1
|
Cherneva TD, Todorova MM, Bakalska RI, Shterev IG, Horkel E, Delchev VB. Experimental and theoretical study of the cytosine tautomerism through excited states. J Mol Model 2023; 29:303. [PMID: 37665380 DOI: 10.1007/s00894-023-05707-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
CONTEXT The irradiation of water solution of cytosine with UV light (λmax = 254 nm) shows oxo-hydroxy tautomerism with a rate constant of 6.297 × 10-3 min-1. The order of the reaction implies a tautomeric conversion. After removing the UV light source, we observed a dark reaction with a rate constant of 1.473 × 10-3 min-1 which leads to a restoration of the initial tautomer as before the irradiation. The mechanism of oxo-hydroxy tautomerism of cytosine in water solution was studied in the excited state. It was found that the transformations occur along the 1πσ* excited-state reaction paths which link the Franck-Condon geometries of the tautomers and the conical intersections S0/S1 connected with the H-detachment processes of the corresponding bonds. Furthermore, we established that the conical intersections S0/S1 are also mutually accessible along the 1πσ* excited-state reaction paths. METHODS The ground-state equilibrium geometries were optimized at the B3LYP/aug-cc-pVDZ level of theory in water environment according to PCM as well as at the CC2/aug-cc-pVDZ level in the gas phase. The TD B3LYP and CC2 methods were applied for the study of the excited states. The tautomerization mechanisms were studied with the use of the linear interpolation in internal coordinates approach using the optimized geometries of tautomers minima and conical intersections S0/S1 at the CASSCF(6,6)/6-31G* level. All calculations were performed with the GAUSSIAN 16 commercial software.
Collapse
Affiliation(s)
- Tsvetina D Cherneva
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria
| | - Mina M Todorova
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria
| | - Rumyana I Bakalska
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria
| | - Ivan G Shterev
- Department of Inorganic and Physical Chemistry, University of Food Technologies, 4002, Plovdiv, Bulgaria
| | - Ernst Horkel
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Vassil B Delchev
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria.
| |
Collapse
|
2
|
Boeije Y, Olivucci M. From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chem Soc Rev 2023; 52:2643-2687. [PMID: 36970950 DOI: 10.1039/d2cs00719c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.
Collapse
Affiliation(s)
- Yorrick Boeije
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Massimo Olivucci
- Chemistry Department, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, USA
| |
Collapse
|
3
|
Cherneva TD, Todorova MM, Bakalska RI, Horkel E, Delchev VB. Non-radiative deactivation of excited cytosine: probing of different DFT functionals and basis sets in solvents with different polarity. J Mol Model 2022; 28:306. [PMID: 36085333 DOI: 10.1007/s00894-022-05313-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
The vertical excitation and emission energies of the cytosine oxo-amino form were calculated at the TD DFT level of theory with several functionals, basis sets, and solvents with different polarity (PCM). They were compared with the experimental UV absorption and fluorescence maxima, revealing that the minimal deviation of the vertical excitation energies from the of UV absorption maxima can be achieved when the hybrid functional B3LYP is applied within the calculations. Regular correlations like curves with saturation between the vertical excitation/emission energies and the dielectric constants were registered. The relaxation of the 1ππ* excited state through an ethylene-like conical intersection S0/S1 should occur through decrease of the decay rate (commented qualitatively here) with the rise of the solvent polarity.
