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Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations

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Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations. / Holroyd, Leo F.; Buehl, Michael; Gaigeot, Marie-Pierre; van Mourik, Tanja.

Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results. ed. / Samantha Jenkins; Steven Kirk; Jean Maruani; Erkki Brandas. Academic Press, 2019. p. 109-128 (Advances of Quantum Chemistry; Vol. 78).

Research output: Chapter in Book/Report/Conference proceedingChapter

Harvard

Holroyd, LF, Buehl, M, Gaigeot, M-P & van Mourik, T 2019, Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations. in S Jenkins, S Kirk, J Maruani & E Brandas (eds), Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results. Advances of Quantum Chemistry, vol. 78, Academic Press, pp. 109-128. https://doi.org/10.1016/bs.aiq.2018.05.001

APA

Holroyd, L. F., Buehl, M., Gaigeot, M-P., & van Mourik, T. (2019). Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations. In S. Jenkins, S. Kirk, J. Maruani, & E. Brandas (Eds.), Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results (pp. 109-128). (Advances of Quantum Chemistry; Vol. 78). Academic Press. https://doi.org/10.1016/bs.aiq.2018.05.001

Vancouver

Holroyd LF, Buehl M, Gaigeot M-P, van Mourik T. Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations. In Jenkins S, Kirk S, Maruani J, Brandas E, editors, Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results. Academic Press. 2019. p. 109-128. (Advances of Quantum Chemistry). https://doi.org/10.1016/bs.aiq.2018.05.001

Author

Holroyd, Leo F. ; Buehl, Michael ; Gaigeot, Marie-Pierre ; van Mourik, Tanja. / Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations. Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results. editor / Samantha Jenkins ; Steven Kirk ; Jean Maruani ; Erkki Brandas. Academic Press, 2019. pp. 109-128 (Advances of Quantum Chemistry).

Bibtex - Download

@inbook{969e090c333040438786e43fcda9bd65,
title = "Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations",
abstract = "We modelled the driving force for aqueous keto-to-enol tautomerisation of 5-bromouracil, a mutagenic thymine analogue, by first-principles molecular dynamics simulations with thermodynamic integration. Using interatomic distance constraints to model the water-assisted (de)protonation of 5-bromouracil in a periodic water box, we show that the free energy for its enolisation is lower than that of the parent compound, uracil, by around 3.0 kcal/mol (BLYP-D2 level), enough to significantly alter the relative tautomeric ratios. Assuming the energetic difference also holds in the cell, this finding is evidence for the “rare tautomer” hypothesis of 5-bromouracil mutagenicity (and, possibly, that of other base analogues). ",
keywords = "Density functional theory, Nucleobases, Solvation effects, Mutagenesis, CPMD, Bromouracil",
author = "Holroyd, {Leo F.} and Michael Buehl and Marie-Pierre Gaigeot and {van Mourik}, Tanja",
note = "The authors acknowledge support from the Engineering and Physical Sciences Research Council (EPSRC) UK National Service for Computational Chemistry Software (NSCCS); from GENCI (Grand {\'e}quipement national de calcul intensif); and from CINES (Centre informatique national de l{\textquoteright}enseignement sup{\'e}rieur). LFH and TvM gratefully acknowledge support from the HPC-EUROPA2 project with the support of the European Commission - Capacities Area - Research Infrastructures. LFH is grateful to the EPSRC for studentship support through the Doctoral Training Account scheme (grant code EP/K503162/1).",
year = "2019",
month = jan,
day = "1",
doi = "10.1016/bs.aiq.2018.05.001",
language = "English",
isbn = "9780128160848",
series = "Advances of Quantum Chemistry",
publisher = "Academic Press",
pages = "109--128",
editor = "Samantha Jenkins and Steven Kirk and Jean Maruani and Erkki Brandas",
booktitle = "Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results",

}

RIS (suitable for import to EndNote) - Download

TY - CHAP

T1 - Thermodynamics of 5-bromouracil tautomerisation from first-principles molecular dynamics simulations

AU - Holroyd, Leo F.

AU - Buehl, Michael

AU - Gaigeot, Marie-Pierre

AU - van Mourik, Tanja

N1 - The authors acknowledge support from the Engineering and Physical Sciences Research Council (EPSRC) UK National Service for Computational Chemistry Software (NSCCS); from GENCI (Grand équipement national de calcul intensif); and from CINES (Centre informatique national de l’enseignement supérieur). LFH and TvM gratefully acknowledge support from the HPC-EUROPA2 project with the support of the European Commission - Capacities Area - Research Infrastructures. LFH is grateful to the EPSRC for studentship support through the Doctoral Training Account scheme (grant code EP/K503162/1).

PY - 2019/1/1

Y1 - 2019/1/1

N2 - We modelled the driving force for aqueous keto-to-enol tautomerisation of 5-bromouracil, a mutagenic thymine analogue, by first-principles molecular dynamics simulations with thermodynamic integration. Using interatomic distance constraints to model the water-assisted (de)protonation of 5-bromouracil in a periodic water box, we show that the free energy for its enolisation is lower than that of the parent compound, uracil, by around 3.0 kcal/mol (BLYP-D2 level), enough to significantly alter the relative tautomeric ratios. Assuming the energetic difference also holds in the cell, this finding is evidence for the “rare tautomer” hypothesis of 5-bromouracil mutagenicity (and, possibly, that of other base analogues).

AB - We modelled the driving force for aqueous keto-to-enol tautomerisation of 5-bromouracil, a mutagenic thymine analogue, by first-principles molecular dynamics simulations with thermodynamic integration. Using interatomic distance constraints to model the water-assisted (de)protonation of 5-bromouracil in a periodic water box, we show that the free energy for its enolisation is lower than that of the parent compound, uracil, by around 3.0 kcal/mol (BLYP-D2 level), enough to significantly alter the relative tautomeric ratios. Assuming the energetic difference also holds in the cell, this finding is evidence for the “rare tautomer” hypothesis of 5-bromouracil mutagenicity (and, possibly, that of other base analogues).

KW - Density functional theory

KW - Nucleobases

KW - Solvation effects

KW - Mutagenesis

KW - CPMD

KW - Bromouracil

UR - https://www.sciencedirect.com/bookseries/advances-in-quantum-chemistry/vol/78/suppl/C

U2 - 10.1016/bs.aiq.2018.05.001

DO - 10.1016/bs.aiq.2018.05.001

M3 - Chapter

SN - 9780128160848

T3 - Advances of Quantum Chemistry

SP - 109

EP - 128

BT - Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results

A2 - Jenkins, Samantha

A2 - Kirk, Steven

A2 - Maruani, Jean

A2 - Brandas, Erkki

PB - Academic Press

ER -

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