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Guzman-Lopez EG, Reina M, Perez-Gonzalez A, Francisco-Marquez M, Hernandez-Ayala LF, Castañeda-Arriaga R, Galano A. CADMA-Chem: A Computational Protocol Based on Chemical Properties Aimed to Design Multifunctional Antioxidants. Int J Mol Sci 2022; 23:13246. [PMID: 36362034 PMCID: PMC9658414 DOI: 10.3390/ijms232113246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 10/12/2023] Open
Abstract
A computational protocol aimed to design new antioxidants with versatile behavior is presented. It is called Computer-Assisted Design of Multifunctional Antioxidants and is based on chemical properties (CADMA-Chem). The desired multi-functionality consists of in different methods of antioxidant protection combined with neuroprotection, although the protocol can also be used to pursue other health benefits. The dM38 melatonin derivative is used as a study case to illustrate the protocol in detail. This was found to be a highly promising candidate for the treatment of neurodegeneration, in particular Parkinson's and Alzheimer's diseases. This also has the desired properties of an oral-drug, which is significantly better than Trolox for scavenging free radicals, and has chelates redox metals, prevents the ●OH production, via Fenton-like reactions, repairs oxidative damage in biomolecules (lipids, proteins, and DNA), and acts as a polygenic neuroprotector by inhibiting catechol-O-methyl transferase (COMT), acetylcholinesterase (AChE) and monoamine oxidase B (MAOB). To the best of our best knowledge, CADMA-Chem is currently the only protocol that simultaneously involves the analyses of drug-like behavior, toxicity, manufacturability, versatile antioxidant protection, and receptor-ligand binding affinities. It is expected to provide a starting point that helps to accelerate the discovery of oral drugs with the potential to prevent, or slow down, multifactorial human health disorders.
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Affiliation(s)
- Eduardo Gabriel Guzman-Lopez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | - Miguel Reina
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Adriana Perez-Gonzalez
- CONACYT-Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | | | - Luis Felipe Hernandez-Ayala
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | - Romina Castañeda-Arriaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
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2
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Schneiker A, Góbi S, Joshi PR, Bazsó G, Lee YP, Tarczay G. Non-energetic, Low-Temperature Formation of C α-Glycyl Radical, a Potential Interstellar Precursor of Natural Amino Acids. J Phys Chem Lett 2021; 12:6744-6751. [PMID: 34264091 DOI: 10.1021/acs.jpclett.1c01306] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The reaction of H atoms with glycine was investigated at 3.1 K in para-H2, a quantum-solid host. The reaction was followed by IR spectroscopy, with the spectral analysis aided by quantum chemical computations. Comparison of the experimental IR spectrum with computed anharmonic frequencies and intensities proved that, regardless of the reactant glycine conformation, Cα-glycyl radical is formed in an H-atom-abstraction process with great selectivity. The product of the second H-atom abstraction, iminoacetic acid, was also observed in a smaller amount. The Cα-glycyl radical is sensitive to UV light and decomposes to iminoacetic acid and H atom upon 280 nm radiation. Since the reactive radical center is located on the Cα-atom, it is suggested that natural α-amino acids can be formed from glycine via the Cα-glycyl radical by non-energetic mechanisms in the solid phase of the interstellar medium.