Collapse
Affiliation(s)
- T D Cherneva
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, Plovdiv, Bulgaria
| | - M M Todorova
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, Plovdiv, Bulgaria
| | - R I Bakalska
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, Plovdiv, Bulgaria
| | - E Horkel
- Inst. Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - V B Delchev
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, Plovdiv, Bulgaria.
| |
Collapse
|
4
|
Lapinski L, Rostkowska H, Nowak MJ. Distinct class of photoinduced hydrogen-atom-transfer processes: phototautomerizations in molecules with no intramolecular hydrogen bond in the structure. INT REV PHYS CHEM 2022. [DOI: 10.1080/0144235x.2022.2030613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Delchev VB, Shterev IG. CRYSTAL STRUCTURE AND PHOTOCHEMISTRY OF 5-AZACYTOSINE: EXPERIMENTAL AND THEORETICAL STUDY. J STRUCT CHEM+ 2022. [DOI: 10.1134/s0022476622030015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Romeo-Gella F, Arpa EM, Corral I. A molecular insight into the photophysics of barbituric acid, a candidate for canonical nucleobases' ancestor. Phys Chem Chem Phys 2022; 24:1405-1414. [PMID: 34982082 DOI: 10.1039/d1cp04987a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This work investigates the photophysics of barbituric acid at different pH conditions using ab initio methods. Our calculations ascribe the most intense bands at ca. 260 nm at neutral pH and 210 nm at acidic pH conditions in the absorption spectra of this chromophore to the lowest lying ππ* transitions. Consistently with the ultrashort excited state lifetimes experimentally registered, the potential energy landscapes of both the neutral and deprotonated forms of barbituric acid combined with the interpretation of their transient absorption spectra suggest the deactivation of these systems along the singlet manifold. Compared to uracil, its closest natural nucleobase, barbituric acid presents a red shifted absorption spectrum, due to the lowering by more than 0.5 eV of the lowest-energy ππ* excited state, and a much more complex topography of the S1 potential energy surface, with several energetically accessible local minima. This fact, however, does not affect the excited state lifetimes, which for barbituric acid were experimentally registered in the sub-ps time scale.
Collapse
Affiliation(s)
- Fernando Romeo-Gella
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Enrique M Arpa
- Departamento de Química, Módulo 13, 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
| |
Collapse
|
8
|
Photoinduced phenomena in water solution of melamine explaining the photostability of the compound. J Mol Model 2021; 27:196. [PMID: 34104983 DOI: 10.1007/s00894-021-04809-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
Two tautomers of melamine (triamino and imino-diamino) were studied at the BLYP/aug-cc-pVDZ theoretical level. It was found that the two tautomers are bridged with the 1πσ* excited-state reaction path. The high photostability of melamine in water solution was explained with the mechanism of ring deformation which occurs along the 1ππ* excited-state reaction path. The two mechanisms are investigated at the TD BLYP level of theory using the linear interpolation in internal coordinates approach.
Collapse
|
9
|
Shahrokh L, Omidyan R, Azimi G. Theoretical insights on the excited-state-deactivation mechanisms of protonated thymine and cytosine. Phys Chem Chem Phys 2021; 23:8916-8925. [PMID: 33876051 DOI: 10.1039/d0cp06673g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ab initio and surface-hopping nonadiabatic dynamics simulation methods were employed to investigate relaxation mechanisms in protonated thymine (TH+) and cytosine (CH+). A few conical intersections were located between 1ππ* and S0 states for each system with the CASSCF (8,8) theoretical model and relevant contributions to the deactivation mechanism of titled systems were addressed by the determination of potential energy profiles at the CASPT2 (12,10) theoretical level. It was revealed that the relaxation of the 1ππ* state of the most stable conformer of both systems to the ground state is mostly governed by the accessible S1/S0 conical intersection resulting from the barrier-free out-of-plane deformation. Interestingly, it was exhibited that the ring puckering coordinate driven from the C6 position of the heterocycle ring in TH+ and CH+ plays the most prominent role in the deactivation mechanism of considered systems. Our ab initio results are also supported by excited-state nonadiabatic dynamics simulations based on ADC(2), describing the ultrashort S1 lifetime of TH+/CH+ by analyzing trajectories leading excited systems to the ground. It was confirmed that the excited-state population mostly relaxes to the ground via the ring puckering coordinate from the C6 moiety. Overall, the theoretical results of this study shed light on the deactivation mechanism of protonated DNA bases.
