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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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2
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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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3
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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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4
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Taherivardanjani S, Wylie L, Dötzer R, Kirchner B. Exploring the Influence of the Phosphorus-Heteroatom Substitution in Nicotine on Its Electronic and Vibrational Spectroscopic Properties. Chemistry 2024; 30:e202302534. [PMID: 37984418 DOI: 10.1002/chem.202302534] [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: 08/03/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
The influence of phosphorus substitution of nitrogen in heterocyclic compounds on the vibrational spectroscopy as well as frontier molecular orbitals are analyzed. Nicotine with two nitrogen atoms in its structure is taken as the sample system to be studied computationally. By replacing the nitrogen atom in one or both rings of this molecule with phosphorus, three nicotine derivatives are created. The vibrational circular dichroism and infrared spectra of these four molecules in their monomer state, as well as the assemblies up to trimers are determined. The aforementioned spectra are calculated using static quantum chemical calculations employing a cluster-weighted approach. The calculated gas phase spectra of nicotine are compared to their respective experimental spectra. It is observed that the nicotine derivatives with phosphorus in the methylpyrrolidine ring have considerably different gas phase and bulk phase vibrational circular dichroism spectra when compared to nicotine. The phosphorus substitution reduces the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital as well as altering the polarizability and reactivity of the investigated molecules.
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Affiliation(s)
- Shima Taherivardanjani
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, Beringstr. 4, D-53115, Bonn, Germany
| | - Luke Wylie
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, Beringstr. 4, D-53115, Bonn, Germany
| | | | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, Beringstr. 4, D-53115, Bonn, Germany
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5
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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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6
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Grassin C, Pollok CH, Kreienborg NM, Merten C. Matrix effects in MI-VCD spectra of two chiral oxiranes and their potential microscopic origin. Phys Chem Chem Phys 2023; 25:31995-32001. [PMID: 37975701 DOI: 10.1039/d3cp05023h] [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
Combining vibrational circular dichroism (VCD) spectroscopy with the matrix isolation (MI) technique opens up interesting possibilities to study chiral molecules. MI involves the isolation of guest species in inert solid matrices at cryogenic temperatures. Hence, MI-VCD measures are solid-state VCD measurements, and as such, can suffer from mostly birefringance-related artefacts in the same way as common solid-state VCD measurements. In this contribution, we demonstrate that the sample preparation condition have tremendous impact on the quality and reliability of the recorded MI-VCD spectra. While MI-IR spectra are basically blind to these artefacts, the variation of deposition temperatures and host flow rates seem to control whether high quality MI-VCD spectra are obtained or if depolarization effects lead to completely obscured spectra. For two selected examples, styrene oxide (SO) and 1-phenyl propylene oxide (PPO), we discuss how the various experimental conditions may lead to the aforementioned effects and give a microscopic description of their origin.
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Affiliation(s)
- Corentin Grassin
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Corina H Pollok
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Nora M Kreienborg
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Christian Merten
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
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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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8
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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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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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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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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.
| | - Ariel Pérez-Mellor
- 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.
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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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12
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Domzalski A, Margent L, Vigo V, Dewan F, Pilarsetty NVK, Xu Y, Kawamura A. Unambiguous Stereochemical Assignment of Cyclo(Phe-Pro), Cyclo(Leu-Pro), and Cyclo(Val-Pro) by Electronic Circular Dichroic Spectroscopy. Molecules 2021; 26:molecules26195981. [PMID: 34641525 PMCID: PMC8512403 DOI: 10.3390/molecules26195981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/21/2022] Open
Abstract
2,5-diketopiperazines (DKPs) are cyclic dipeptides ubiquitously found in nature. In particular, cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) are frequently detected in many microbial cultures. Each of these DKPs has four possible stereoisomers due to the presence of two chirality centers. However, absolute configurations of natural DKPs are often ambiguous due to the lack of a simple, sensitive, and reproducible method for stereochemical assignment. This is an important problem because stereochemistry is a key determinant of biological activity. Here, we report a synthetic DKP library containing all stereoisomers of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro). The library was subjected to spectroscopic characterization using mass spectrometry, NMR, and electronic circular dichroism (ECD). It turned out that ECD can clearly differentiate DKP stereoisomers. Thus, our ECD dataset can serve as a reference for unambiguous stereochemical assignment of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) samples from natural sources. The DKP library was also subjected to a biological screening using assays for E. coli growth and biofilm formation, which revealed distinct biological effects of cyclo(D-Phe-L-Pro).