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Affiliation(s)
- Anita Schneiker
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
| | - Sándor Góbi
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
| | - Prasad Ramesh Joshi
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Gábor Bazsó
- Wigner Research Centre for Physics, P. O. Box 49, H-1525 Budapest, Hungary
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 300093, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
| | - György Tarczay
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
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3
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Castañeda-Arriaga R, Pérez-González A, Reina M, Galano A. Computer-designed melatonin derivatives: potent peroxyl radical scavengers with no pro-oxidant behavior. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02641-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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4
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Orján EM, Nacsa AB, Czakó G. Conformers of dehydrogenated glycine isomers. J Comput Chem 2020; 41:2001-2014. [DOI: 10.1002/jcc.26375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Erik M. Orján
- MTA‐SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials ScienceInstitute of Chemistry, University of Szeged Szeged Hungary
| | - András B. Nacsa
- MTA‐SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials ScienceInstitute of Chemistry, University of Szeged Szeged Hungary
| | - Gábor Czakó
- MTA‐SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials ScienceInstitute of Chemistry, University of Szeged Szeged Hungary
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5
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Hamid AKM, Salvatore JC, Wang K, Murahari P, Guljas A, Rágyanszki A, Owen M, Jójárt B, Szőri M, Csizmadia IG, Viskolcz B, Fiser B. Oxidatively-mediated in silico epimerization of a highly amyloidogenic segment in the human calcitonin hormone (hCT15-19). Comput Biol Chem 2019; 80:259-269. [DOI: 10.1016/j.compbiolchem.2019.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
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6
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Chan B, Radom L. An ONIOM investigation of the effect of conformation on bond dissociation energies in peptides. J Comput Chem 2018; 40:82-88. [DOI: 10.1002/jcc.25538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Bun Chan
- Graduate School of Engineering Nagasaki University Bunkyo 1‐14, Nagasaki‐shi, Nagasaki, 852‐8521 Japan
| | - Leo Radom
- School of Chemistry University of Sydney New South Wales, 2006 Australia
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7
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Zhou C, Song Z, Yang H, Wu H, Wang B, Yu J, Sun L. Insight into elemental mercury (Hg 0) removal from flue gas using UV/H 2O 2 advanced oxidation processes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:21097-21105. [PMID: 29770935 DOI: 10.1007/s11356-018-2271-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
Elemental mercury (Hg0) emitted from coal-fired power plants and municipal solid waste (MSW) incinerators has caused great harm to the environment and human beings. The strong oxidized •OH radicals produced by UV/H2O2 advanced oxidation processes were studied to investigate the performance of Hg0 removal from simulated flue gases. The results showed that when H2O2 concentration was 1.0 mol/L and the solution pH value was 4.1, the UV/H2O2 system had the highest Hg0 removal efficiency. The optimal reaction temperature was approximately 50 °C and Hg0 removal was inhibited when the temperature was higher or lower. The yield of •OH radicals during UV/H2O2 reaction was studied by electron paramagnetic resonance (EPR) analysis. UV radiation was the determining factor to remove Hg0 in UV/H2O2 system due to •OH generation during H2O2 decomposition. SO2 had little influence on Hg0 removal whereas NO had an inhibitory effect on Hg0 removal. The detailed findings for Hg0 removal reactions over UV/H2O2 make it an attractive method for mercury control from flue gases.
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Affiliation(s)
- Changsong Zhou
- Engineering Laboratory of Energy System Process Conversion and Emission Reduction Technology of Jiangsu Province, School of Energy and Mechanical Engineering, Nanjing Normal University, Nanjing, 210042, China.
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China.
- School of Energy and Mechanical Engineering, Nanjing Normal University, Nanjing, 210042, Jiangsu, China.
| | - Zijian Song
- State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongmin Yang
- Engineering Laboratory of Energy System Process Conversion and Emission Reduction Technology of Jiangsu Province, School of Energy and Mechanical Engineering, Nanjing Normal University, Nanjing, 210042, China
| | - Hao Wu
- Engineering Laboratory of Energy System Process Conversion and Emission Reduction Technology of Jiangsu Province, School of Energy and Mechanical Engineering, Nanjing Normal University, Nanjing, 210042, China
| | - Ben Wang
- State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jie Yu
- State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lushi Sun
- State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan, 430074, China.