Collapse
Affiliation(s)
- Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441, Isfahan, Iran.
| | | | | |
Collapse
|
10
|
Zhang K, Wang F, Jiang Y, Wang X, Pan H, Sun Z, Sun H, Xu J, Chen J. New Insights about the Photostability of DNA/RNA Bases: Triplet nπ* State Leads to Effective Intersystem Crossing in Pyrimidinones. J Phys Chem B 2021; 125:2042-2049. [PMID: 33600186 DOI: 10.1021/acs.jpcb.0c10611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The high photostability of DNA/RNA nucleobases is attributed to the effective internal conversions of their bright 1ππ* states to the ground state through conical intersections. Intersystem crossing (ISC) from singlet to triplet excited states is a minor decay pathway in nucleobases and it is observed with ∼1-2% quantum yields (QYs) in pyrimidine bases. Presumably, ISC in pyrimidines takes place from the dark singlet 1nπ* state to the lowest triplet 3ππ* state. However, recent studies showed that ISC from the initial populated bright 1ππ* state to higher energy triplet 3nπ* states indeed occurs in the subpicosecond timescale. Such a mechanism is still poorly understood since direct observation of this pathway is challenging. Herein, excited state dynamics of three pyrimidinones, which share the same skeleton with pyrimidine bases, is investigated in different solvents. Compared to canonical pyrimidine bases, removing the oxygen atom at the C4 position revokes the low-lying dark 1nπ* state in pyrimidinones, resulting in direct ISC from the S1 (1ππ*) state to triplet T3 (3nπ*) state with much higher QYs. Meanwhile, hydrogen bonding between the carbonyl group in pyrimidinones and protic solvents can accelerate vibrational cooling of the hot S1 (1ππ*) state, leading to higher fluorescence QYs and smaller ISC rate constants. These results not only evidence the hypothesis of the direct 1ππ* → 3nπ* ISC mechanism, but also contribute to a better understanding of triplet formation in pyrimidines.
Collapse
Affiliation(s)
- Kun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Fufang Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
11
|
Noble JA, Marceca E, Dedonder C, Phasayavan W, Féraud G, Inceesungvorn B, Jouvet C. Influence of the N atom position on the excited state photodynamics of protonated azaindole. Phys Chem Chem Phys 2020; 22:27280-27289. [PMID: 33227118 DOI: 10.1039/d0cp03608k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a study of the photofragmentation of three protonated azaindole molecules - 7-azaindole, 6-azaindole, and 5-azaindole - consisting of fused pyrrole-pyridine bicyclic aromatic systems, in which the pyridinic (protonated) nitrogen heteroatom is located at the 7, 6, and 5 positions, respectively. Photofragmentation electronic spectra of the isolated aforementioned azaindolinium cations reveal that their photodynamics extends over timescales covering nine orders of magnitude and provide evidence about the resultant fragmentation pathways. Moreover, we show how the position of the heteroatom in the aromatic skeleton influences the excited state energetics, fragmentation pathways, and fragmentation timescales. Computed ab initio adiabatic transition energies are used to assist the assignation of the spectra, while geometry optimisation in the excited electronic states as well as ab initio calculations along the potential surfaces demonstrate the role of ππ*/πσ* coupling and/or large geometry changes in the dynamics of these species. Evidence supporting the formation of Dewar valence isomers as intermediates involved in sub-picosecond relaxation processes is discussed.
Collapse
Affiliation(s)
- Jennifer A Noble
- CNRS, Aix Marseille Univ., PIIM, Physique des Interactions Ioniques et Moléculaires, UMR 7345, 13397, Marseille, France.
| | | | | | | | | | | | | |
Collapse
|
12
|
Omidyan R, Abedini F, Shahrokh L, Azimi G. Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies. J Phys Chem A 2020; 124:5089-5097. [PMID: 32469520 DOI: 10.1021/acs.jpca.0c02284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have conducted here a theoretical exploration, discussing the distinct excited state lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this regard, the first-principal computational levels as well as the nonadiabatic surface hopping dynamics have been employed. It has been revealed that relaxation of the 1ππ* state of enol-enol form (EE+) to the ground is barrier-free via out-of-plane coordinates, resulting in an ultrashort S1 lifetime of this species. For the second most stable isomer (EK+), however, a significant barrier predicted in the CASPT2 S1 potential energy profile along the twisting coordinate has been proposed to explain the relevant long lifetime reported experimentally.
