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Krupová M, Leszczenko P, Sierka E, Hamplová SE, Klepetářová B, Pelc R, Andrushchenko V. Vibrational circular dichroism of adenosine crystals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124381. [PMID: 38838602 DOI: 10.1016/j.saa.2024.124381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024]
Abstract
Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution. Here, we present the first vibrational circular dichroism (VCD) spectroscopic study of adenosine crystals in solid state. Highly regular arrangement of adenosine molecules in a crystal resulted in a strongly enhanced supramolecular VCD signal originating from long-range coupling of vibrations. The data suggested that adenosine crystals, in contrast to guanosine ones, do not imbibe atmospheric water. Relatively large dimensions of the adenosine crystals resulted in scattering and substantial orientational artifacts affecting the spectra. Several strategies for tackling the artifacts have been proposed and tested. Atypical features in IR absorption spectra of crystalline adenosine (e.g., extremely low absorption in mid-IR spectral range) were observed and attributed to refractive properties of adenosine crystals.
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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; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348 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
| | - Blanka Klepetářová
- 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; 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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2
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Sklenář A, Růžičková L, Schrenková V, Bednárová L, Pazderková M, Chatziadi A, Zmeškalová Skořepová E, Šoóš M, Kaminský J. Solid-state vibrational circular dichroism for pharmaceutical applications: Polymorphs and cocrystal of sofosbuvir. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124478. [PMID: 38788502 DOI: 10.1016/j.saa.2024.124478] [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: 09/25/2023] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024]
Abstract
X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD's ability to differentiate between various crystal structures of the same molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible, and artifact-free results with maximal signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finally, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicate that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations, and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir.
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Affiliation(s)
- Adam Sklenář
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic; University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic
| | - Lucie Růžičková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic; Imperial College London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Věra Schrenková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic
| | - Argyro Chatziadi
- University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic
| | - Eliška Zmeškalová Skořepová
- University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic; Institute of Physics of the CAS, Na Slovance 1999/2, Prague 182 21, Czech Republic
| | - Miroslav Šoóš
- University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic.
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3
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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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Liu Y, Hao A, Xing P. Ultrasensitive Solvatochirochromism of Single Benzene Chromophores. Chemistry 2024; 30:e202400059. [PMID: 38409631 DOI: 10.1002/chem.202400059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Solvents influence the structure, aggregation and folding behaviors of solvatochromic compounds. Ultrasensitive solvent mediated chiroptical response is conducive to the fabrication of molecular platform for sensing and recognition, which however, remains great challenges in conceptual or applicable design. Here we report a cysteine-based single benzene chromophore system that shows ultrasensitivity to solvents. Compared to the ratiometrically responsive systems, the chiroptical activities could be triggered or inverted depending on the substituents of chiral entities with an ultralow solvent volume fraction (<1 vol %). One drop of dipolar solvents shall significantly induce the emergence or inversion of chiroptical signals in bulky phases. Based on the experimental and computational studies, the ultrasensitivity is contributed to the intimate interplay between solvents and chiral compounds that anchors the specific chiral conformation. It illustrates that structurally simple organic compounds without aggregation or folding behaviors possess pronounced solvatochiroptical properties, which sheds light on the next-generation of chiroptical sensors and switches.
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Affiliation(s)
- Yiping Liu
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, People's Republic of China
| | - Aiyou Hao
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, People's Republic of China
| | - Pengyao Xing
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, People's Republic of China
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5
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Bowles J, Jähnigen S, Agostini F, Vuilleumier R, Zehnacker A, Calvo F, Clavaguéra C. Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases. Chemphyschem 2024; 25:e202300982. [PMID: 38318765 DOI: 10.1002/cphc.202300982] [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: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/07/2024]
Abstract
Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of the IR and VCD spectra is examined and found to be more demanding in the latter case. Comparisons with experimental frequencies are also provided for the condensed phases.
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Affiliation(s)
- Jessica Bowles
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Sascha Jähnigen
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Anne Zehnacker
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay UMR8214, 91405, Orsay, France
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LIPhy, 38000, Grenoble, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
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6
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Rode JE, Wasilczenko J, Górecki M. Differentiation of solvatomorphs of active pharmaceutical ingredients (API) by solid-state vibrational circular dichroism (VCD). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123851. [PMID: 38295593 DOI: 10.1016/j.saa.2024.123851] [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: 07/18/2023] [Revised: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Here, we present the new application of solid-state Vibrational Circular Dichroism (VCD) spectroscopy to differentiate several dutasteride (DS) solvatomorphs - the model active pharmaceutical ingredient (API). Several crystalline DS hydrochloride hydrates solvated with methanol, ethanol, acetonitrile, acetone, and acetic acid were prepared. In contrast to almost identical IR spectra, the VCD ones were very sensitive to changes in the sample composition. We marked significant differences in the shape of VCD spectra of studied DS solvatomorphs, DS hydrates, and DS polymorphic forms. Our findings, supported by DFT calculations, show that VCD spectroscopy has the pronounced ability to distinguish their crystal arrangements. We believe that this contribution will extend the use of VCD in the pharmaceutical industry for developing and designing new chiral drug products for the identification, description, and in-depth probing of several pharmaceutical solvatomorphs in the future.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, Dorodna 16 St., 03-195 Warsaw, Poland
| | - Justyna Wasilczenko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland.