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8
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Castañeda-Arriaga R, Pérez-González A, Reina M, Alvarez-Idaboy JR, Galano A. Comprehensive Investigation of the Antioxidant and Pro-oxidant Effects of Phenolic Compounds: A Double-Edged Sword in the Context of Oxidative Stress? J Phys Chem B 2018; 122:6198-6214. [PMID: 29771524 DOI: 10.1021/acs.jpcb.8b03500] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Oxidative stress (OS) is a health-threatening process that is involved, at least partially, in the development of several diseases. Although antioxidants can be used as a chemical defense against OS, they might also exhibit pro-oxidant effects, depending on environmental conditions. In this work, such a dual behavior was investigated for phenolic compounds (PhCs) within the framework of the density functional theory and based on kinetic data. Multiple reaction mechanisms were considered in both cases. The presence of redox metals, the pH, and the possibility that PhCs might be transformed into benzoquinones were identified as key aspects in the antioxidant versus pro-oxidant effects of these compounds. The main virtues of PhCs as antioxidants are their radical trapping activity, their regeneration under physiological conditions, and their behavior as OH-inactivating ligands. The main risks of PhCs as pro-oxidants are predicted to be the role of phenolate ions in the reduction of metal ions, which can promote Fenton-like reactions, and the formation of benzoquinones that might cause protein arylation at cysteine sites. Although the benefits seem to overcome the hazards, to properly design chemical strategies against OS using PhCs, it is highly recommended to carefully explore their duality in this context.
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Affiliation(s)
- Romina Castañeda-Arriaga
- Departamento de Química , Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186 , Col. Vicentina, Iztapalapa , C.P. 09340 México City , México
| | - Adriana Pérez-González
- CONACYT-Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina, Iztapalapa , C.P. 09340 México City , México
| | - Miguel Reina
- Departamento de Química , Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186 , Col. Vicentina, Iztapalapa , C.P. 09340 México City , México
| | - J Raúl Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica , Universidad Nacional Autónoma de México , C.P. 04510 México City , México
| | - Annia Galano
- Departamento de Química , Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186 , Col. Vicentina, Iztapalapa , C.P. 09340 México City , México
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9
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Uranga J, Mujika JI, Grande-Aztatzi R, Matxain JM. Oxidation of Acid, Base, and Amide Side-Chain Amino Acid Derivatives via Hydroxyl Radical. J Phys Chem B 2018; 122:4956-4971. [PMID: 29676577 DOI: 10.1021/acs.jpcb.7b12450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydroxyl radical (•OH) is known to be highly reactive. Herein, we analyze the oxidation of acid (Asp and Glu), base (Arg and Lys), and amide (Asn and Gln) containing amino acid derivatives by the consecutive attack of two •OH. In this work, we study the reaction pathway by means of density functional theory. The oxidation mechanism is divided into two steps: (1) the first •OH can abstract a H atom or an electron, leading to a radical amino acid derivative, which is the intermediate of the reaction and (2) the second •OH can abstract another H atom or add itself to the formed radical, rendering the final oxidized products. The studied second attack of •OH is applicable to situations where high concentration of •OH is found, e.g., in vitro. Carbonyls are the best known oxidation products for these reactions. This work includes solvent dielectric and confirmation's effects of the reaction, showing that both are negligible. Overall, the most favored intermediates of the oxidation process at the side chain correspond to the secondary radicals stabilized by hyperconjugation. Intermediates show to be more stable in those cases where the spin density of the unpaired electron is lowered. Alcohols formed at the side chains are the most favored products, followed by the double-bond-containing ones. Interestingly, Arg and Lys side-chain scission leads to the most favored carbonyl-containing oxidation products, in line with experimental results.