Collapse
Affiliation(s)
- Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Fatemeh Abedini
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Gholamhassan Azimi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| |
Collapse
|
13
|
Excited-state photocycodimerization of 6-azauracil to oxazetidine cyclodimer: A mechanism elucidation in water surroundings. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
14
|
Dimitrov BH, Bakalska RI, Delchev VB. Phototautomerism of Isocytosine in a Water Medium: Theoretical and Experimental Study. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619060040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Karsili TN, Marchetti B, Ashfold MN. The role of 1πσ∗ states in the formation of adenine radical-cations in DNA duplexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
16
|
Yankov EP, Bakalska RI, Horkel E, Svatunek D, Delchev VB. Experimental and theoretical study of the excited-state tautomerism of 6-azauracil in water surroundings. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
17
|
Ghafur O, Crane SW, Ryszka M, Bockova J, Rebelo A, Saalbach L, De Camillis S, Greenwood JB, Eden S, Townsend D. Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source. J Chem Phys 2018; 149:034301. [DOI: 10.1063/1.5034419] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Omair Ghafur
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Stuart W. Crane
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Michal Ryszka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jana Bockova
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Andre Rebelo
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
- CEFITEC, Departamento de Física, FCT–Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal
| | - Lisa Saalbach
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Simone De Camillis
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jason B. Greenwood
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Samuel Eden
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| |
Collapse
|
18
|
Baker LA, Marchetti B, Karsili TNV, Stavros VG, Ashfold MNR. Photoprotection: extending lessons learned from studying natural sunscreens to the design of artificial sunscreen constituents. Chem Soc Rev 2018; 46:3770-3791. [PMID: 28580469 DOI: 10.1039/c7cs00102a] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Evolution has ensured that plants and animals have developed effective protection mechanisms against the potentially harmful effects of incident ultraviolet radiation (UVR). Tanning is one such mechanism in humans, but tanning only occurs post-exposure to UVR. Hence, there is ever growing use of commercial sunscreens to pre-empt overexposure to UVR. Key requirements for any chemical filter molecule used in such a photoprotective capacity include a large absorption cross-section in the UV-A and UV-B spectral regions and the availability of one or more mechanisms whereby the absorbed photon energy can be dissipated without loss of the molecular integrity of the chemical filter. Here we summarise recent experimental (mostly ultrafast pump-probe spectroscopy studies) and computational progress towards unravelling various excited state decay mechanisms that afford the necessary photostability in chemical filters found in nature and those used in commercial sunscreens. We also outline ways in which a better understanding of the photophysics and photochemistry of sunscreen molecules selected by nature could aid the design of new and improved commercial sunscreen formulations.
Collapse
Affiliation(s)
- Lewis A Baker
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Barbara Marchetti
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | | | - Vasilios G Stavros
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| |
Collapse
|
19
|
Al-Ansari IAZ. Role of Solvent Polarity and Hydrogen-Bonding on Excited-State Fluorescence of 3-[(E)-{4-[Dimethylamino]benzylidene}amino]-2-naphthoic Acid (DMAMN): Isomerization vs Rotomerization. J Phys Chem A 2018; 122:1838-1854. [PMID: 29381869 DOI: 10.1021/acs.jpca.7b11623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present experimental and theoretical study on a new chromophore DMAMN of the type push-π-pull (push = dimethylaniline, π = imine, pull = 2-naphthoic acid), allows understanding of the mechanism by which the molecular conformational undergoes isomerization/rotomerization following electronic excitation. The steady-state fluorescence spectra of this compound, carried out in solvents of different polarities and proticities, showed significant changes in both the shape and peak positions. The wavelength and intensity change depend on the polarity and hydrogen-bonding environment. In highly polar solvents, the emission is weak and red-shifted compared to that for cyclohexane, but it is more red-shifted in moderate aprotic polar solvents. In hydroxyl solvents, a new weak low-energy emission band appears at ∼525 nm, attributed to the intermolecularly H-bonded open conformer. On the basis of the generated potential energy landscapes of the ground state and low-lying excited state in the gas phase and solution, we found that selective photon absorption, brings this molecule to a "bright" state, from which N═C isomerization Z → E, takes place. This isomerization in gas-phase and low-polarity solvents leads to two minima with a barrier, whereas in highly polar-protic media, it gives one minimum on the S1 surface with low ΔES1/T1 (0.17 eV), facilitating deactivation via ISC.
