The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode

Publication type:
Journal article
Metadata:
Autoren
  • Francesca Costanzo
  • Marialore Sulpizi
  • Raffaele Guido Della Valle
  • Michiel Sprik
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000292331900042&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1063/1.3597603
eISSN
1089-7690
Externe Identifier
  • Clarivate Analytics Document Solution ID: 786TX
  • PubMed Identifier: 21721644
ISSN
0021-9606
Ausgabe der Veröffentlichung
24
Zeitschrift
JOURNAL OF CHEMICAL PHYSICS
Schlüsselwörter
  • charge exchange
  • density functional theory
  • dissociation
  • free energy
  • molecular dynamics method
  • organic compounds
  • oxidation
  • solvation
  • solvent effects
  • thermochemistry
Artikelnummer
ARTN 244508
Datum der Veröffentlichung
2011
Status
Published
Titel
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
Sub types
  • Article
Ausgabe der Zeitschrift
134

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:p>The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H+) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H3O+). Using the computed solvation free energy of H+ as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pKa and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]10.1063/1.3250438. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pKa, NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.</jats:p>
Autoren
  • Francesca Costanzo
  • Marialore Sulpizi
  • Raffaele Guido Della Valle
  • Michiel Sprik
DOI
10.1063/1.3597603
eISSN
1089-7690
ISSN
0021-9606
Ausgabe der Veröffentlichung
24
Zeitschrift
The Journal of Chemical Physics
Sprache
en
Online publication date
2011
Datum der Veröffentlichung
2011
Status
Published
Herausgeber
AIP Publishing
Herausgeber URL
http://dx.doi.org/10.1063/1.3597603
Datum der Datenerfassung
2023
Titel
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
Ausgabe der Zeitschrift
134

Data source: Crossref

Abstract
The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.
Addresses
  • Dipartimento di Chimica Fisica e Inorganica, Università di Bologna and INSTM-UdR Bologna, Bologna, Italy. costanzo@ms.fci.unibo.it
Autoren
  • Francesca Costanzo
  • Marialore Sulpizi
  • Raffaele Guido Della Valle
  • Michiel Sprik
DOI
10.1063/1.3597603
eISSN
1089-7690
Externe Identifier
  • PubMed Identifier: 21721644
Funding acknowledgements
  • Engineering and Physical Sciences Research Council: EP/F005636/1
Open access
false
ISSN
0021-9606
Ausgabe der Veröffentlichung
24
Zeitschrift
The Journal of chemical physics
Schlüsselwörter
  • Protons
  • Hydrogen
  • Tryptophan
  • Tyrosine
  • Electrodes
  • Oxidation-Reduction
  • Electrons
  • Quantum Theory
  • Thermodynamics
  • Molecular Dynamics Simulation
Sprache
eng
Medium
Print
Paginierung
244508
Datum der Veröffentlichung
2011
Status
Published
Datum der Datenerfassung
2011
Titel
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode.
Sub types
  • Research Support, Non-U.S. Gov't
  • Journal Article
Ausgabe der Zeitschrift
134

Data source: Europe PubMed Central

Abstract
The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.
Autoren
  • Francesca Costanzo
  • Marialore Sulpizi
  • Raffaele Guido Della Valle
  • Michiel Sprik
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/21721644
DOI
10.1063/1.3597603
eISSN
1089-7690
Ausgabe der Veröffentlichung
24
Zeitschrift
J Chem Phys
Schlüsselwörter
  • Electrodes
  • Electrons
  • Hydrogen
  • Molecular Dynamics Simulation
  • Oxidation-Reduction
  • Protons
  • Quantum Theory
  • Thermodynamics
  • Tryptophan
  • Tyrosine
Sprache
eng
Country
United States
Paginierung
244508
Datum der Veröffentlichung
2011
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2011
Titel
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode.
Sub types
  • Journal Article
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
134

Data source: PubMed

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