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Affiliation(s)
- Jon Uranga
- Kimika Fakultatea-Chemistry Department , Euskal Herriko Unibertsitatea (UPV/EHU) , P.K. 1072 , 20080 Donostia , Euskadi , Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal 4 , 20018 Donostia , Euskadi , Spain
| | - Jon I Mujika
- Donostia International Physics Center (DIPC) , Manuel Lardizabal 4 , 20018 Donostia , Euskadi , Spain
| | - Rafael Grande-Aztatzi
- Donostia International Physics Center (DIPC) , Manuel Lardizabal 4 , 20018 Donostia , Euskadi , Spain
| | - Jon M Matxain
- Kimika Fakultatea-Chemistry Department , Euskal Herriko Unibertsitatea (UPV/EHU) , P.K. 1072 , 20080 Donostia , Euskadi , Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal 4 , 20018 Donostia , Euskadi , Spain
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10
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Yu CP, Gerlei KZ, Rágyanszki A, Jensen SJK, Viskolcz B, Csizmadia IG. Reactivity of Ala-Gly dipeptide with β-turn secondary structure. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.12.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Chan B, Radom L. Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides. Aust J Chem 2018. [DOI: 10.1071/ch17621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.
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Castañeda-Arriaga R, Galano A. Exploring Chemical Routes Relevant to the Toxicity of Paracetamol and Its meta-Analogue at a Molecular Level. Chem Res Toxicol 2017; 30:1286-1301. [DOI: 10.1021/acs.chemrestox.7b00024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Romina Castañeda-Arriaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina.
Iztapalapa, C. P. 09340, México D. F., México
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina.
Iztapalapa, C. P. 09340, México D. F., México
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13
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Protein Stability and Unfolding Following Glycine Radical Formation. Molecules 2017; 22:molecules22040655. [PMID: 28422069 PMCID: PMC6154654 DOI: 10.3390/molecules22040655] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 02/02/2023] Open
Abstract
Glycine (Gly) residues are particularly susceptible to hydrogen abstraction; which results in the formation of the capto-dative stabilized Cα-centered Gly radical (GLR) on the protein backbone. We examined the effect of GLR formation on the structure of the Trp cage; tryptophan zipper; and the villin headpiece; three fast-folding and stable miniproteins; using all-atom (OPLS-AA) molecular dynamics simulations. Radicalization changes the conformation of the GLR residue and affects both neighboring residues but did not affect the stability of the Trp zipper. The stability of helices away from the radical center in villin were also affected by radicalization; and GLR in place of Gly15 caused the Trp cage to unfold within 1 µs. These results provide new evidence on the destabilizing effects of protein oxidation by reactive oxygen species.
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Castañeda-Arriaga R, Domínguez-Castro A, Lee J, Alvarez-Idaboy JR, Mora-Diez N. Chemical repair of protein carbon-centred radicals: long-distance dynamic factors. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0230] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The thermodynamic and kinetic study of the repair reactions of three damaged aliphatic amino acids (alanine, valine, and leucine) with dihydrolipoic acid (DHLA) in a polar and a nonpolar solvent is presented in this work. Two simplified protein models were explored in the most common conformations (alpha helix and beta sheet). Calculations are performed at the M06-2X-SMD/6-31++G(d,p) level of theory. DHLA has shown to be an excellent antioxidant repair agent through hydrogen-transfer reaction involving the thiol groups, with rate constants close to diffusion control in most cases. The stability of the initial protein radical is not the most important factor determining the rate of the repair reaction because stabilizing intermolecular interactions involving the protein and the antioxidant can provide additional stability to some transition states accelerating the repair of sites that would otherwise not be so quickly repaired.
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Affiliation(s)
- Romina Castañeda-Arriaga
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, México DF 04510, México
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
| | | | - JinGyu Lee
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
| | - J. Raul Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, México DF 04510, México
| | - Nelaine Mora-Diez
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
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15
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Tryptophan versus nitric oxide, nitrogen dioxide and carbonate radicals: differences in reactivity and implications for oxidative damage to proteins. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1913-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Uranga J, Lakuntza O, Ramos-Cordoba E, Matxain JM, Mujika JI. A computational study of radical initiated protein backbone homolytic dissociation on all natural amino acids. Phys Chem Chem Phys 2016; 18:30972-30981. [DOI: 10.1039/c6cp06529e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydroxyl radical (˙OH) is known to be one of the most reactive species. The attack of this radical onto the backbone of all natural amino acids is investigated.
