1
|
Domin D, Braïda B, Bergès J. Influence of Water on the Oxidation of Dimethyl Sulfide by the ·OH Radical. J Phys Chem B 2017; 121:9321-9330. [DOI: 10.1021/acs.jpcb.7b05796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Dominik Domin
- Direction
de la Recherche Fondamentale, Maison de la Simulation, Bâtiment
565 − Digiteo, Commissariat à l’Énergie Atomique, centre de Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Benoît Braïda
- UPMC Université Paris 06, CNRS UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, 75252 Paris, France
| | - Jacqueline Bergès
- UPMC Université Paris 06, CNRS UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, 75252 Paris, France
| |
Collapse
|
2
|
Zeida A, Guardia CM, Lichtig P, Perissinotti LL, Defelipe LA, Turjanski A, Radi R, Trujillo M, Estrin DA. Thiol redox biochemistry: insights from computer simulations. Biophys Rev 2014; 6:27-46. [PMID: 28509962 PMCID: PMC5427810 DOI: 10.1007/s12551-013-0127-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/03/2013] [Indexed: 12/13/2022] Open
Abstract
Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.
Collapse
Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Carlos M Guardia
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Pablo Lichtig
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Laura L Perissinotti
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada, T2N 2N4
| | - Lucas A Defelipe
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina.
| |
Collapse
|
3
|
Vallejos MM, Peruchena NM. Preferential Formation of the Different Hydrogen Bonds and Their Effects in Tetrahydrofuran and Tetrahydropyran Microhydrated Complexes. J Phys Chem A 2012; 116:4199-210. [DOI: 10.1021/jp301498n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Margarita M. Vallejos
- Laboratorio de Estructura
Molecular y Propiedades,
Área de Química Física, Departamento de Química,
Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460,
(3400) Corrientes, Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura
Molecular y Propiedades,
Área de Química Física, Departamento de Química,
Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460,
(3400) Corrientes, Argentina
| |
Collapse
|
4
|
Dupont C, Dumont É, Jacquemin D. Superior performance of range-separated hybrid functionals for describing σ* ← σ UV-vis signatures of three-electron two-center anions. J Phys Chem A 2012; 116:3237-46. [PMID: 22376324 DOI: 10.1021/jp211875r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We assess the efficiency of density functionals for the description of UV-vis signatures of temporary anions featuring a three-electron two-center bond, along a representative set of systems ranging from (pseudo)dihalides to disulfide radical anions (dimethyl disulfide and lipoate). While BH&HLYP and B3LYP have been predominantly applied to perform such simulations so far, we outline the significantly improved performance of several recently proposed functionals, including range-separated hybrids for the computation of these specific vertical transitions.
Collapse
Affiliation(s)
- Céline Dupont
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | | | | |
Collapse
|
5
|
Angelina EL, Peruchena NM. Strength and Nature of Hydrogen Bonding Interactions in Mono- and Di-Hydrated Formamide Complexes. J Phys Chem A 2011; 115:4701-10. [DOI: 10.1021/jp1105168] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emilio L. Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
| |
Collapse
|