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Park W, Filatov (Gulak) M, Sadiq S, Gerasimov I, Lee S, Joo T, Choi CH. A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate. J Phys Chem Lett 2022; 13:7072-7080. [PMID: 35900137 PMCID: PMC9358713 DOI: 10.1021/acs.jpclett.2c01694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/11/2022] [Indexed: 05/28/2023]
Abstract
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.
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Affiliation(s)
- Woojin Park
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | | | - Saima Sadiq
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Igor Gerasimov
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Taiha Joo
- Department
of Chemistry, Pohang University of Science
and Technology (POSTECH), Pohang 37673, South Korea
| | - Cheol Ho Choi
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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2
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Vos E, Hoehn SJ, Krul SE, Crespo-Hernández CE, González-Vázquez J, Corral I. Disclosing the Role of C4-Oxo Substitution in the Photochemistry of DNA and RNA Pyrimidine Monomers: Formation of Photoproducts from the Vibrationally Excited Ground State. J Phys Chem Lett 2022; 13:2000-2006. [PMID: 35191712 PMCID: PMC8900130 DOI: 10.1021/acs.jpclett.2c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure on early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases' ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S1(ππ*) state, which decays to the vibrationally excited ground state in a few hundred femtoseconds. Analysis of the postirradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(Iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core.
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Affiliation(s)
- Eva Vos
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Sean J. Hoehn
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Sarah E. Krul
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E. Crespo-Hernández
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jesús González-Vázquez
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Corral
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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3
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Domcke W, Ehrmaier J, Sobolewski AL. Solar Energy Harvesting with Carbon Nitrides and N-Heterocyclic Frameworks: Do We Understand the Mechanism? CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201800144] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wolfgang Domcke
- Department of Chemistry; Technical University of Munich; 85747 Garching Germany
| | - Johannes Ehrmaier
- Department of Chemistry; Technical University of Munich; 85747 Garching Germany
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Ehrmaier J, Janicki MJ, Sobolewski AL, Domcke W. Mechanism of photocatalytic water splitting with triazine-based carbon nitrides: insights from ab initio calculations for the triazine–water complex. Phys Chem Chem Phys 2018; 20:14420-14430. [DOI: 10.1039/c8cp01998c] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Valuable theoretical insights into the mechanism of photocatalytic water-splitting using triazine as a model system for carbon-nitride materials.
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Affiliation(s)
- Johannes Ehrmaier
- Department of Chemistry
- Technical University of Munich
- D-85747 Garching
- Germany
| | - Mikołaj J. Janicki
- Department of Chemistry
- Technical University of Munich
- D-85747 Garching
- Germany
| | | | - Wolfgang Domcke
- Department of Chemistry
- Technical University of Munich
- D-85747 Garching
- Germany
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Chakraborty P, Karsili TNV, Marchetti B, Matsika S. Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution. Faraday Discuss 2018; 207:329-350. [DOI: 10.1039/c7fd00188f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanistic details of well-known photohydrate lesions are explored using state-of-the-art computational methods.
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Baltrusaitis J, Patterson EV, O'Connor M, Qu S, Kolodziej EP, Cwiertny DM. Reversible Photohydration of Trenbolone Acetate Metabolites: Mechanistic Understanding of Product-to-Parent Reversion through Complementary Experimental and Theoretical Approaches. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6753-61. [PMID: 26800354 DOI: 10.1021/acs.est.5b03905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Photolysis experiments (in H2O and D2O) and quantum chemical calculations were performed to explore the pH-dependent, reversible photohydration of trenbolone acetate (TBA) metabolites. Photohydration of 17α-trenbolone (17α-TBOH) and 17β-trenbolone (17β-TBOH) occurred readily in simulated sunlight to yield hydrated products with incorporated H(+) at C4 and OH(-) at either C5 (5-OH-TBOH) or C12 (12-OH-TBOH) in the tetracyclic steroid backbone. Although unable to be elucidated analytically, theory suggests preferred orientations of cis-12-OH-TBOH (relative to C13 methyl) and trans-5-OH-TBOH, with the former most thermodynamically stable overall. Both experiment and theory indicate limited stability of trans-5-OH-TBOH at acidic pH where it undergoes concurrent, carbocation-mediated thermal rearrangement to cis-12-OH-TBOH and dehydration to regenerate its parent structure. Experiments revealed cis-12-OH-TBOH to be more stable at acidic pH, which is the only condition where its reversion to parent TBA metabolite occurred. At basic pH cis-12-OH-TBOH decayed quickly via hydroxide/water addition, behavior that theory attributes to the formation of a stable enolate resistant to dehydration but prone to thermal hydration. In a noteworthy deviation from predicted theoretical stability, 17α-TBOH photohydration yields major trans-5-OH-TBOH and minor cis-12-OH-TBOH, a distribution also opposite that observed for 17β-TBOH. Because H(+) and OH(-) loss from adjacent carbon centers allows trans-5-OH-TBOH to dehydrate at all pH values, the presumed kinetically controlled yield of 17α-TBOH photohydrates results in a greater propensity for 17α-TBOH reversion than 17β-TBOH. Additional calculations explored minor, but potentially bioactive, trenbolone analogs that could be generated via alternative rearrangement of the acidic carbocation intermediate.