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Affiliation(s)
- Jon Uranga
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Oier Lakuntza
- Institut Catala d'Investigacio Quimica (ICIQ)
- 43007 Tarragona
- Spain
| | - Eloy Ramos-Cordoba
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
- Department of Chemistry
| | - Jon M. Matxain
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Jon I. Mujika
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
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17
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Lam AT, Faragó EP, Owen MC, Fiser B, Jójárt B, Jensen SJK, Csizmadia IG, Viskolcz B. The effect of oxidative stress on the bursopentin peptide structure: a theoretical study. Phys Chem Chem Phys 2015; 16:9602-9. [PMID: 24730022 DOI: 10.1039/c3cp54799j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bursopentin (BP(5), H-Cys(1)-Lys(2)-Arg(3)-Val(4)-Tyr(5)-OH), found in the bursa Fabricius of the chicken, is a pentapeptide that protects the organism from oxidative stress by reducing the intracellular generation of reactive oxygen species. Hydrogen abstraction, a common oxidative reaction occurring in proteins, often results in the formation of d amino acid residues. To study the effect of this phenomenon on the structure of bursopentin, each of its residues were converted from the l configuration to the d configuration, and the structures of these peptide epimers were compared to that of the wild-type bursopentin. The conformations, secondary structures, compactness and hydrogen bonding of bursopentin were compared to its epimers using molecular dynamics simulations and first principles quantum chemical computations. It was discovered that the repulsion between the side chains of Lys(2) and Arg(3) influenced the conformation of the peptide regardless of the configuration of these residues. Epimerisation of the Val(4) and Tyr(5) caused a reduction in the compactness of bursopentin. In all cases, the occurrence of a turn structure was relatively high, especially when Arg(3) was in the d configuration. Thermodynamic analysis of the epimerisation process showed that the formation of d amino acid residues is favourable.
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Affiliation(s)
- A T Lam
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, Ontario, CanadaM5S
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18
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Szórád JJ, Faragó EP, Rágyanszki A, Cimino FA, Fiser B, Owen MC, Jójárt B, Morgado CA, Szőri M, Jensen SJK, Csizmadia IG, Viskolcz B. Conformation change of opiorphin derivates. A theoretical study of the radical initiated epimerization of opiorphin. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Salamone M, Basili F, Bietti M. Reactivity and selectivity patterns in hydrogen atom transfer from amino acid C-H bonds to the cumyloxyl radical: polar effects as a rationale for the preferential reaction at proline residues. J Org Chem 2015; 80:3643-50. [PMID: 25774567 DOI: 10.1021/acs.joc.5b00549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Absolute rate constants for hydrogen atom transfer (HAT) from the C-H bonds of N-Boc-protected amino acids to the cumyloxyl radical (CumO(•)) were measured by laser flash photolysis. With glycine, alanine, valine, norvaline, and tert-leucine, HAT occurs from the α-C-H bonds, and the stability of the α-carbon radical product plays a negligible role. With leucine, HAT from the α- and γ-C-H bonds was observed. The higher kH value measured for proline was explained in terms of polar effects, with HAT that predominantly occurs from the δ-C-H bonds, providing a rationale for the previous observation that proline residues represent favored HAT sites in the reactions of peptides and proteins with (•)OH. Preferential HAT from proline was also observed in the reactions of CumO(•) with the dipeptides N-BocProGlyOH and N-BocGlyGlyOH. The rate constants measured for CumO(•) were compared with the relative rates obtained previously for the corresponding reactions of different hydrogen-abstracting species. The behavior of CumO(•) falls between those observed for the highly reactive radicals Cl(•) and (•)OH and the significantly more stable Br(•). Taken together, these results provide a general framework for the description of the factors that govern reactivity and selectivity patterns in HAT reactions from amino acid C-H bonds.