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7
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Liu JZ, Chai XY, Huang J, Li RS, Li CM, Ling J, Cao QE, Huang CZ. Chiral Assembly of Perovskite Nanocrystals: Sensitive Discrimination of Amino Acid Enantiomers. Anal Chem 2024; 96:4282-4289. [PMID: 38469640 DOI: 10.1021/acs.analchem.3c05941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Chirality is a widespread phenomenon in nature and in living organisms and plays an important role in living systems. The sensitive discrimination of chiral molecular enantiomers remains a challenge in the fields of chemistry and biology. Establishing a simple, fast, and efficient strategy to discriminate the spatial configuration of chiral molecular enantiomers is of great significance. Chiral perovskite nanocrystals (PNCs) have attracted much attention because of their excellent optical activity. However, it is a challenge to prepare perovskites with both chiral and fluorescence properties for chiral sensing. In this work, we synthesized two chiral fluorescent perovskite nanocrystal assembly (PNA) enantiomers by using l- or d-phenylalanine (Phe) as chiral ligands. PNA exhibited good fluorescence recognition for l- and d-proline (Pro). Homochiral interaction led to fluorescence enhancement, while heterochiral interaction led to fluorescence quenching, and there is a good linear relationship between the fluorescence changing rate and l- or d-Pro concentration. Mechanism studies show that homochiral interaction-induced fluorescence enhancement is attributed to the disassembly of chiral PNA, while no disassembly of chiral PNA was found in heterochiral interaction-induced fluorescence quenching, which is attributed to the substitution of Phe on the surface of chiral PNA by heterochiral Pro. This work suggests that chiral perovskite can be used for chiral fluorescence sensing; it will inspire the development of chiral nanomaterials and chiral optical sensors.
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Affiliation(s)
- Jin-Zhou Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Xin-Yi Chai
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Jingtao Huang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Rong Sheng Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jian Ling
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Qiu-E Cao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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8
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Majka Z, Kwiecień K, Kaczor A. Vibrational Optical Activity of Amyloid Fibrils. Chempluschem 2024:e202400091. [PMID: 38421108 DOI: 10.1002/cplu.202400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
Amyloid fibrils are supramolecular systems showing distinct chirality at different levels of their complex multilayered architectures. Due to the regular long-range chiral organization, amyloid fibrils exhibit the most intense Vibrational Optical Activity (VOA) signal observed up to now, making VOA techniques: Vibrational Circular Dichroism (VCD) and Raman Optical Activity (ROA) very promising tools to explore their structures, handedness and intricate polymorphism. This concept article reviews up-to-date experimental studies on VOA applications to investigate amyloid fibrils highlighting its future potential in analyzing of these unique supramolecular systems, in particular in the context of biomedicine and nanotechnology.
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Affiliation(s)
- Zuzanna Majka
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387, Krakow, Poland
| | - Karolina Kwiecień
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387, Krakow, Poland
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Prof. St. Łojasiewicza 11 Str., Krakow, Poland
- Łukasiewicz Research Network-Institute of Microelectronics and Photonics, 39 Zabłocie Str., 30-701, Krakow, Poland
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387, Krakow, Poland
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9
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O'Neill N, Lima TA, Furlan Ferreira F, Alvarez NJ, Schweitzer-Stenner R. Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I' bands in FTIR, VCD, and Raman spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123584. [PMID: 37956526 DOI: 10.1016/j.saa.2023.123584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I' band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA; Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210-580, Brazil
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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10
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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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11
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Blasius J, Drysch K, Pilz FH, Frömbgen T, Kielb P, Kirchner B. Efficient Prediction of Mole Fraction Related Vibrational Frequency Shifts. J Phys Chem Lett 2023; 14:10531-10536. [PMID: 37972218 DOI: 10.1021/acs.jpclett.3c02761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
While so far it has been possible to calculate vibrational spectra of mixtures at a particular composition, we present here a novel cluster approach for a fast and robust calculation of mole fraction dependent infrared and vibrational circular dichroism spectra at the example of acetonitrile/(R)-butan-2-ol mixtures. By assigning weights to a limited number of quantum chemically calculated clusters, vibrational spectra can be obtained at any desired composition by a weighted average of the single cluster spectra. In this way, peak positions carrying information about intermolecular interactions can be predicted. We show that mole fraction dependent peak shifts can be accurately modeled and, that experimentally recorded infrared spectra can be reproduced with high accuracy over the entire mixing range. Because only a very limited number of clusters is required, the presented approach is a valuable and computationally efficient tool to access mole fraction dependent spectra of mixtures on a routine basis.