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Affiliation(s)
- Jonas Baltrusaitis
- Department of Chemical and Biomolecular Engineering, Lehigh University , B336 Iacocca Hall, 111 Research Drive, Bethlehem, Pennsylvania 18015, United States
- College of Public Health, University of Iowa , Iowa City, Iowa 52242, United States
| | - Eric V Patterson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Meghan O'Connor
- Department of Civil and Environmental Engineering, University of Iowa , 4105 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
| | - Shen Qu
- Department of Civil and Environmental Engineering, University of Iowa , 4105 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
| | - Edward P Kolodziej
- Interdisciplinary Arts and Sciences, University of Washington , Tacoma, Tacoma Washington 98402, United States
- Civil and Environmental Engineering, University of Washington , Seattle, Washington 98195, United States
| | - David M Cwiertny
- Department of Civil and Environmental Engineering, University of Iowa , 4105 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
- Department of Chemical and Biochemical Engineering, University of Iowa , Iowa City, Iowa 52242, United States
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Theoretical investigations on the stability of alkali metal substituted phenylpentazole. J Mol Model 2016; 22:106. [DOI: 10.1007/s00894-016-2971-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/24/2016] [Indexed: 10/21/2022]
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8
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Franzen S, Cochran KH, Weng J, Bartolotti L, Delley B. The quadrapolar character of the Markovnikov reaction transition state. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2015.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Liang K, Chen X, Guo Z, Hou T, Zhang X, Li Y. Lithium intercalation and diffusion in TiO2 nanotubes: a first-principles investigation. Phys Chem Chem Phys 2016; 18:24370-6. [DOI: 10.1039/c6cp03830a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The effective diffusion barriers between the outer and inner surfaces of the O2c–TiO2 NT can be as low as 0.53 eV.
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Affiliation(s)
- Ke Liang
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Xue Chen
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Zhenyu Guo
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Xiaohong Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
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Theoretical investigations on stability of pyridylpentazoles, pyridazylpentazoles, triazinylpentazoles, tetrazinylpentazoles, and pentazinylpentazole searching for a replacement of phenylpentazole as N5 (-) source. J Mol Model 2015; 21:318. [PMID: 26615562 DOI: 10.1007/s00894-015-2867-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022]
Abstract
Stabilities of pyridylpentazoles, pyridazylpentazoles, triazinylpentazoles, tetrazinylpentazoles, and pentazinylpentazole were studied using density functional theory to assess their potentials as the source of pentazole anion (N5 (-)) for replacement of phenylpentazole (PhN 5 ). Replacing the aryl group of PhN 5 by six-member heterocycle weakens pentazole ring. Compared to PhN 5 , title molecules have longer N-N bonds and lower activation energy (E a,1) needed for the N5 ring breaking. E a,1 decreases with the increasing number of nitrogen atoms of heterocycle. The ortho nitrogen of heterocycle most obviously lowers the stability of pentazole. The central C-N bond dissociation energies (BDEs) of title molecules are lower than that of PhN 5 . For the molecule with 0~1 ortho-nitrogen, H rearrangement happens during the central C-N bond breaking. The energy (E a,2) required for H rearrangement is considerably smaller than the corresponding BDE. ΔE a,2 (E a,2(PhN5) - E a,2 = 7.5~35.7 kJ mol(-1)) is larger than ΔE a,1 (E a,2(PhN5) - E a,2 = 4.6~15.5 kJ mol(-1)), while ΔE a,2/E a,2(PhN5) (2~9.5 %) is smaller than ΔE a,1/E a,1(PhN5) ( 4.4~15.0 %). The larger ΔE a,1/E a,1(PhN5) suggests that title molecules can not be the better N5 (-) than PhN 5 .
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11
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Zhang X, Yang J, Lu M, Gong X. Pyridylpentazole and its derivatives: a new source of N5−? RSC Adv 2015. [DOI: 10.1039/c5ra00813a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pyridylpentazole (PyN5) and its derivatives with 1–2 electron withdrawing groups were studied using the density functional theory to assess their potentials as the source of pentazole anion N5− for replacement of phenylpentazole (PhN5).
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Affiliation(s)
- Xueli Zhang
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Junqing Yang
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Ming Lu
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Xuedong Gong
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
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12
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Zhang X, Yang J, Lu M, Gong X. Theoretical studies on the stability of phenylpentazole and its substituted derivatives of –OH, –OCH3, –OC2H5and –N(CH3)2. RSC Adv 2014. [DOI: 10.1039/c4ra10669e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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