Collapse
Affiliation(s)
- Ibrahim Ahmed Z Al-Ansari
- Department of Chemistry & Earth Sciences, College of Arts & Sciences, Qatar University , P.O. Box 2713, Doha, Qatar
| |
Collapse
|
20
|
Karsili TNV, Marchetti B, Matsika S. Origins of Photodamage in Pheomelanin Constituents: Photochemistry of 4-Hydroxybenzothiazole. J Phys Chem A 2018; 122:1986-1993. [DOI: 10.1021/acs.jpca.7b09690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tolga N. V. Karsili
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Barbara Marchetti
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
21
|
Marchetti B, Karsili TNV, Ashfold MNR, Domcke W. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs. Phys Chem Chem Phys 2018; 18:20007-27. [PMID: 26980149 DOI: 10.1039/c6cp00165c] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.
Collapse
Affiliation(s)
- Barbara Marchetti
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Tolga N V Karsili
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| |
Collapse
|
22
|
Bil A, Latajka Z, Biczysko M. Hydrogen detachment driven by a repulsive 1πσ* state – an electron localization function study of 3-amino-1,2,4-triazole. Phys Chem Chem Phys 2018; 20:5210-5216. [DOI: 10.1039/c7cp06744e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron localization function analysis reveals the details of a charge induced hydrogen detachment mechanism of 3-amino-1,2,4-triazole, identified recently as responsible for phototautomerization of the molecule.
Collapse
Affiliation(s)
- Andrzej Bil
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | | | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures (ICQMS)
- College of Sciences
- Shanghai University
- 200444 Shanghai
- China
| |
Collapse
|
23
|
Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
| |
Collapse
|
24
|
Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| |
Collapse
|
25
|
Shterev IG, Delchev VB. Phototransformations in m-aminophenol: A theoretical and experimental study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
26
|
Keefer D, Thallmair S, Matsika S, de Vivie-Riedle R. Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment. J Am Chem Soc 2017; 139:5061-5066. [DOI: 10.1021/jacs.6b12033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Keefer
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Sebastian Thallmair
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | | |
Collapse
|
27
|
Pino GA, Feraud G, Broquier M, Grégoire G, Soorkia S, Dedonder C, Jouvet C. Non-radiative processes in protonated diazines, pyrimidine bases and an aromatic azine. Phys Chem Chem Phys 2016; 18:20126-34. [PMID: 27110833 DOI: 10.1039/c6cp01345g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state lifetimes of DNA bases are often very short due to very efficient non-radiative processes assigned to the ππ*-nπ* coupling. A set of protonated aromatic diazine molecules (pyridazine, pyrimidine and pyrazine C4H5N2(+)) and protonated pyrimidine DNA bases (cytosine, uracil and thymine), as well as the protonated pyridine (C5H6N(+)), have been investigated. For all these molecules except one tautomer of protonated uracil (enol-keto), electronic spectroscopy exhibits vibrational line broadening. Excited state geometry optimization at the CC2 level has been conducted to find out whether the excited state lifetimes measured from line broadening can be correlated to the calculated ordering of the ππ* and nπ* states and the ππ*-nπ* energy gap. The short lifetimes, observed when one nitrogen atom of the ring is not protonated, can be rationalized by relaxation of the ππ* state to the nπ* state or directly to the electronic ground state through ring puckering.