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Affiliation(s)
- Jan Blasius
- Mulliken Center for Theoretical Chemistry, Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115 Bonn, Germany
| | - Katrin Drysch
- Mulliken Center for Theoretical Chemistry, Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115 Bonn, Germany
| | - Frank Hendrik Pilz
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, D-53115 Bonn, Germany
| | - Tom Frömbgen
- Mulliken Center for Theoretical Chemistry, Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115 Bonn, Germany
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Patrycja Kielb
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, D-53115 Bonn, Germany
- Transdisciplinary Research Area "Building Blocks of Matter and Fundamental Interactions" (TRA Matter), University of Bonn, D-53115 Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115 Bonn, Germany
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12
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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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13
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Bowles J, Jähnigen S, Vuilleumier R, Calvo F, Clavaguéra C, Agostini F. Influence of the environment on the infrared spectrum of alanine: An effective mode analysis. J Chem Phys 2023; 158:094305. [PMID: 36889973 DOI: 10.1063/5.0135608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm-1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.
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Affiliation(s)
- Jessica Bowles
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Sascha Jähnigen
- 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
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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14
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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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15
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Galimberti DR. Vibrational Circular Dichroism from DFT Molecular Dynamics: The AWV Method. J Chem Theory Comput 2022; 18:6217-6230. [PMID: 36112978 PMCID: PMC9558311 DOI: 10.1021/acs.jctc.2c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The paper illustrates the Activity Weighted Velocities
(AWV) methodology
to compute Vibrational Circular Dichroism (VCD) anharmonic spectra
from Density Functional Theory (DFT) molecular dynamics. AWV calculates
the spectra by the Fourier Transform of the time correlation functions
of velocities, weighted by specific observables: the Atomic Polar
Tensors (APTs) and the Atomic Axial Tensors (AATs). Indeed, AWV shows
to correctly reproduce the experimental spectra for systems in the
gas and liquid phases, both in the case of weakly and strongly interacting
systems. The comparison with the experimental spectra is striking
especially in the fingerprint region, as demonstrated by the three
benchmark systems discussed: (1S)-Fenchone in the
gas phase, (S)-(−)-Propylene oxide in the
liquid phase, and (R)-(−)-2-butanol in the
liquid phase. The time evolution of APTs and AATs can be adequately
described by a linear combination of the tensors of a small set of
appropriate reference structures, strongly reducing the computational
cost without compromising accuracy. Additionally, AWV allows the partition
of the spectral signal in its molecular components without any expensive
postprocessing and any localization of the charge density or the wave
function.
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Affiliation(s)
- Daria Ruth Galimberti
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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16
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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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17
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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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18
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Chao YK, Praveena NM, Yang KC, Gowd EB, Ho RM. Crystallization of polylactides examined by vibrational circular dichroism of intra- and inter-chain chiral interactions. SOFT MATTER 2022; 18:2722-2725. [PMID: 35234247 DOI: 10.1039/d2sm00060a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Herein, vibrational circular dichroism (VCD) measurements were carried out to study the kinetics of cold-crystallized poly(D-lactide) (PDLA) at the molecular level via qualitative analysis. The amplification of the VCD signals from intra- and inter-chain chiral interactions suggests the formation of partially ordered PDLA, followed by heterogeneous nucleation for crystallization. These results were further supported by differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD) and Fourier transform infrared (FTIR) spectroscopy analyses.
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Affiliation(s)
- Yi-Kuan Chao
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, Republic of China.
| | - N M Praveena
- Materials Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Industrial Estate (P.O.) Pappanamcode, Trivandrum 695 019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Kai-Chieh Yang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, Republic of China.
| | - E Bhoje Gowd
- Materials Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Industrial Estate (P.O.) Pappanamcode, Trivandrum 695 019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Rong-Ming Ho
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, Republic of China.
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19
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Dupont J, Lepère V, Zehnacker A, Hartweg S, Garcia GA, Nahon L. Photoelectron Circular Dichroism as a Signature of Subtle Conformational Changes: The Case of Ring Inversion in 1-Indanol. J Phys Chem Lett 2022; 13:2313-2320. [PMID: 35245057 DOI: 10.1021/acs.jpclett.2c00074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chirality plays a fundamental role in the molecular recognition processes. Molecular flexibility is also crucial in molecular recognition, allowing the interacting molecules to adjust their structures and hence optimize the interaction. Methods probing simultaneously chirality and molecular conformation are therefore crucially needed. Taking advantage of a possible control in the gas phase of the conformational distribution between the equatorial and axial conformers resulting from a ring inversion in jet-cooled 1-indanol, we demonstrate here the sensitivity of valence-shell photoelectron circular dichroism (PECD) to both chirality and subtle conformational changes, in a case where the photoelectron spectra of the two conformers are identical. For the highest occupied orbital, we observe a dramatic inversion of the PECD-induced photoelectron asymmetries, while the photoionization cross-section and usual anisotropy (β) parameter are completely insensitive to conformational isomerism. Such a sensitivity is a major asset for the ongoing developments of PECD-based techniques as a sensitive chiral (bio)chemical analytical tool in the gas phase.
