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Manna D, Lo R, Vacek J, Miriyala VM, Bouř P, Wu T, Osifová Z, Nachtigallová D, Dračinský M, Hobza P. The Stability of Hydrogen-Bonded Ion-Pair Complex Unexpectedly Increases with Increasing Solvent Polarity. Angew Chem Int Ed Engl 2024; 63:e202403218. [PMID: 38497312 DOI: 10.1002/anie.202403218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
The generally observed decrease of the electrostatic energy in the complex with increasing solvent polarity has led to the assumption that the stability of the complexes with ion-pair hydrogen bonds decreases with increasing solvent polarity. Besides, the smaller solvent-accessible surface area (SASA) of the complex in comparison with the isolated subsystems results in a smaller solvation energy of the latter, leading to a destabilization of the complex in the solvent compared to the gas phase. In our study, which combines Nuclear Magnetic Resonance, Infrared Spectroscopy experiments, quantum chemical calculations, and molecular dynamics (MD) simulations, we question the general validity of this statement. We demonstrate that the binding free energy of the ion-pair hydrogen-bonded complex between 2-fluoropropionic acid and n-butylamine (CH3CHFCOO-…NH3But+) increases with increased solvent polarity. This phenomenon is rationalized by a substantial charge transfer between the subsystems that constitute the ion-pair hydrogen-bonded complex. This unexpected finding introduces a new perspective to our understanding of solvation dynamics, emphasizing the interplay between solvent polarity and molecular stability within hydrogen-bonded systems.
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Affiliation(s)
- Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
- Faculty of Science, Palacký University Olomouc, 17. Listopadu 1192/12, 779 00, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Tao Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
| | - Martin Dračinský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
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2
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Ramundo A, Hurtová M, Božek I, Osifová Z, Russo M, Ngoy BP, Křen V, Klán P. Multimodal Carbon Monoxide Photorelease from Flavonoids. Org Lett 2024; 26:708-712. [PMID: 38227978 PMCID: PMC10825817 DOI: 10.1021/acs.orglett.3c04141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/18/2024]
Abstract
Photooxygenation of flavonoids leads to the release of carbon monoxide (CO). Our structure-photoreactivity study, employing several structurally different flavonoids, including their 13C-labeled analogs, revealed that CO can be produced via two completely orthogonal pathways, depending on their hydroxy group substitution pattern and the reaction conditions. While photooxygenation of the enol 3-OH group has previously been established as the CO liberation channel, we show that the catechol-type hydroxy groups of ring B can predominantly participate in photodecarbonylation.
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Affiliation(s)
- Andrea Ramundo
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Martina Hurtová
- Laboratory
of Biotransformation, Institute of Microbiology
of the Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Igor Božek
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Zuzana Osifová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 166 00 Prague, Czech Republic
| | - Marina Russo
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Bokolombe Pitchou Ngoy
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Vladimír Křen
- Laboratory
of Biotransformation, Institute of Microbiology
of the Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Petr Klán
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
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3
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Osifová Z, Kalvoda T, Galgonek J, Culka M, Vondrášek J, Bouř P, Bednárová L, Andrushchenko V, Dračínský M, Rulíšek L. What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments. Chem Sci 2024; 15:594-608. [PMID: 38179543 PMCID: PMC10763034 DOI: 10.1039/d3sc04960d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.
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Affiliation(s)
- Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University Hlavova 2030 Prague 128 00 Czech Republic
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
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Osifová Z, Šála M, Dračínský M. Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives. ACS Omega 2023; 8:25538-25548. [PMID: 37483191 PMCID: PMC10357537 DOI: 10.1021/acsomega.3c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
Hydrogen bonding between nucleobases is a crucial noncovalent interaction for life on Earth. Canonical nucleobases form base pairs according to two main geometries: Watson-Crick pairing, which enables the static functions of nucleic acids, such as the storing of genetic information; and Hoogsteen pairing, which facilitates the dynamic functions of these biomacromolecules. This precisely tuned system can be affected by oxidation or substitution of nucleobases, leading to changes in their hydrogen-bonding patterns. This paper presents an investigation into the intermolecular interactions of various 8-substituted purine derivatives with their hydrogen-bonding partners. The systems were analyzed using nuclear magnetic resonance spectroscopy and density functional theory calculations. Our results demonstrate that the stability of hydrogen-bonded complexes, or base pairs, depends primarily on the number of intermolecular H-bonds and their donor-acceptor alternation. No strong preferences for a particular geometry, either Watson-Crick or Hoogsteen, were found.
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Affiliation(s)
- Zuzana Osifová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
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5
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Osifová Z, Socha O, Mužíková Čechová L, Šála M, Janeba Z, Dračínský M. Hydrogen‐Bonding Interactions of Methylated Adenine Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University Hlavova 2030 Prague 128 00 Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Lucie Mužíková Čechová
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
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