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Phosphodiester bond rupture in 5 ' and 3 ' cytosine monophosphate in aqueous environment and the effect of low-energy electron attachment: A Car-Parrinello QM/MM molecular dynamics study
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0001-8748-3890
2008 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 462, no 4-6, 289-294 p.Article in journal (Refereed) Published
Abstract [en]

In this study we have explored the effect of low-energy electrons (LEEs) when rupturing the C3'-O3' and C5'-O5' bonds in 3' and 5' cytosine monophosphate in an aqueous environment. This has been done using a hybrid quantum mechanics/classical mechanics (QM/MM) setup within the framework of Car-Parrinello molecular dynamics (CPMD). Our results are in agreement with experimental findings and indicate that LEEs do not drastically lower the energy barrier for breaking the 3' or 5' phosphodiester bonds for single cytosine nucleotides in aqueous environment.

Place, publisher, year, edition, pages
2008. Vol. 462, no 4-6, 289-294 p.
Keyword [en]
dna-strand breaks, density-functional theory, pyrimidine nucleotides, damage, single, thymidine, cleavage, biomolecules, simulations, nucleosides
URN: urn:nbn:se:kth:diva-17792DOI: 10.1016/j.cplett.2008.07.106ISI: 000258830900031ScopusID: 2-s2.0-50349097694OAI: diva2:335837
QC 20100525Available from: 2010-08-05 Created: 2010-08-05Bibliographically approved

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