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Affiliation(s)
- Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Sebastian Hartweg
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192 Gif sur Yvette, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192 Gif sur Yvette, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192 Gif sur Yvette, France
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20
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Rode JE, Lyczko K, Kosińska K, Matalińska J, Dyniewicz J, Misicka A, Dobrowolski JC, Lipiński PFJ. The solid state VCD of a novel N-acylhydrazone trifluoroacetate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120761. [PMID: 34954483 DOI: 10.1016/j.saa.2021.120761] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
A novel N-acylhydrazone with pharmaceutical importance was subject of structural and IR/VCD investigations in the solid state. In the crystal structure, dimers of anion-cation pairs are stabilized by H-bonding and ionic interactions. Some less common interaction types, like C=N···C-NH3+ (σ-hole) interactions, hydrazone-aromatic interactions and dispersive contacts of the CF3 groups are also present in the crystal. Satisfactory reproduction of the solid state IR and VCD spectra required that quantum-chemical calculations be done on a tetramer (four cation-anion pairs) cut out from the crystal structure, exhibiting key intermolecular interactions. Ten DFT functionals were assessed as to the agreement between the calculated and experimental spectra. Various approaches to scaling of the calculated frequencies were applied. The best results were yielded with individual (optimized) frequency scaling factors (FSFs) and band half-widths at half maximum-(HWHM) for four separate spectral subregions. The best matching between the experimental and theoretical spectra (according to SimIR, SimVCD and SimVDF indices) was found for the B3PW91 functional, however, a few other functionals follow closely in the ranking. Based on the quantum chemical calculations, spectral assignments have been made.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, PL 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, PL 03-195 Warsaw, Poland
| | - Katarzyna Kosińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Jolanta Dyniewicz
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Jan Cz Dobrowolski
- Department for Medicines Biotechnology and Bioinformatics, National Medicines Institute, 30/34 Chełmska Street, PL 00-725 Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland.
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21
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Kirchner B, Blasius J, Alizadeh V, Gansäuer A, Hollóczki O. Chemistry Dissolved in Ionic Liquids. A Theoretical Perspective. J Phys Chem B 2022; 126:766-777. [PMID: 35034453 DOI: 10.1021/acs.jpcb.1c09092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The theoretical treatment of ionic liquids must focus now on more realistic models while at the same time keeping an accurate methodology when following recent ionic liquids research trends or allowing predictability to come to the foreground. In this Perspective, we summarize in three cases of advanced ionic liquid research what methodological progress has been made and point out difficulties that need to be overcome. As particular examples to discuss we choose reactions, chirality, and radicals in ionic liquids. All these topics have in common that an explicit or accurate treatment of the electronic structure and/or intermolecular interactions is required (accurate methodology), while at the same time system size and complexity as well as simulation time (realistic model) play an important role and must be covered as well.