Collapse
Affiliation(s)
- Gustavo A Pino
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC) CONICET - UNC. Dpto. de Fisicoquímica - Facultad de Ciencias Químicas - Centro Láser de Ciencias Moleculares - Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Géraldine Feraud
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France.
| | - Michel Broquier
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France and Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Gilles Grégoire
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France and Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Satchin Soorkia
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France and Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Claude Dedonder
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France.
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France.
| |
Collapse
|
28
|
Kancheva P, Tuna D, Delchev VB. Comparative study of radiationless deactivation mechanisms in cytosine and 2,4-diaminopyrimidine. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
29
|
Shterev IG, Delchev VB. Excited-state deactivation channels via internal conversions in two position isomers of hydroxy-methyl-pyridine: a theoretical study. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ivan G. Shterev
- Department Inorganic and Physical Chemistry; University of Food Technologies; 4002 Plovdiv Bulgaria
| | - Vassil B. Delchev
- Department of Physical Chemistry; University of Plovdiv; 4000 Plovdiv Bulgaria
| |
Collapse
|
30
|
Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S, Pollum M, Marquetand P, González L, Corral I. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J Am Chem Soc 2015; 137:4368-81. [PMID: 25763596 PMCID: PMC4410903 DOI: 10.1021/ja512536c] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/20/2022]
Abstract
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.
Collapse
Affiliation(s)
- Carlos E. Crespo-Hernández
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| | - Clemens Rauer
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Christian Reichardt
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Marvin Pollum
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Inés Corral
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
31
|
Féraud G, Berdakin M, Dedonder C, Jouvet C, Pino GA. Excited states of proton-bound DNA/RNA base homodimers: pyrimidines. J Phys Chem B 2014; 119:2219-28. [PMID: 25046334 DOI: 10.1021/jp505756a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homodimers. Only the thymine dimer exhibits a well structured vibrational progression, while the protonated monomer shows broad vibrational bands. This shows that proton bonding can block some nonradiative processes present in the monomer.
Collapse
Affiliation(s)
- Géraldine Féraud
- Physique des Interactions Ioniques et Moléculaires (PIIM), UMR 7345, CNRS, Aix-Marseille Université , 13397 Marseille Cedex 20, France
| | | | | | | | | |
Collapse
|
32
|
Franzen S, Skalski B, Bartolotti L, Delley B. The coupling of tautomerization to hydration in the transition state on the pyrimidine photohydration reaction path. Phys Chem Chem Phys 2014; 16:20164-74. [DOI: 10.1039/c4cp02160f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Park JW, Rhee YM. Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian. Chemphyschem 2014; 15:3183-93. [DOI: 10.1002/cphc.201402226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/13/2022]
|
34
|
Berdakin M, Féraud G, Dedonder-Lardeux C, Jouvet C, Pino GA. Effect of Ag(+) on the Excited-State Properties of a Gas-Phase (Cytosine)2Ag(+) Complex: Electronic Transition and Estimated Lifetime. J Phys Chem Lett 2014; 5:2295-2301. [PMID: 26279549 DOI: 10.1021/jz5009455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recently, DNA molecules have received great attention because of their potential applications in material science. One interesting example is the production of highly fluorescent and tunable DNA-Agn clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine···Ag(+)···cytosine (C2Ag(+)) and cytosine···H(+)···cytosine (C2H(+)) complexes together with theoretical calculations. In both cases, the excitation energy does not differ significantly from that of isolated cytosine or protonated cytosine, indicating that the excitation takes place on the DNA base. However, the excited-state lifetime of the C2H(+) (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C2Ag(+) (τ > 5000 fs). The increased excited-state lifetime upon silver complexation is quite unexpected, and it clearly opens the question about what factors are controlling the nonradiative decay in pyrimidine DNA bases. This is an important result for the expanding field of metal-mediated base pairing and may also be important to the photophysical properties of DNA-templated fluorescent silver clusters.
