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Marquetand P, Nogueira JJ, Mai S, Plasser F, González L. Challenges in Simulating Light-Induced Processes in DNA. Molecules 2016. [PMCID: PMC6155660 DOI: 10.3390/molecules22010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.
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Mai S, Pollum M, Martínez-Fernández L, Dunn N, Marquetand P, Corral I, Crespo-Hernández CE, González L. The origin of efficient triplet state population in sulfur-substituted nucleobases. Nat Commun 2016; 7:13077. [PMID: 27703148 PMCID: PMC5059480 DOI: 10.1038/ncomms13077] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/01/2016] [Indexed: 12/19/2022] Open
Abstract
Elucidating the photophysical mechanisms in sulfur-substituted nucleobases (thiobases) is essential for designing prospective drugs for photo- and chemotherapeutic applications. Although it has long been established that the phototherapeutic activity of thiobases is intimately linked to efficient intersystem crossing into reactive triplet states, the molecular factors underlying this efficiency are poorly understood. Herein we combine femtosecond transient absorption experiments with quantum chemistry and nonadiabatic dynamics simulations to investigate 2-thiocytosine as a necessary step to unravel the electronic and structural elements that lead to ultrafast and near-unity triplet-state population in thiobases in general. We show that different parts of the potential energy surfaces are stabilized to different extents via thionation, quenching the intrinsic photostability of canonical DNA and RNA nucleobases. These findings satisfactorily explain why thiobases exhibit the fastest intersystem crossing lifetimes measured to date among bio-organic molecules and have near-unity triplet yields, whereas the triplet yields of canonical nucleobases are nearly zero.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Marvin Pollum
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | | | - Nicholas Dunn
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Inés Corral
- Universidad Autónoma de Madrid, Departamento de Química, Cantoblanco, Madrid 28049, Spain
| | - Carlos E. Crespo-Hernández
- Center for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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53
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Pollum M, Jockusch S, Crespo-Hernández CE. Increase in the photoreactivity of uracil derivatives by doubling thionation. Phys Chem Chem Phys 2016; 17:27851-61. [PMID: 26439833 DOI: 10.1039/c5cp04822b] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability of 4-thiouracil to strongly absorb UVA radiation and to populate a reactive triplet state in high yield has enabled its use as a versatile photocrosslinker for nearly 50 years. In this contribution, we present a detailed spectroscopic and photochemical investigation of the 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil series in an effort to further advance this chemistry and to scrutinize the photoreactivity of 2,4-dithiouracil. Our results reveal that excitation of 2,4-dithiouracil leads to intersystem crossing to the triplet manifold in 220 ± 40 fs, which enables the population of the reactive triplet state with near unity yield (ΦT = 0.90 ± 0.15) and ultimately leads to a ca. 50% singlet oxygen generation (ΦΔ = 0.49 ± 0.02)-one of the highest singlet oxygen yields reported to date for a photoexcited thiobase. In addition, the long-lived triplet state of 2,4-dithiouracil reacts efficiently with the nucleic acid base adenine 5'-monophosphate through a direct, oxygen-independent photocycloaddition mechanism and at a rate that is at least 3-fold faster than that of 4-thiouracil under equal conditions. The new physico-chemical insights reported for these RNA-thiobase derivatives are compared to those of the DNA and RNA bases and the DNA-thiobase derivatives. Furthermore, the strong near-visible absorption and increased photoreactivity measured for 2,4-dithiouracil lays a solid foundation for developing RNA-targeted photocrosslinking and phototherapeutic agents that are more effective than those currently available.
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Affiliation(s)
- M Pollum
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, OH 44106, USA.
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54
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Yi J, Xiong Y, Cheng K, Li M, Chu G, Pu X, Xu T. A Combination of Chemometrics and Quantum Mechanics Methods Applied to Analysis of Femtosecond Transient Absorption Spectrum of Ortho-Nitroaniline. Sci Rep 2016; 6:19364. [PMID: 26781083 PMCID: PMC4726040 DOI: 10.1038/srep19364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/11/2015] [Indexed: 12/19/2022] Open
Abstract
A combination of the advanced chemometrics method with quantum mechanics calculation was for the first time applied to explore a facile yet efficient analysis strategy to thoroughly resolve femtosecond transient absorption spectroscopy of ortho-nitroaniline (ONA), served as a model compound of important nitroaromatics and explosives. The result revealed that the ONA molecule is primarily excited to S3 excited state from the ground state and then ultrafast relaxes to S2 state. The internal conversion from S2 to S1 occurs within 0.9 ps. One intermediate state S* was identified in the intersystem crossing (ISC) process, which is different from the specific upper triplet receiver state proposed in some other nitroaromatics systems. The S1 state decays to the S* one within 6.4 ps and then intersystem crossing to the lowest triplet state within 19.6 ps. T1 was estimated to have a lifetime up to 2 ns. The relatively long S* state and very long-lived T1 one should play a vital role as precursors to various nitroaromatic and explosive photoproducts.