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Affiliation(s)
- Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4+6, D-53115 Bonn, Germany
| | - Jan Blasius
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4+6, D-53115 Bonn, Germany
| | - Vahideh Alizadeh
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4+6, D-53115 Bonn, Germany
| | - Andreas Gansäuer
- Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, D-53121 Bonn, Germany
| | - Oldamur Hollóczki
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4+6, D-53115 Bonn, Germany.,Department of Physical Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary
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22
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Yamagishi A, Takimoto K, Tamura K, Sato F, Sato H. Chiral Discrimination of Dansylated Alanine Methyl Ester on a Modified Clay Surface: Vibrational Circular Dichroism Approach. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Akihiko Yamagishi
- Department of Medicine, Faculty of Medicine, Toho University, Ota-ku, Tokyo 143-8540, Japan
- Research Center for Functional Materials, National Institute of Materials Science, Tsukuba, Ibaraki 305-0044, Japan
| | - Kazuyoshi Takimoto
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Kenji Tamura
- Research Center for Functional Materials, National Institute of Materials Science, Tsukuba, Ibaraki 305-0044, Japan
| | - Fumi Sato
- Department of Medicine, Faculty of Medicine, Toho University, Ota-ku, Tokyo 143-8540, Japan
| | - Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
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23
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Le Barbu-Debus K, Zehnacker A. Competition between inter and intramolecular hydrogen bond evidenced by vibrational circular dichroism spectroscopy: The case of (1S,2R)-(-)-cis-1-amino-2-indanol. Chirality 2021; 33:858-874. [PMID: 34570370 DOI: 10.1002/chir.23362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 02/06/2023]
Abstract
The infrared (IR) absorption and vibrational circular dichroism (VCD) spectra of an intramolecularly hydrogen-bonded chiral amino-alcohol, (1S,2R)-(-)-cis-1-amino-2-indanol, are studied in DMSO-d6 . The spectra are simulated at the density functional theory (DFT) level within the frame of the cluster-in-the-liquid model. Both IR and VCD spectra show a clear signature of the formation of intermolecular hydrogen bonds at the detriment of the intramolecular OH … N interaction present in the isolated molecule. Two solvent molecules are necessary to reproduce the experimental spectra. Whereas the first DMSO molecule captures the main spectral modifications due to hydrogen bond formation between the solute and the solvent, the second DMSO molecule is necessary for a good description of the Boltzmann contribution of the different complexes, based on their Gibbs free energy.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, Orsay, France
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24
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Jähnigen S, Sebastiani D, Vuilleumier R. The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution. Phys Chem Chem Phys 2021; 23:17232-17241. [PMID: 34369531 DOI: 10.1039/d1cp03106f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss the effect of the hydrogen bond network on the aggregation behaviour of the acid: while aggregates of the solute represent conditions encountered in a weakly interacting solvent, the presence of water drastically interferes with the clusters - more strongly than originally anticipated. For both scenarios we computed the VCD spectra by means of nuclear velocity perturbation theory (NVPT). The comparison with experimental data allows us to establish a VCD-structure relationship that includes the solvent network around the chiral solute. We suggest that fundamental modes with strong polarisation such as the carbonyl stretching vibration can borrow VCD from the chirally restructured solvent cage, which extends the common explanatory models of VCD generation in aqueous solution.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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25
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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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26
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Yamagishi H, Sato H, Kawamura I. Vibrational circular dichroism of D-amino acid-containing peptide NdWFamide in the crystal form. Chirality 2021; 33:652-659. [PMID: 34313360 DOI: 10.1002/chir.23343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 01/31/2023]
Abstract
Microcrystals of l-Asn-d-Trp-l-Phe-NH2 (NdWFamide), a tripeptide derived from Aplysia kurodai that exhibits invertebrate cardiac activity, were evaluated by vibrational circular dichroism (VCD). The chirality of the tryptophan residue at the second position in NdWFamide was associated with the conformation and biological characteristics. The VCD spectrum of NdWFamide was a mirror image of its enantiomer; however, it was significantly different from that of its diastereomer, NWFamide, which is its precursor. The obtained VCD signals of NdWFamide were in good agreement with the VCD signals that were calculated based on the optimized aggregates of NdWFamide, which formed a helical-like backbone conformation. The evaluation of the VCD results revealed the conformation of NdWFamide in the crystalline state and succeeded in distinguishing its stereoisomers. Therefore, this study demonstrates VCD as a useful method for the structural analysis of naturally occurring d-amino acid-containing peptides.
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Affiliation(s)
- Hiroki Yamagishi
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | - Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
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27
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Hesser M, Thursch LJ, Lewis TR, Lima TA, Alvarez NJ, Schweitzer-Stenner R. Concentration Dependence of a Hydrogel Phase Formed by the Deprotonation of the Imidazole Side Chain of Glycylhistidylglycine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6935-6946. [PMID: 34077210 DOI: 10.1021/acs.langmuir.1c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Upon deprotonation of its imidazole group at ∼pH 6, the unblocked tripeptide glycylhistidylglycine (GHG) self-assembles into very long crystalline fibrils on a 10-1000 μm scale which are capable of forming a volume spanning network, that is, hydrogel. The critical peptide concentration for self-assembly at a pH of 6 lies between 50 and 60 mM. The fraction of peptides that self-assemble into fibrils depends on the concentration of deprotonated GHG. While IR spectra seem to indicate the formation of fibrils with standard amyloid fibril β-sheet structures, vibrational circular dichroism spectra show a strongly enhanced amide I' signal, suggesting that the formed fibrils exhibit significant chirality. The fibril chirality appears to be a function of peptide concentration. Rheological measurements reveal that the rate of gelation is concentration-dependent and that there is an optimum gel strength at intermediate peptide concentrations of ca. 175 mM. This paper outlines the unique properties of the GHG gel phase which is underlain by a surprisingly dense fibril network with an exceptionally strong modulus that make them potential additives for biomedical applications.