Collapse
Affiliation(s)
- Matias Berdakin
- †INFIQC (CONICET - UNC), Departamento de Fisicoquı́mica, Facultad de Ciencias Quı́micas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Géraldine Féraud
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix Marseille Université: UMR-7345, 13397 Marseille, France
| | - Claude Dedonder-Lardeux
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix Marseille Université: UMR-7345, 13397 Marseille, France
| | - Christophe Jouvet
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix Marseille Université: UMR-7345, 13397 Marseille, France
| | - Gustavo A Pino
- †INFIQC (CONICET - UNC), Departamento de Fisicoquı́mica, Facultad de Ciencias Quı́micas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| |
Collapse
|
35
|
Shterev IG, Delchev VB. Solvent influence on the excited states of the oxo form of barbituric acid and the mechanisms of the out-of-plane non-radiative elongation of the N-H bond: a comparative theoretical and experimental study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 125:384-390. [PMID: 24566117 DOI: 10.1016/j.saa.2014.01.124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/07/2014] [Accepted: 01/26/2014] [Indexed: 06/03/2023]
Abstract
The solvent influence on the excited states, emission and absorption energies of the oxo for of barbituric acid was studied with experimental (UV and fluorescence spectra) and theoretical methods. The excited-state reaction paths of the out-pf-plane elongation of the N-H bond of the oxo form of barbituric acid were also investigated (TD DFT level) to the conical intersections mediating internal conversions to the ground state. The (1)nσ* excited state was found to be the driven electronic state. We found that the increase of the polarity of the solvent reduces the (1)nσ* excited state decay rate through a non-planar conical intersection and increases its energy. Thus, solvents with higher polarity disfavor the non-radiative decay through conical intersections.
Collapse
Affiliation(s)
- Ivan G Shterev
- Dept. Inorganic and Physical Chemistry, University of Food Technologies, Maritza 26 Str., 4002 Plovdiv, Bulgaria
| | - Vassil B Delchev
- Dept. Physical Chemistry, University of Plovdiv, Tzar Assen 24 Str., 4000 Plovdiv, Bulgaria.
| |
Collapse
|
36
|
Fingerhut BP, Dorfman KE, Mukamel S. Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations. J Chem Theory Comput 2014; 10:1172-1188. [PMID: 24803857 PMCID: PMC3958139 DOI: 10.1021/ct401012u] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 11/29/2022]
Abstract
![]()
Nonadiabatic electron
and nuclear dynamics of photoexcited molecules
involving conical intersections is of fundamental importance in many
reactions such as the self-protection mechanism of DNA and RNA bases
against UV irradiation. Nonlinear vibrational spectroscopy can provide
an ultrafast sensitive probe for these processes. We employ a simulation
protocol that combines nonadiabatic on-the-fly molecular dynamics
with a mode-tracking algorithm for the simulation of femtosecond stimulated
Raman spectroscopy (SRS) signals of the high frequency C–H-
and N–H-stretch vibrations of the photoexcited RNA base uracil.
The simulations rely on a microscopically derived expression that
takes into account the path integral of the excited state evolution
and the pulse shapes. Analysis of the joint time/frequency resolution
of the technique reveals a matter chirp contribution that limits the
inherent temporal resolution. Characteristic signatures of relaxation
dynamics mediated in the vicinity of conical intersection are predicted.
The C–H and N–H spectator modes provide high sensitivity
to their local environment and act as local probes with submolecular
and high temporal resolution.