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Affiliation(s)
- Michela Salamone
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Federica Basili
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
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20
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Castañeda-Arriaga R, Mora-Diez N, Alvarez-Idaboy JR. Modelling the chemical repair of protein carbon-centered radicals formed via oxidative damage with dihydrolipoic acid. RSC Adv 2015. [DOI: 10.1039/c5ra20618a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dihydrolipoic acid repairs carbon-centred radicals at diffusion-controlled rates via HAT mechanism.
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Affiliation(s)
- Romina Castañeda-Arriaga
- Facultad de Química
- Departamento de Física y Química Teórica
- Universidad Nacional Autónoma de México
- México DF 04510
- México
| | | | - J. Raul Alvarez-Idaboy
- Facultad de Química
- Departamento de Física y Química Teórica
- Universidad Nacional Autónoma de México
- México DF 04510
- México
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21
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Salamone M, Basili F, Mele R, Cianfanelli M, Bietti M. Reactions of the cumyloxyl radical with secondary amides. The influence of steric and stereoelectronic effects on the hydrogen atom transfer reactivity and selectivity. Org Lett 2014; 16:6444-7. [PMID: 25474754 DOI: 10.1021/ol503277r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A time-resolved kinetic study of the hydrogen atom transfer (HAT) reactions from secondary alkanamides to the cumyloxyl radical was carried out in acetonitrile. HAT predominantly occurs from the N-alkyl α-C-H bonds, and a >60-fold decrease in kH was observed by increasing the steric hindrance of the acyl and N-alkyl groups. The role of steric and stereoelectronic effects on the reactivity and selectivity is discussed in the framework of HAT reactions from peptides.
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Affiliation(s)
- Michela Salamone
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata" , Via della Ricerca Scientifica, 1 I-00133 Rome, Italy
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22
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Gerlei KZ, Yarligan Uysal S. A comparison of l- and d-Asp and Asn α-radicals a case study for atropisomerism. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Sheykhkarimli D, Choo KL, Owen M, Fiser B, Jójárt B, Csizmadia IG, Viskolcz B. Molecular ageing: free radical initiated epimerization of thymopentin--a case study. J Chem Phys 2014; 140:205102. [PMID: 24880333 DOI: 10.1063/1.4871684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The epimerization of amino acid residues increases with age in living organisms. In the present study, the structural consequences and thermodynamic functions of the epimerization of thymopentin (TP-5), the active site of the thymic hormone thymopoietin, were studied using molecular dynamics and density functional theory methods. The results show that free radical-initiated D-amino acid formation is energetically favoured (-130 kJmol(-1)) for each residue and induces significant changes to the peptide structure. In comparison to the wild-type (each residue in the L-configuration), the radius of gyration of the D-Asp(3) epimer of the peptide decreased by 0.5 Å, and disrupted the intramolecular hydrogen bonding of the native peptide. Beyond establishing important structural, energetic and thermodynamic benchmarks and reference data for the structure of TP-5, these results disseminate the understanding of molecular ageing, the epimerization of amino acid residues.
