ArticleThe journal of physical chemistry. B2011
An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Zirconium Coordination Chemistry and Its Role in Optimizing Hydroxymate Chelation: Insights from Molecular Dynamics.ACS omega · 2023Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Screening of Suitable Ionic Liquids as Green Solvents for Extraction of Eicosapentaenoic Acid (EPA) from Microalgae Biomass Using COSMO-RS Model.Molecules (Basel, Switzerland) · 2019Article
- Photolyase: Dynamics and electron-transfer mechanisms of DNA repair.Archives of biochemistry and biophysics · 2017Review
- Dynamics and mechanisms of DNA repair by photolyase.Physical chemistry chemical physics : PCCP · 2015Review
- Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: a computational study.Journal of the American Chemical Society · 2014Article
- Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase.Journal of the American Chemical Society · 2012Article
- Dynamics and mechanism of DNA repair in a biomimetic system: flavin-thymine dimer adduct.Journal of the American Chemical Society · 2012Article
- Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5' and C6-C6' bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Nonequilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects. Throughout the splitting of C5-C5' and C6-C6' bonds, a significant amount of excess charge is delocalized onto the solvent. We have verified that this is not an artifact of the electronic density functional theory (DFT) method used for this anionic system with Schrödinger equation-based quantum chemical cluster calculations. The amount and variability of charge delocalization changes with the course of the reaction. The splitting of the C6-C6' bond is accompanied by both an increase in electron density on the C6 and C6' carbon atoms and an increase in the water density near those atoms. These features are observed both in our equilibrium umbrella sampling simulations and nonequilibrium trajectories.
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Registered trials
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