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Affiliation(s)
- Morgan Hesser
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Lavenia J Thursch
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Todd R Lewis
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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28
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Sato H, Shimizu M, Watanabe K, Yoshida J, Kawamura I, Koshoubu J. Multidimensional Vibrational Circular Dichroism Apparatus Equipped with Quantum Cascade Laser and Its Use for Investigating Some Peptide Systems Containing d-Amino Acids. Anal Chem 2021; 93:2742-2748. [DOI: 10.1021/acs.analchem.0c02990] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Masaru Shimizu
- JASCO Corporation, Ishikawa 2967-5, Hachioji, Tokyo 192-8537, Japan
| | - Keisuke Watanabe
- JASCO Corporation, Ishikawa 2967-5, Hachioji, Tokyo 192-8537, Japan
| | - Jun Yoshida
- Department of Chemistry, School of Science, Kitasato University, Kitasato 1-15-1, Sagamihara 252-0373, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Jun Koshoubu
- JASCO Corporation, Ishikawa 2967-5, Hachioji, Tokyo 192-8537, Japan
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29
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Ouyang J, Swartjes A, Geerts M, Gilissen PJ, Wang D, Teeuwen PCP, Tinnemans P, Vanthuyne N, Chentouf S, Rutjes FPJT, Naubron JV, Crassous J, Elemans JAAW, Nolte RJM. Absolute configuration and host-guest binding of chiral porphyrin-cages by a combined chiroptical and theoretical approach. Nat Commun 2020; 11:4776. [PMID: 32963222 PMCID: PMC7508876 DOI: 10.1038/s41467-020-18596-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022] Open
Abstract
Porphyrin cage-compounds are used as biomimetic models and substrate-selective catalysts in supramolecular chemistry. In this work we present the resolution of planar-chiral porphyrin cages and the determination of their absolute configuration by vibrational circular dichroism in combination with density functional theory calculations. The chiral porphyrin-cages form complexes with achiral and chiral viologen-guests and upon binding one of the axial enantiomorphs of the guest is bound selectively, as is indicated by induced-electronic-dichroism-spectra in combination with calculations. This host-guest binding also leads to unusual enhanced vibrational circular dichroism, which is the result of a combination of phenomena, such as rigidification of the host and guest structures, charge transfer, and coupling of specific vibration modes of the host and guest. The results offer insights in how the porphyrin cage-compounds may be used to construct a future molecular Turing machine that can write chiral information onto polymer chains. Vibrational circular dichroism (VCD) spectroscopy can be useful for determining the absolute configuration of chiral molecules, as long as the signal intensities are high enough. Here, the authors establish the absolute configurations of two large chiral porphyrin cages and, notably, discover that host-guest binding enhances their VCD intensities.
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Affiliation(s)
- Jiangkun Ouyang
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Anne Swartjes
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Marc Geerts
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Pieter J Gilissen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Danni Wang
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paula C P Teeuwen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul Tinnemans
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nicolas Vanthuyne
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Sara Chentouf
- FSCM - Spectropole, FR1739, Aix-Marseille University, CNRS, Centrale Marseille, 13397 Cedex 20, Marseille, France
| | - Floris P J T Rutjes
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jean-Valère Naubron
- FSCM - Spectropole, FR1739, Aix-Marseille University, CNRS, Centrale Marseille, 13397 Cedex 20, Marseille, France.
| | - Jeanne Crassous
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, ISCR-UMR 6226, F-35000, Rennes, France.
| | - Johannes A A W Elemans
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Roeland J M Nolte
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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30
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Albano G, Pescitelli G, Di Bari L. Chiroptical Properties in Thin Films of π-Conjugated Systems. Chem Rev 2020; 120:10145-10243. [PMID: 32892619 DOI: 10.1021/acs.chemrev.0c00195] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chiral π-conjugated molecules provide new materials with outstanding features for current and perspective applications, especially in the field of optoelectronic devices. In thin films, processes such as charge conduction, light absorption, and emission are governed not only by the structure of the individual molecules but also by their supramolecular structures and intermolecular interactions to a large extent. Electronic circular dichroism, ECD, and its emission counterpart, circularly polarized luminescence, CPL, provide tools for studying aggregated states and the key properties to be sought for designing innovative devices. In this review, we shall present a comprehensive coverage of chiroptical properties measured on thin films of organic π-conjugated molecules. In the first part, we shall discuss some general concepts of ECD, CPL, and other chiroptical spectroscopies, with a focus on their applications to thin film samples. In the following, we will overview the existing literature on chiral π-conjugated systems whose thin films have been characterized by ECD and/or CPL, as well other chiroptical spectroscopies. Special emphasis will be put on systems with large dissymmetry factors (gabs and glum) and on the application of ECD and CPL to derive structural information on aggregated states.
