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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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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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Zakrzewski J, Liberka M, Wang J, Chorazy S, Ohkoshi SI. Optical Phenomena in Molecule-Based Magnetic Materials. Chem Rev 2024; 124:5930-6050. [PMID: 38687182 PMCID: PMC11082909 DOI: 10.1021/acs.chemrev.3c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Since the last century, we have witnessed the development of molecular magnetism which deals with magnetic materials based on molecular species, i.e., organic radicals and metal complexes. Among them, the broadest attention was devoted to molecule-based ferro-/ferrimagnets, spin transition materials, including those exploring electron transfer, molecular nanomagnets, such as single-molecule magnets (SMMs), molecular qubits, and stimuli-responsive magnetic materials. Their physical properties open the application horizons in sensors, data storage, spintronics, and quantum computation. It was found that various optical phenomena, such as thermochromism, photoswitching of magnetic and optical characteristics, luminescence, nonlinear optical and chiroptical effects, as well as optical responsivity to external stimuli, can be implemented into molecule-based magnetic materials. Moreover, the fruitful interactions of these optical effects with magnetism in molecule-based materials can provide new physical cross-effects and multifunctionality, enriching the applications in optical, electronic, and magnetic devices. This Review aims to show the scope of optical phenomena generated in molecule-based magnetic materials, including the recent advances in such areas as high-temperature photomagnetism, optical thermometry utilizing SMMs, optical addressability of molecular qubits, magneto-chiral dichroism, and opto-magneto-electric multifunctionality. These findings are discussed in the context of the types of optical phenomena accessible for various classes of molecule-based magnetic materials.
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Affiliation(s)
- Jakub
J. Zakrzewski
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Lojasiewicza
11, 30-348 Krakow, Poland
| | - Michal Liberka
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Lojasiewicza
11, 30-348 Krakow, Poland
| | - Junhao Wang
- Department
of Materials Science, Faculty of Pure and Applied Science, University of Tsukuba, 1-1-1 Tonnodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Szymon Chorazy
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Shin-ichi Ohkoshi
- Department
of Chemistry, School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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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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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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