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Affiliation(s)
- Alison Domzalski
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, New York, NY 10016, USA; (A.D.); (F.D.); (Y.X.)
- Department of Chemistry, Hunter College of CUNY, New York, NY 10065, USA; (L.M.); (V.V.)
| | - Liliana Margent
- Department of Chemistry, Hunter College of CUNY, New York, NY 10065, USA; (L.M.); (V.V.)
| | - Valeria Vigo
- Department of Chemistry, Hunter College of CUNY, New York, NY 10065, USA; (L.M.); (V.V.)
| | - Faizunnahar Dewan
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, New York, NY 10016, USA; (A.D.); (F.D.); (Y.X.)
- Department of Chemistry, Hunter College of CUNY, New York, NY 10065, USA; (L.M.); (V.V.)
| | | | - Yujia Xu
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, New York, NY 10016, USA; (A.D.); (F.D.); (Y.X.)
- Department of Chemistry, Hunter College of CUNY, New York, NY 10065, USA; (L.M.); (V.V.)
- Chemistry Ph.D. Program, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Akira Kawamura
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, New York, NY 10016, USA; (A.D.); (F.D.); (Y.X.)
- Department of Chemistry, Hunter College of CUNY, New York, NY 10065, USA; (L.M.); (V.V.)
- Chemistry Ph.D. Program, The Graduate Center of CUNY, New York, NY 10016, USA
- Correspondence: ; Tel.: +1-212-772-5339
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13
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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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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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15
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Li X, Porcino M, Martineau-Corcos C, Guo T, Xiong T, Zhu W, Patriarche G, Péchoux C, Perronne B, Hassan A, Kümmerle R, Michelet A, Zehnacker-Rentien A, Zhang J, Gref R. Efficient incorporation and protection of lansoprazole in cyclodextrin metal-organic frameworks. Int J Pharm 2020; 585:119442. [PMID: 32445910 DOI: 10.1016/j.ijpharm.2020.119442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 01/01/2023]
Abstract
Lansoprazole (LPZ) is an acid pump inhibitor, which readily degrades upon acidic or basic conditions and under heating. We investigated here LPZ stability upon incorporation in particles made of cyclodextrin metal-organic frameworks (CD-MOFs). LPZ loaded CD-MOFs were successfully synthesized, reaching high LPZ payloads of 23.2 ± 2.1 wt%, which correspond to a molar ratio of 1:1 between LPZ and γ-CD. The homogeneity of LPZ loaded CD-MOFs in terms of component distribution was confirmed by elemental mapping by STEM-EDX. Both CTAB, the surfactant used in the CD-MOFs synthesis, and LPZ compete for their inclusion in the CD cavities. CTAB allowed obtaining regular cubic particles of around 5 µm with 15 wt% residual CTAB amounts. When LPZ was incorporated, the residual CTAB amount was less than 0.1 wt%, suggesting a higher affinity of LPZ for the CDs than CTAB. These findings were confirmed by molecular simulations. Vibrational circular dichroism studies confirmed the LPZ incorporation inside the CDs. Solid-state NMR showed that LPZ was located in the CDs and that it remained intact even after three years storage. Remarkably, the CD-MOFs matrix protected the drug upon thermal decomposition. This study highlights the interest of CD-MOFs for the incorporation and protection of LPZ.
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Affiliation(s)
- Xue Li
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Marianna Porcino
- Université d'Orléans, CEMHTI UPR CNRS 3079, F-45071 Orléans, France
| | - Charlotte Martineau-Corcos
- Université d'Orléans, CEMHTI UPR CNRS 3079, F-45071 Orléans, France; Université Paris Saclay, ILV UMR CNRS 8180, Université de Versailles St-Quentin en Yvelines, 78035 Versailles, France; Institut Universitaire de France (IUF), 75005 Paris, France
| | - Tao Guo
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201210 Shanghai, China
| | - Ting Xiong
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, 330004 Nanchang, China
| | - Weifeng Zhu
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, 330004 Nanchang, China
| | - Gilles Patriarche
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120 Palaiseau, France
| | - Christine Péchoux
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | | | - Alia Hassan
- Bruker Biospin Corporation, 8117 Fällanden, Switzerland
| | | | | | - Anne Zehnacker-Rentien
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Jiwen Zhang
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201210 Shanghai, China; Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, 330004 Nanchang, China
| | - Ruxandra Gref
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
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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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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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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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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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