Collapse
Affiliation(s)
- Benjamin P Fingerhut
- Department of Chemistry, University of California , Irvine, California 92697-2025, United States
| | - Konstantin E Dorfman
- Department of Chemistry, University of California , Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department of Chemistry, University of California , Irvine, California 92697-2025, United States
| |
Collapse
|
37
|
Roberts GM, Stavros VG. The role of πσ* states in the photochemistry of heteroaromatic biomolecules and their subunits: insights from gas-phase femtosecond spectroscopy. Chem Sci 2014. [DOI: 10.1039/c3sc53175a] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
|
38
|
|
39
|
Matsika S, Spanner M, Kotur M, Weinacht TC. Ultrafast Relaxation Dynamics of Uracil Probed via Strong Field Dissociative Ionization. J Phys Chem A 2013; 117:12796-801. [DOI: 10.1021/jp408073d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | | | - Marija Kotur
- Department
of Physics, Lund University, 221 00 Lund, Sweden
| | - Thomas C. Weinacht
- Department
of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11790, United States
| |
Collapse
|
40
|
Delchev VB, Domcke W. Ab initio study of the cyclodimerization of uracil through butane-like and oxetane-like conical intersections. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
41
|
Fingerhut BP, Dorfman KE, Mukamel S. Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy. J Phys Chem Lett 2013; 4:1933-1942. [PMID: 23914288 PMCID: PMC3728908 DOI: 10.1021/jz400776r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale.
Collapse
Affiliation(s)
| | | | - Shaul Mukamel
- Chemistry Department, University of California, Irvine, California 92697-2025, USA
| |
Collapse
|
42
|
Excited-state relaxation paths of oxo/hydroxy and N9H/N7H tautomers of guanine: a CC2 theoretical study. J Mol Model 2013; 19:2299-308. [DOI: 10.1007/s00894-013-1774-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 01/15/2013] [Indexed: 11/30/2022]
|
43
|
Villabona-Monsalve JP, Islas RE, Rodríguez-Córdoba W, Matsika S, Peón J. Ultrafast Excited State Dynamics of Allopurinol, a Modified DNA Base. J Phys Chem A 2013; 117:898-904. [DOI: 10.1021/jp3107815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan P. Villabona-Monsalve
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, 04510,
D.F., México
| | - Rosa E. Islas
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, 04510,
D.F., México
| | - William Rodríguez-Córdoba
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, 04510,
D.F., México
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, 13th and
Norris Streets, Philadelphia,
Pennsylvania 19122, United States
| | - Jorge Peón
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, 04510,
D.F., México
| |
Collapse
|
44
|
Excitation of Nucleobases from a Computational Perspective I: Reaction Paths. Top Curr Chem (Cham) 2013; 355:57-97. [DOI: 10.1007/128_2013_501] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
45
|
Yang YL, Ho YC, Dyakov YA, Hsu WH, Ni CK, Sun YL, Tsai WC, Hu WP. Effects of intramolecular hydrogen bonding on the excited state dynamics of phenol chromophores. Phys Chem Chem Phys 2013; 15:7182-90. [DOI: 10.1039/c3cp44674c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Fingerhut BP, Oesterling S, Haiser K, Heil K, Glas A, Schreier WJ, Zinth W, Carell T, de Vivie-Riedle R. ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization. J Chem Phys 2012; 136:204307. [PMID: 22667560 DOI: 10.1063/1.4720090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.
Collapse
Affiliation(s)
- Benjamin P Fingerhut
- Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Comparative study of the relaxation mechanisms of the excited states of cytosine and isocytosine. J Mol Model 2012; 18:5133-46. [DOI: 10.1007/s00894-012-1506-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
|
48
|
Delchev VB, Ivanova IP. Theoretical study of the excited-state reaction paths of the OH and NH dissociation processes in barbituric acid. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-012-0766-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
49
|
Excited-state deactivation of the monohydrated complexes of cytosine, uracil, and thymine through S0/S1 conical intersections. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-012-0720-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
50
|
Yamazaki S, Taketsugu T. Nonradiative Deactivation Mechanisms of Uracil, Thymine, and 5-Fluorouracil: A Comparative ab Initio Study. J Phys Chem A 2011; 116:491-503. [DOI: 10.1021/jp206546g] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shohei Yamazaki
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| |
Collapse
|