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Affiliation(s)
- Dayag Sheykhkarimli
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ken-Loon Choo
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Michael Owen
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Béla Fiser
- Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
| | - Balázs Jójárt
- Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
| | - Imre G Csizmadia
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Béla Viskolcz
- Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
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24
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Gerlei KZ, Élő L, Fiser B, Owen MC, Jákli I, Knak Jensen SJ, Csizmadia IG, Perczel A, Viskolcz B. Impairment of a model peptide by oxidative stress: Thermodynamic stabilities of asparagine diamide Cα-radical foldamers. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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25
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Signorelli S, Coitiño EL, Borsani O, Monza J. Molecular mechanisms for the reaction between (˙)OH radicals and proline: insights on the role as reactive oxygen species scavenger in plant stress. J Phys Chem B 2013; 118:37-47. [PMID: 24328335 DOI: 10.1021/jp407773u] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The accumulation of proline (Pro) and overproduction of reactive oxygen species (ROS) by plants exposed to stress is well-documented. In vitro assays show that enzyme inactivation by hydroxyl radicals ((•)OH) can be avoided in the presence of Pro, suggesting this amino acid might act as a (•)OH scavenger. Although production of hydroxyproline (Hyp) has been hypothesized in connection with such antioxidant activity, no evidence on the detailed mechanism of scavenging has been reported. To elucidate whether and how Hyp might be produced, we used density functional theory calculations coupled to a polarizable continuum model to explore 27 reaction channels including H-abstraction by (•)OH and (•)OH/H2O addition. The structure and energetics of stable species and transition states for each reaction channel were characterized at the PCM-(U)M06/6-31G(d,p) level in aqueous solution. Evidence is found for a main pathway in which Pro scavenges (•)OH by successive H-abstractions (ΔG(‡,298) = 4.1 and 7.5 kcal mol(-1)) to yield 3,4-Δ-Pro. A companion pathway with low barriers yielding Δ(1)-pyrroline-5-carboxylate (P5C) is also supported, linking with 5-Hyp through hydration. However, this connection remains unlikely in stressed plants because P5C would be efficiently recycled to Pro (contributing to its accumulation) by P5C reductase, hypothesis coined here as the "Pro-Pro cycle".
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Affiliation(s)
- Santiago Signorelli
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República , Av. E. Garzón 780, CP 12900 Montevideo, Uruguay
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26
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Gerlei KZ, Jákli I, Szőri M, Jensen SJK, Viskolcz B, Csizmadia IG, Perczel A. Atropisomerism of the Asn α radicals revealed by Ramachandran surface topology. J Phys Chem B 2013; 117:12402-9. [PMID: 24015919 DOI: 10.1021/jp4070906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
C radicals are typically trigonal planar and thus achiral, regardless of whether they originate from a chiral or an achiral C-atom (e.g., C-H + (•)OH → C• + H2O). Oxidative stress could initiate radical formation in proteins when, for example, the H-atom is abstracted from the Cα-carbon of an amino acid residue. Electronic structure calculations show that such a radical remains achiral when formed from the achiral Gly, or the chiral but small Ala residues. However, when longer side-chain containing proteogenic amino acid residues are studied (e.g., Asn), they provide radicals of axis chirality, which in turn leads to atropisomerism observed for the first time for peptides. The two enantiomeric extended backbone structures, •βL and •βD, interconvert via a pair of enantiotopic reaction paths, monitored on a 4D Ramachandran surface, with two distinct transition states of very different Gibbs-free energies: 37.4 and 67.7 kJ/mol, respectively. This discovery requires the reassessment of our understanding on radical formation and their conformational and stereochemical behavior. Furthermore, the atropisomerism of proteogenic amino acid residues should affect our understanding on radicals in biological systems and, thus, reframes the role of the D-residues as markers of molecular aging.
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Affiliation(s)
- Klára Z Gerlei
- Department of Chemical Informatics, Faculty of Education, University of Szeged , 6726 Szeged, Hungary
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27
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Mujika JI, Uranga J, Matxain JM. Computational study on the attack of ·OH radicals on aromatic amino acids. Chemistry 2013; 19:6862-73. [PMID: 23536477 DOI: 10.1002/chem.201203862] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/15/2013] [Indexed: 01/24/2023]
Abstract
The attack of hydroxyl radicals on aromatic amino acid side chains, namely phenylalanine, tyrosine, and tryptophan, have been studied by using density functional theory. Two reaction mechanisms were considered: 1) Addition reactions onto the aromatic ring atoms and 2) hydrogen abstraction from all of the possible atoms on the side chains. The thermodynamics and kinetics of the attack of a maximum of two hydroxyl radicals were studied, considering the effect of different protein environments at two different dielectric values (4 and 80). The obtained theoretical results explain how the radical attacks take place and provide new insight into the reasons for the experimentally observed preferential mechanism. These results indicate that, even though the attack of the first (·)OH radical on an aliphatic C atom is energetically favored, the larger delocalization and concomitant stabilization that are obtained by attack on the aromatic side chain prevail. Thus, the obtained theoretical results are in agreement with the experimental evidence that the aromatic side chain is the main target for radical attack and show that the first (·)OH radical is added onto the aromatic ring, whereas a second radical abstracts a hydrogen atom from the same position to obtain the oxidized product. Moreover, the results indicate that the reaction can be favored in the buried region of the protein.