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Affiliation(s)
- Jing Yi
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Ying Xiong
- Institute of Chemical Material, China Academy of Engineering Physics (CAEP), Mianyang 621900, People's Republic of China
| | - Kemei Cheng
- Institute of Chemical Material, China Academy of Engineering Physics (CAEP), Mianyang 621900, People's Republic of China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Genbai Chu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, People's Republic of China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Tao Xu
- Institute of Chemical Material, China Academy of Engineering Physics (CAEP), Mianyang 621900, People's Republic of China
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55
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Stephansen AB, Larsen MAB, Sølling TI. The involvement of triplet receiver states in the ultrafast excited state processes of small esters. Phys Chem Chem Phys 2016; 18:24484-97. [DOI: 10.1039/c6cp04046b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The photoinduced processes of methyl formate and methyl acetate have been probed by femtosecond time-resolved mass spectrometry and photoelectron spectroscopy experiments supported by quantum chemical calculations.
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Affiliation(s)
- A. B. Stephansen
- Department of Chemistry
- Københavns Universitet Det Natur- og Biovidenskabelige Fakultet
- København Ø
- Denmark
| | - M. A. B. Larsen
- Department of Chemistry
- Københavns Universitet Det Natur- og Biovidenskabelige Fakultet
- København Ø
- Denmark
| | - T. I. Sølling
- Department of Chemistry
- Københavns Universitet Det Natur- og Biovidenskabelige Fakultet
- København Ø
- Denmark
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56
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Brister MM, Pollum M, Crespo-Hernández CE. Photochemical etiology of promising ancestors of the RNA nucleobases. Phys Chem Chem Phys 2016; 18:20097-103. [DOI: 10.1039/c6cp00639f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Barbituric acid and 2,4,6-triaminopyrimidine dissipate ultraviolet radiation efficiently as heat to the environment, thus supporting their feasibility as prebiotic ancestors to the RNA nucleobases.
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Affiliation(s)
- M. M. Brister
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- Cleveland
- USA
| | - M. Pollum
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- Cleveland
- USA
| | - C. E. Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- Cleveland
- USA
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57
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Brister MM, Crespo-Hernández CE. Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil. J Phys Chem Lett 2015; 6:4404-9. [PMID: 26538051 DOI: 10.1021/acs.jpclett.5b01901] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations.
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Affiliation(s)
- Matthew M Brister
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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Chaiwongwattana S, Sapunar M, Ponzi A, Decleva P, Došlić N. Exploration of Excited State Deactivation Pathways of Adenine Monohydrates. J Phys Chem A 2015; 119:10637-44. [DOI: 10.1021/acs.jpca.5b07496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Marin Sapunar
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Aurora Ponzi
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Piero Decleva
- Dipartimento di
Scienze Chimiche, Università di Trieste, 34127 Trieste, Italy
| | - Nađa Došlić
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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59
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Mai S, Marquetand P, González L. A Static Picture of the Relaxation and Intersystem Crossing Mechanisms of Photoexcited 2-Thiouracil. J Phys Chem A 2015; 119:9524-33. [PMID: 26284285 PMCID: PMC4568544 DOI: 10.1021/acs.jpca.5b06639] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/17/2015] [Indexed: 12/02/2022]
Abstract
Accurate excited-state quantum chemical calculations on 2-thiouracil, employing large active spaces and up to quadruple-ζ quality basis sets in multistate complete active space perturbation theory calculations, are reported. The results suggest that the main relaxation path for 2-thiouracil after photoexcitation should be S2 → S1 → T2 → T1, and that this relaxation occurs on a subpicosecond time scale. There are two deactivation pathways from the initially excited bright S2 state to S1, one of which is nearly barrierless and should promote ultrafast internal conversion. After relaxation to the S1 minimum, small singlet-triplet energy gaps and spin-orbit couplings of about 130 cm(-1) are expected to facilitate intersystem crossing to T2, from where very fast internal conversion to T1 occurs. An important finding is that 2-thiouracil shows strong pyramidalization at the carbon atom of the thiocarbonyl group in several excited states.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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