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Sobornova VV, Belov KV, Krestyaninov MA, Khodov IA. Influence of Solvent Polarity on the Conformer Ratio of Bicalutamide in Saturated Solutions: Insights from NOESY NMR Analysis and Quantum-Chemical Calculations. Int J Mol Sci 2024; 25:8254. [PMID: 39125824 PMCID: PMC11311660 DOI: 10.3390/ijms25158254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.
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Affiliation(s)
| | | | | | - Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
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2
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Khodov I, Sobornova V, Mulloyarova V, Belov K, Dyshin A, de Carvalho LB, Tolstoy P, Kiselev M. Exploring the Conformational Equilibrium of Mefenamic Acid Released from Silica Aerogels via NMR Analysis. Int J Mol Sci 2023; 24:ijms24086882. [PMID: 37108046 PMCID: PMC10138679 DOI: 10.3390/ijms24086882] [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: 03/09/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
This study examines the influence of mefenamic acid on the physical and chemical properties of silica aerogels, as well as its effect on the sorption characteristics of the composite material. Solid state magic angle spinning nuclear magnetic resonance (MAS NMR) and high-pressure 13C NMR kinetic studies were conducted to identify the presence of mefenamic acid and measure the kinetic rates of CO2 sorption. Additionally, a high-pressure T1-T2 relaxation-relaxation correlation spectroscopy (RRCOSY) study was conducted to estimate the relative amount of mefenamic acid in the aerogel's pores, and a high-pressure nuclear Overhauser effect spectoscopy (NOESY) study was conducted to investigate the conformational preference of mefenamic acid released from the aerogel. The results indicate that mefenamic acid is affected by the chemical environment of the aerogel, altering the ratio of mefenamic acid conformers from 75% to 25% in its absence to 22% to 78% in the presence of aerogel.
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Affiliation(s)
- Ilya Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
| | - Valentina Sobornova
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
| | - Valeriya Mulloyarova
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg 198504, Russia
| | - Konstantin Belov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
| | - Alexey Dyshin
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
| | - Luís Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Peter Tolstoy
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg 198504, Russia
| | - Michael Kiselev
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
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Structures Controlled by Entropy: The Flexibility of Strychnine as Example. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227987. [PMID: 36432085 PMCID: PMC9692940 DOI: 10.3390/molecules27227987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term TΔS of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and 3JHH couplings as well.
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Khodov IA, Belov KV, Krestyaninov MA, Kiselev MG. Conformational Equilibria of a Thiadiazole Derivative in Solvents of Different Polarities: an NMR Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422040148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Belov KV, Dyshin AA, Kiselev MG, Krestyaninov MA, Sobornova VV, Khodov IA. Determination of the Spatial Structure of Lidocaine in SC-CO2 by the 2D NOESY Method. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793121080145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Spatial structure and conformations of hydrazones derived from pyridoxal 5′-phosphate and 2-, 3-pyridinecarbohydrazide in the light of NMR study and quantum chemical calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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7
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Mamardashvili G, Kaigorodova E, Dmitrieva O, Koifman O, Mamardashvili N. Molecular Recognition of Imidazole Derivatives by Co(III)-Porphyrinsin Phosphate Buffer (pH = 7.4) and Cetylpyridinium Chloride Containing Solutions. Molecules 2021; 26:molecules26040868. [PMID: 33562133 PMCID: PMC7915429 DOI: 10.3390/molecules26040868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 02/05/2023] Open
Abstract
Bymeans of spectrophotometric titration and NMR spectroscopy, the selective binding ability ofthe Co(III)-5,15-bis-(3-hydroxyphenyl)-10,20-bis-(4-sulfophenyl)porphyrin (Со(III)Р1) andCo(III)-5,15-bis-(2-hydroxyphenyl)-10,20-bis-(4-sulfophenyl)porphyrin (Со(III)Р2) towards imidazole derivatives of various nature (imidazole (L1), metronidazole (L2), and histamine (L3)) in phosphate buffer (pH 7.4) has been studied. It was found that in the case of L2, L3 the binding of the "first" ligand molecule by porphyrinatesCo(III)P1 and Co(III)P2 occurs with the formation of complexes with two binding sites (donor-acceptor bond at the center and hydrogen bond at the periphery of the macrocycle), while the "second" ligand molecule is added to the metalloporphyrin only due to the formation of the donor-acceptor bond at the macrocycle coordination center. The formation of stable complexes with two binding sites has been confirmed by density functional theory method (DFT) quantum chemical calculations and two-dimensional NMR experiments. It was shown that among the studied porphyrinates, Co(III)P2 is more selective towards to L1-L3 ligands, and localization of cobalt porphyrinates in cetylpyridinium chloride (CPC) micelles does not prevent the studied imidazole derivatives reversible binding. The obtained materials can be used to develop effective receptors for recognition, delivery, and prolonged release of drug compounds to the sites of their functioning. Considering that cetylpyridinium chloride is a widely used cationic biocide as a disinfectant, the designed materials may also prove to be effective antimicrobial agents.