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Affiliation(s)
- J I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center, PK 1072, 20080 Donostia, Euskadi, Spain.
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28
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Salamone M, DiLabio GA, Bietti M. Reactions of the cumyloxyl and benzyloxyl radicals with strong hydrogen bond acceptors. Large enhancements in hydrogen abstraction reactivity determined by substrate/radical hydrogen bonding. J Org Chem 2012; 77:10479-87. [PMID: 23153316 DOI: 10.1021/jo3019889] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A kinetic study on hydrogen abstraction from strong hydrogen bond acceptors such as DMSO, HMPA, and tributylphosphine oxide (TBPO) by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out in acetonitrile. The reactions with CumO(•) were described in terms of a direct hydrogen abstraction mechanism, in line with the kinetic deuterium isotope effects, k(H)/k(D), of 2.0 and 3.1 measured for reaction of this radical with DMSO/DMSO-d(6) and HMPA/HMPA-d(18). Very large increases in reactivity were observed on going from CumO(•) to BnO(•), as evidenced by k(H)(BnO(•))/k(H)(CumO(•)) ratios of 86, 4.8 × 10(3), and 1.6 × 10(4) for the reactions with HMPA, TBPO, and DMSO, respectively. The k(H)/k(D) of 0.91 and 1.0 measured for the reactions of BnO(•) with DMSO/DMSO-d(6) and HMPA/HMPA-d(18), together with the k(H)(BnO(•))/k(H)(CumO(•)) ratios, were explained on the basis of the formation of a hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the oxygen atom of the substrates followed by hydrogen abstraction. This is supported by theoretical calculations that show the formation of relatively strong prereaction complexes. These observations confirm that in alkoxyl radical reactions specific hydrogen bond interactions can dramatically influence the hydrogen abstraction reactivity, pointing toward the important role played by structural and electronic effects.
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Affiliation(s)
- Michela Salamone
- Dipartimento di Scienze e Tecnologie Chimiche, Università Tor Vergata, Via della Ricerca Scientifica, 1 I-00133 Rome, Italy
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29
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Owen MC, Tóth L, Jojárt B, Komáromi I, Csizmadia IG, Viskolcz B. The Effect of Newly Developed OPLS-AA Alanyl Radical Parameters on Peptide Secondary Structure. J Chem Theory Comput 2012; 8:2569-80. [DOI: 10.1021/ct300059f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael C. Owen
- Materials Science Research Institute,
Faculty of Dentistry, Semmelweis University, Üllöi út 26. H-1085 Budapest, Hungary
- Department of Chemical
Informatics,
Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
- Global Institute of Computational Molecular and Materials Science
- Drug Discovery Research Center
| | - László Tóth
- Thrombosis and Haemostasis Research
Group of the Hungarian Academy of Sciences at the University of Debrecen, H-4010, Hungary
| | - Balázs Jojárt
- Department of Chemical
Informatics,
Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
- Drug Discovery Research Center
| | - István Komáromi
- Thrombosis and Haemostasis Research
Group of the Hungarian Academy of Sciences at the University of Debrecen, H-4010, Hungary
| | - Imre G. Csizmadia
- Materials Science Research Institute,
Faculty of Dentistry, Semmelweis University, Üllöi út 26. H-1085 Budapest, Hungary
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6,
Canada
- Department of Chemical
Informatics,
Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
- Global Institute of Computational Molecular and Materials Science
- Drug Discovery Research Center
| | - Bela Viskolcz
- Department of Chemical
Informatics,
Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary
- Drug Discovery Research Center
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