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Affiliation(s)
- Gianluigi Albano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
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31
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Solid-state vibrational circular dichroism studies on the conformation of an amino acid molecule in crystalline state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140439. [DOI: 10.1016/j.bbapap.2020.140439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/18/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022]
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32
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Blasius J, Elfgen R, Hollóczki O, Kirchner B. Glucose in dry and moist ionic liquid: vibrational circular dichroism, IR, and possible mechanisms. Phys Chem Chem Phys 2020; 22:10726-10737. [PMID: 32150178 DOI: 10.1039/c9cp06798a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionic liquids and their mixtures with water show remarkable features in cellulose processing. For this reason, understanding the behavior of carbohydrates in ionic liquids is important. In the present study, we investigated three d-glucose isomers (α, β and open-chain) in 1-ethyl-3-methylimidazolium acetate in the presence and absence of water, through ab initio molecular dynamics simulations. In the complex hydrogen bonding network of these mixtures, the most interesting observation is that upon water addition every hydrogen bond elongates, except the glucose-glucose hydrogen bond for the open-chain and the α-form which shortens, clearly showing the beginning of the crystallization process. The ring glucose rearranges from on-top to in-plane and the open form changes from a coiled to a more linear arrangement when adding water which explains the contradiction that the center of mass distances of the glucose molecules with other glucose molecules grow while the hydrogen bonds shorten. The appearance of coiled open forms indicates that the previously suggested isomerization between these forms is possible and might play a role in the solubility of the related carbohydrates. The calculated IR and VCD spectra reveal insight into the intermolecular interactions, with good to excellent agreements with experimental spectra. Investigating the role of the cation, distances between the acidic carbon atom of the cation and the glucose carbon atom where ring closure and opening occurs are found, which are way shorter than dispersion-like interactions between aliphatic hydrocarbons.
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Affiliation(s)
- Jan Blasius
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4 + 6, D-53115 Bonn, Germany.
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33
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Krupová M, Kessler J, Bouř P. Recent Trends in Chiroptical Spectroscopy: Theory and Applications of Vibrational Circular Dichroism and Raman Optical Activity. Chempluschem 2020; 85:561-575. [DOI: 10.1002/cplu.202000014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and PhysicsCharles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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34
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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35
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Nafie LA. Vibrational optical activity: From discovery and development to future challenges. Chirality 2020; 32:667-692. [DOI: 10.1002/chir.23191] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
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36
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Sato H. A new horizon for vibrational circular dichroism spectroscopy: a challenge for supramolecular chirality. Phys Chem Chem Phys 2020; 22:7671-7679. [DOI: 10.1039/d0cp00713g] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of the solid state and time-step VCD methods opened a new horizon to reveal the mechanism of chirality amplification from microscopic to supramolecular scales.
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Affiliation(s)
- Hisako Sato
- Department of Chemistry
- Graduate School of Science and Engineering
- Ehime University
- Matsuyama 790-8577
- Japan
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37
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Le Barbu-Debus K, Bowles J, Jähnigen S, Clavaguéra C, Calvo F, Vuilleumier R, Zehnacker A. Assessing cluster models of solvation for the description of vibrational circular dichroism spectra: synergy between static and dynamic approaches. Phys Chem Chem Phys 2020; 22:26047-26068. [DOI: 10.1039/d0cp03869e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solvation effects are essential for defining the shape of vibrational circular dichroism (VCD) spectra.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Université Paris-Saclay
- F-91405 Orsay
- France
| | - Jessica Bowles
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique
- UMR8000
- 91405 Orsay
| | - Sascha Jähnigen
- PASTEUR
- Département de Chimie
- Ecole Normale Supérieure
- PSL University
- Sorbonne Université
| | - Carine Clavaguéra
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique
- UMR8000
- 91405 Orsay
| | - Florent Calvo
- Université Grenoble Alpes
- CNRS
- LiPhy
- F-38000 Grenoble
- France
| | - Rodolphe Vuilleumier
- PASTEUR
- Département de Chimie
- Ecole Normale Supérieure
- PSL University
- Sorbonne Université
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Université Paris-Saclay
- F-91405 Orsay
- France
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38
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Sato H, Takimoto K, Kawamura I, Aisawa S. Application of Solid-State Vibrational Circular Dichroism for Intercalation Compounds of Layered Double Hydroxide and Amino Acids: Conformation of an Intercalated Phenylalanine. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hisako Sato
- Department of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Kazuyoshi Takimoto
- Department of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan
| | - Sumio Aisawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
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39
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Declerck V, Pérez‐Mellor A, Guillot R, Aitken DJ, Mons M, Zehnacker A. Vibrational circular dichroism as a probe of solid‐state organisation of derivatives of cyclic β‐amino acids:
Cis
‐ and
trans
‐2‐aminocyclobutane‐1‐carboxylic acid. Chirality 2019; 31:547-560. [DOI: 10.1002/chir.23083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Valérie Declerck
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182Université Paris Sud, Université Paris‐Saclay Orsay France
| | - Ariel Pérez‐Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris‐SudUniversité Paris‐Saclay Orsay France
| | - Régis Guillot
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182Université Paris Sud, Université Paris‐Saclay Orsay France
| | - David J. Aitken
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182Université Paris Sud, Université Paris‐Saclay Orsay France
| | - Michel Mons
- Laboratoire Interactions Dynamiques et Lasers (LIDYL)Université Paris Saclay Paris France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris‐SudUniversité Paris‐Saclay Orsay France
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40
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Kawamura I, Sato H. Solid-state vibrational circular dichroism studies of L- and D-serine. Anal Biochem 2019; 580:14-20. [PMID: 31153871 DOI: 10.1016/j.ab.2019.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/26/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
d-Serine is considered a key endogenous substance involved in several enzymatic reactions in the human body. In this study, solid-state vibrational circular dichroism (VCD) measurements of enantiomeric serine were performed for spectroscopic distinction between d- and l-serine. The mirror-image VCD signals of the isomers in the KBr pellets were observed in the mid-infrared range of 1800-1250 cm-1. The calculated infrared (IR) and VCD spectra for the optimized serine structures were in good agreement with the corresponding observed spectra. In addition, the chemical shift values estimated from the shielding constants of the optimized structure of serine corresponded with the observed values in 13C and 15N solid-state nuclear magnetic resonance spectra, supporting the VCD assignments. Our results suggest the need for further study of VCD to develop a sensitive and high-resolution spectroscopic technique for the detection of d-amino acids.