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Exposing Hidden Conformations of Carbamazepine Appearing Due to Interaction With the Solid Phase by 2D 1H- 15N HMBC NMR Spectroscopy. J Pharm Sci 2021; 110:1533-1539. [PMID: 33421434 DOI: 10.1016/j.xphs.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 11/20/2022]
Abstract
Two-dimensional 1H-15N HMBC NMR spectra of the well-known anticonvulsant carbamazepine dissolved in different organic solvents, recorded on an NMR spectrometer prove the existence of hidden conformers in saturated solutions. Obtained conformer distribution arises due to the presence of the solid phase in saturated solution. A weak influence of ring currents was revealed for different molecular conformations of carbamazepine dissolved in a saturated solution, which provides a simple approach to discovering hidden conformations. Hidden conformers were found in three different solvents: dimethyl sulfoxide, chloroform, and dichloromethane.
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Khodov I, Dyshin A, Efimov S, Ivlev D, Kiselev M. High-pressure NMR spectroscopy in studies of the conformational composition of small molecules in supercritical carbon dioxide. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113113] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Pestryaev EM. Molecular Dynamics Simulation of the Cage Effect
in a Wide Packing Fraction Range. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418070221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Theoretical and experimental study of imine-enamine tautomerism of condensation products of propanal with 4-aminobenzoic acid in ethanol. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1701-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rakhmatullin IZ, Galiullina LF, Balandina AA, Garipov MR, Strelnik AD, Galiullina AS, Shtyrlin YG, Klochkov VV. Stereodynamics of some pyridoxine derivatives. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:304-311. [PMID: 27663994 DOI: 10.1002/mrc.4528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
The conformational properties of three pyridoxine derivatives were studied by 1 H dynamic NMR spectroscopy. Conformational exchange caused by a rotation of 2-nytrophenyl group around one single C-C bond, of 2,4-dinitrophenyl substituent around two single C-O bonds, and twist-twist transformations of the seven-membered ketal cycle was observed by NMR experiments at low temperatures. Meanwhile, the conformational exchange of the acetal ring remains fast in the NMR timescale even at 198 K. The energy barriers for all observed conformational exchange processes were determined by the lineshape analysis of dynamic NMR spectra. The activation barriers of the 2-nitrophenyl group rotation were almost the same for all studied compounds, about 40-41 kJ/mol. The energy barriers of the conformational exchange processes of the 2,4-nitrophenyl group and the ketal cycle increased significantly up to 10 kJ/mol in comparison with previously studied compounds with similar structure. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- I Z Rakhmatullin
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - L F Galiullina
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - A A Balandina
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - M R Garipov
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - A D Strelnik
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - A S Galiullina
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - Y G Shtyrlin
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - V V Klochkov
- Kazan (Volga Region) Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
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Khodov IA, Maltceva OV, Klochkov VV, Koifman OI, Mamardashvili NZ. N-Confused porphyrins: complexation and 1H NMR studies. NEW J CHEM 2017. [DOI: 10.1039/c7nj01814b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complexation of 2-aza-21-carba-tetraphenylporphyrin and 2-aza-2-methyl-5,10,15,20-tetraphenyl-21-carbaporphyrin with nickel and zinc acetates in organic solvents has been investigated by UV-Vis spectroscopy and 1H NMR.
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Affiliation(s)
- Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
- Kazan Federal University
- Kazan
| | - Olga V. Maltceva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
| | | | - Oscar I. Koifman
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
- Research Institute of Macroheterocycles
- Ivanovo State University of Chemistry and Technology
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14
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Rakhmatullin I, Galiullina L, Garipov M, Strel’nik A, Shtyrlin Y, Klochkov V. 1H NMR Characterization of Two New Pyridoxine Derivatives. BIONANOSCIENCE 2016. [DOI: 10.1007/s12668-016-0214-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Thiele CM, Kolmer A. Response to "Comment on "Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone" by I.A. Khodov, M.G. Kiselev, V.V. Klochkov, S.V. Efimov [http://dx.doi.org/ 10.1016/j.jmr.2016.02.009]" - Or Life is about compromises. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:69-72. [PMID: 26947752 DOI: 10.1016/j.jmr.2016.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
| | - Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
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