PMID: 34310135 DOI: 10.1021/acs.jpclett.1c01682] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1S,2S)-trans-1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. Because the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins. The new formalism reconnects the periodic model with the finite physical system and restores gauge freedom. It nevertheless fully accounts for nonlocal spatial couplings from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level.
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Affiliation(s)
- Sascha Jähnigen
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS,, 75005 Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS,, 75005 Paris, France
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43
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Li G, Alshalalfeh M, Yang Y, Cheeseman JR, Bouř P, Xu Y. Can One Measure Resonance Raman Optical Activity? Angew Chem Int Ed Engl 2021; 60:22004-22009. [PMID: 34347923 DOI: 10.1002/anie.202109345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/10/2022]
Abstract
Resonance Raman optical activity (RROA) is commonly measured as the difference in intensity of Raman scattered right and left circularly polarized light, IR -IL , when a randomly polarized light is in resonance with a chiral molecule. Strong and sometimes mono-signate experimental RROA spectra of several chiral solutes were reported previously, although their signs and relative intensities could not be reproduced theoretically. By examining multiple light-matter interaction events which can occur simultaneously under resonance, we show that a new form of chiral Raman spectroscopy, eCP-Raman, a combination of electronic circular dichroism and circularly polarized Raman, prevails. By incorporating the finite-lifetime approach for resonance, the experimental patterns of the model chiral solutes are captured theoretically by eCP-Raman, without any RROA contribution. The results open opportunity for applications of eCP-Raman spectroscopy and for extracting true RROA experimentally.
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Affiliation(s)
- Guojie Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Mutasem Alshalalfeh
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yanqing Yang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - James R Cheeseman
- Gaussian Inc., 340 Quinnipiac St., Bldg. 40, Wallingford, CT, 06492-4050, USA
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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44
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Greenfield JL, Wade J, Brandt JR, Shi X, Penfold TJ, Fuchter MJ. Pathways to increase the dissymmetry in the interaction of chiral light and chiral molecules. Chem Sci 2021; 12:8589-8602. [PMID: 34257860 PMCID: PMC8246297 DOI: 10.1039/d1sc02335g] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022] Open
Abstract
The dissymmetric interaction between circularly polarised (CP) light and chiral molecules is central to a range of areas, from spectroscopy and imaging to next-generation photonic devices. However, the selectivity in absorption or emission of left-handed versus right-handed CP light is low for many molecular systems. In this perspective, we assess the magnitude of the measured chiroptical response for a variety of chiral systems, ranging from small molecules to large supramolecular assemblies, and highlight the challenges towards enhancing chiroptical activity. We explain the origins of low CP dissymmetry and showcase recent examples in which molecular design, and the modification of light itself, enable larger responses. Our discussion spans spatial extension of the chiral chromophore, manipulation of transition dipole moments, exploitation of forbidden transitions and creation of macroscopic chiral structures; all of which can increase the dissymmetry. Whilst the specific strategy taken to enhance the dissymmetric interaction will depend on the application of interest, these approaches offer hope for the development and advancement of all research fields that involve interactions of chiral molecules and light.
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Affiliation(s)
- Jake L Greenfield
- Department of Chemistry and Molecular Sciences Research Hub, Imperial College London, White City Campus 82 Wood Lane London W12 0BZ UK
| | - Jessica Wade
- Department of Materials, Imperial College London Exhibition Road SW7 2AZ UK
- Centre for Processable Electronics, Imperial College London, South Kensington Campus London SW7 2AZ UK
| | - Jochen R Brandt
- Department of Chemistry and Molecular Sciences Research Hub, Imperial College London, White City Campus 82 Wood Lane London W12 0BZ UK
- Centre for Processable Electronics, Imperial College London, South Kensington Campus London SW7 2AZ UK
| | - Xingyuan Shi
- Department of Chemistry and Molecular Sciences Research Hub, Imperial College London, White City Campus 82 Wood Lane London W12 0BZ UK
- Centre for Processable Electronics, Imperial College London, South Kensington Campus London SW7 2AZ UK
| | - Thomas J Penfold
- Chemistry - School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Matthew J Fuchter
- Department of Chemistry and Molecular Sciences Research Hub, Imperial College London, White City Campus 82 Wood Lane London W12 0BZ UK
- Centre for Processable Electronics, Imperial College London, South Kensington Campus London SW7 2AZ UK
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45
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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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46
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Chiral resolution and absolute configuration determination of new metal-based photodynamic therapy antitumor agents. J Pharm Biomed Anal 2021; 204:114233. [PMID: 34252819 DOI: 10.1016/j.jpba.2021.114233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022]
Abstract
The advent of cisplatin as a cancer drug in the late 1960s generated considerable interest in the use of transition metal complexes as cancer therapy agents. Despite enhanced research in this area, there has yet to be any non-platinum-based transition metal complex cancer drugs approved by the Food and Drug Administration (FDA). Recently a Ru(II) metal-organic dyad (TLD1433) has provided promising results as a photodynamic therapy (PDT) agent for some types of cancer. This particularly effective PDT compound has an oligothiophene chain appended to an imidazophenanthroline ligand which chelates Ru(II). The entire complex is chiral and is synthesized as a racemate. Five such chiral Ru(II) and Os(II) PDT agents were synthesized and their enantiomers separated for the first time. The enantiomers of these compounds are not easily crystalized. However, preparative LC provided sufficient amounts of these novel PDT agents to determine their absolute configurations by vibrational circular dichroism (VCD). The synthesis, separation and absolute configuration determinations are described and discussed in detail.
