A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate
It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" groun...
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ftcaltechauth:oai:authors.library.caltech.edu:0wq6y-hd503 2024-06-23T07:54:25+00:00 A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate Park, Woojin Filatov (Gulak), Michael Sadiq, Saima Gerasimov, Igor Lee, Seunghoon Joo, Taiha Choi, Cheol Ho 2022-08-04 https://doi.org/10.1021/acs.jpclett.2c01694 https://www.ncbi.nlm.nih.gov/pmc/PMC9358713 unknown American Chemical Society https://doi.org/10.1021/acs.jpclett.2c01694 oai:authors.library.caltech.edu:0wq6y-hd503 https://www.ncbi.nlm.nih.gov/pmc/PMC9358713 eprintid:115961 resolverid:CaltechAUTHORS:20220729-722028000 info:eu-repo/semantics/openAccess Other Journal of Physical Chemistry Letters, 13(30), 7072-7080, (2022-08-04) Energy Hydration Mathematical methods Pyrimidine Uracil General Materials Science Physical and Theoretical Chemistry info:eu-repo/semantics/article 2022 ftcaltechauth https://doi.org/10.1021/acs.jpclett.2c01694 2024-06-12T06:19:42Z It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50–200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate. © 2022 The Authors. Published by American Chemical Society. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). Received 4 June 2022. Accepted 11 July 2022. Published online 28 July 2022. The support by Samsung Science and Technology Foundations Grant SSTF-BA1701-12 and Grants 2020R1A2C2008246 and 2020R1A5A1019141 funded by the Ministry of Science and ICT is acknowledged. This work was also supported by the Korea Polar Research Institute (KOPRI, PE21120). The authors declare no competing financial interest. Published - jz2c01694.pdf Supplemental Material - jz2c01694_si_001.pdf Supplemental Material - jz2c01694_si_002.mp4 Article in Journal/Newspaper Korea Polar Research Institute Caltech Authors (California Institute of Technology) The Journal of Physical Chemistry Letters 13 30 7072 7080 |
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Open Polar |
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Caltech Authors (California Institute of Technology) |
op_collection_id |
ftcaltechauth |
language |
unknown |
topic |
Energy Hydration Mathematical methods Pyrimidine Uracil General Materials Science Physical and Theoretical Chemistry |
spellingShingle |
Energy Hydration Mathematical methods Pyrimidine Uracil General Materials Science Physical and Theoretical Chemistry Park, Woojin Filatov (Gulak), Michael Sadiq, Saima Gerasimov, Igor Lee, Seunghoon Joo, Taiha Choi, Cheol Ho A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate |
topic_facet |
Energy Hydration Mathematical methods Pyrimidine Uracil General Materials Science Physical and Theoretical Chemistry |
description |
It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50–200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate. © 2022 The Authors. Published by American Chemical Society. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). Received 4 June 2022. Accepted 11 July 2022. Published online 28 July 2022. The support by Samsung Science and Technology Foundations Grant SSTF-BA1701-12 and Grants 2020R1A2C2008246 and 2020R1A5A1019141 funded by the Ministry of Science and ICT is acknowledged. This work was also supported by the Korea Polar Research Institute (KOPRI, PE21120). The authors declare no competing financial interest. Published - jz2c01694.pdf Supplemental Material - jz2c01694_si_001.pdf Supplemental Material - jz2c01694_si_002.mp4 |
format |
Article in Journal/Newspaper |
author |
Park, Woojin Filatov (Gulak), Michael Sadiq, Saima Gerasimov, Igor Lee, Seunghoon Joo, Taiha Choi, Cheol Ho |
author_facet |
Park, Woojin Filatov (Gulak), Michael Sadiq, Saima Gerasimov, Igor Lee, Seunghoon Joo, Taiha Choi, Cheol Ho |
author_sort |
Park, Woojin |
title |
A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate |
title_short |
A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate |
title_full |
A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate |
title_fullStr |
A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate |
title_full_unstemmed |
A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate |
title_sort |
plausible mechanism of uracil photohydration involves an unusual intermediate |
publisher |
American Chemical Society |
publishDate |
2022 |
url |
https://doi.org/10.1021/acs.jpclett.2c01694 https://www.ncbi.nlm.nih.gov/pmc/PMC9358713 |
genre |
Korea Polar Research Institute |
genre_facet |
Korea Polar Research Institute |
op_source |
Journal of Physical Chemistry Letters, 13(30), 7072-7080, (2022-08-04) |
op_relation |
https://doi.org/10.1021/acs.jpclett.2c01694 oai:authors.library.caltech.edu:0wq6y-hd503 https://www.ncbi.nlm.nih.gov/pmc/PMC9358713 eprintid:115961 resolverid:CaltechAUTHORS:20220729-722028000 |
op_rights |
info:eu-repo/semantics/openAccess Other |
op_doi |
https://doi.org/10.1021/acs.jpclett.2c01694 |
container_title |
The Journal of Physical Chemistry Letters |
container_volume |
13 |
container_issue |
30 |
container_start_page |
7072 |
op_container_end_page |
7080 |
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1802646567280181248 |