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Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, 240-8501, Yokohama, Japan.
| | - Hisako Sato
- (b)Graduate School of Science and Engineering, Ehime University, 790-8577, Matsuyama, Japan.
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41
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Ozawa Y, Sato H, Kayano Y, Yamaki N, Izato YI, Miyake A, Naito A, Kawamura I. Self-assembly of tripeptides into γ-turn nanostructures. Phys Chem Chem Phys 2019; 21:10879-10883. [PMID: 30968092 DOI: 10.1039/c9cp00233b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Self-assembling phenylalanine-based peptides have garnered interest owing to their potential for creating new functional materials. Here, we designed four diastereomers, l-Phe-l-Phe-l-Phe (FFF), d-Phe-l-Phe-l-Phe (fFF), l-Phe-d-Phe-l-Phe (FfF) and l-Phe-l-Phe-d-Phe (FFf), to analyze the effect of the d-isomer on the self-assembly. Using SEM, TG, VCD, and solid-state NMR measurements, we found that only FFf forms a γ-turn conformation and self-assembles into a nanoplate with higher thermal stability. The supramolecular structure of FFf consists of intra- and intermolecular hydrogen bonds and π-π stackings. From our results, we have discovered that FFf forms a new type of self-assembling γ-turn conformation, clarifying the structural role of a d-amino acid residue in supramolecular formation.
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Affiliation(s)
- Yumi Ozawa
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan.
| | - Hisako Sato
- Department of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Yohei Kayano
- Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Nana Yamaki
- Graduate School of Environment and Information Sciences, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yu-Ichiro Izato
- Graduate School of Environment and Information Sciences, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Atsumi Miyake
- Institute of Advanced Sciences, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan.
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan. and Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
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42
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Sidler D, Bleiziffer P, Riniker S. Beyond the Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions. J Chem Theory Comput 2019; 15:2492-2503. [PMID: 30802403 DOI: 10.1021/acs.jctc.8b01156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The difference in absorption of left and right circularly polarized light by chiral molecules can be described by the Rosenfeld equation for isotropic samples. It allows the assignment of the absolute stereochemistry by comparing experimental and computationally derived spectra. Despite the simple form of the Rosenfeld equation, its evaluation in the infrared regime remained challenging, as the contribution from the magnetic dipole operator is zero within the Born-Oppenheimer (BO) approximation. In order to resolve this issue, "beyond BO" theories had to be developed, among which Stephen's magnetic field perturbation (MFP) approach offers a computationally easily accessible form. In this work, optical activity is discussed for cylindrically symmetric solutions, which cannot be described anymore by Rosenfeld's equation due to broken spherical symmetry. Mathematical properties of natural and electric-field induced anisotropies are discussed on the basis of the gauge-independent theoretical framework of Buckingham and Dunn. The issue of achiral noise arising from external field perturbations is considered, and potential remedies are introduced. Natural anisotropic vibrational circular dichroism (VCD) equations are solved numerically by applying the MFP approach within the Hartree-Fock (HF) formalism. Properties of anisotropic VCD spectra are discussed for R-(+)-methyloxirane and (1 S,2 S)-cyclopropane-1,2-dicarbonitrile. In particular, by using a group theoretical argument, a gauge-independent lower bound for the quadrupole contribution of C2-symmetric molecules can be identified, which allows the importance of additional quadrupole terms in anisotropic VCD spectra calculation to be assessed.
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Affiliation(s)
- Dominik Sidler
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Patrick Bleiziffer
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
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