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47
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Aerts R, Vanhove J, Herrebout W, Johannessen C. Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity. Chem Sci 2021; 12:5952-5964. [PMID: 35342545 PMCID: PMC8867523 DOI: 10.1039/d1sc01446c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 01/06/2023] Open
Abstract
It is crucial for fundamental physical chemistry techniques to find their application in tackling real-world challenges. Hitherto, Raman optical activity (ROA) spectroscopy is one of the examples where a promising future within the pharmaceutical sector is foreseen, but has not yet been established. Namely, the technique is believed to be able to contribute in investigating the conformational behaviour of drug candidates. We, herein, strive towards the alignment of the ROA analysis outcome and the pharmaceutical expectations by proposing a fresh strategy that ensures a more complete, reliable, and transferable ROA study. The strategy consists of the treatment of the conformational space by means of a principal component analysis (PCA) and a clustering algorithm, succeeded by a thorough ROA spectral analysis and a novel way of estimating the contributions of the different chemical fragments to the total ROA spectral intensities. Here, vancomycin, an antibiotic glycopeptide, has been treated; it is the first antibiotic glycopeptide studied by means of ROA and is a challenging compound in ROA terms. By applying our approach we discover that ROA is capable of independently identifying the correct conformation of vancomycin in aqueous solution. In addition, we have a clear idea of what ROA can and cannot tell us regarding glycopeptides. Finally, the glycopeptide class turns out to be a spectroscopically curious case, as its spectral responses are unlike the typical ROA spectral responses of peptides and carbohydrates. This preludes future ROA studies of this intriguing molecular class. Raman optical activity tackles the complex conformational space of glycopeptide antibiotics.![]()
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Affiliation(s)
- Roy Aerts
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Jente Vanhove
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
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48
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Chamberlain BT, Vincent M, Nafie J, Müller P, Greka A, Wagner FF. Multigram Preparation of BRD4780 Enantiomers and Assignment of Absolute Stereochemistry. J Org Chem 2021; 86:4281-4289. [PMID: 33618515 DOI: 10.1021/acs.joc.0c02520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a multigram synthesis of 3-exo-isopropylbicyclo[2.2.1]heptan-2-endo-amine hydrochloride (1) (also known as BRD4780 and AGN-192403) is described. The process involves protection of the amine as 4-nitrobenzyl carbamate, pNZ, which enables chiral SFC chromatography. The absolute configuration (AC) of the individual enantiomers has been determined by Mosher's amide method, VCD spectroscopy, and X-ray crystallography. We highlight the VCD approach as a rapid and effective means of AC determination that can be deployed directly on the target compounds.
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Affiliation(s)
- Brian T Chamberlain
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Mathilde Vincent
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Jordan Nafie
- BioTools, Inc., 17546 Bee Line Highway, Jupiter Florida 33458, United States
| | - Peter Müller
- Massachusetts Institute of Technology, Massachusetts Avenue 2-235, Cambridge, Massachusetts 02139, United States
| | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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49
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Gogoi A, Konwer S, Zhuo GY. Polarimetric Measurements of Surface Chirality Based on Linear and Nonlinear Light Scattering. Front Chem 2021; 8:611833. [PMID: 33644001 PMCID: PMC7902787 DOI: 10.3389/fchem.2020.611833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023] Open
Abstract
A molecule, molecular aggregate, or protein that cannot be superimposed on its mirror image presents chirality. Most living systems are organized by chiral building blocks, such as amino acids, peptides, and carbohydrates, and any change in their molecular structure (i.e., handedness or helicity) alters the biochemical and pharmacological functions of the molecules, many of which take place at surfaces. Therefore, studying surface chirogenesis at the nanoscale is fundamentally important and derives various applications. For example, since proteins contain highly ordered secondary structures, the intrinsic chirality can be served as a signature to measure the dynamics of protein adsorption and protein conformational changes at biological surfaces. Furthermore, a better understanding of chiral recognition and separation at bio-nanointerfaces is helpful to standardize chiral drugs and monitor the synthesis of adsorbents with high precision. Thus, exploring the changes in surface chirality with polarized excitations would provide structural and biochemical information of the adsorbed molecules, which has led to the development of label-free and noninvasive measurement tools based on linear and nonlinear optical effects. In this review, the principles and selected applications of linear and nonlinear optical methods for quantifying surface chirality are introduced and compared, aiming to conceptualize new ideas to address critical issues in surface biochemistry.
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Affiliation(s)
- Ankur Gogoi
- Department of Physics, Jagannath Barooah College, Jorhat, India
| | - Surajit Konwer
- Department of Chemistry, Dibrugarh University, Dibrugarh, India
| | - Guan-Yu Zhuo
- Institute of New Drug Development, China Medical University, Taichung, Taiwan.,Integrative Stem Cell Center, China Medical University Hospital, Taichung, Taiwan
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50
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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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