101
|
Wang X, Martínez-Fernández L, Zhang Y, Zhang K, Improta R, Kohler B, Xu J, Chen J. Solvent-Dependent Stabilization of a Charge Transfer State is the Key to Ultrafast Triplet State Formation in an Epigenetic DNA Nucleoside. Chemistry 2021; 27:10932-10940. [PMID: 33860588 DOI: 10.1002/chem.202100787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/10/2022]
Abstract
2'-Deoxy-5-formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time-resolved mid-IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM-TD-DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine-to-formyl charge-transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark 1 nπ* state with a lifetime of ∼3 ps. CT-induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non-radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited-state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.
Collapse
Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid Campus de Excelencia UAM-CSIC Cantoblanco, 28049, Madrid, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Kun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, P. R. China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, P. R. China
| |
Collapse
|
102
|
Zhou P, Tang Z, Li P, Liu J. Unraveling the Mechanism for Tuning the Fluorescence of Fluorescein Derivatives: The Role of the Conical Intersection and nπ* State. J Phys Chem Lett 2021; 12:6478-6485. [PMID: 34240884 DOI: 10.1021/acs.jpclett.1c01774] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although a large number of fluorescein derivatives have been developed and applied in many different fields, the general mechanisms for tuning the fluorescence of fluorescein derivatives still remain uncovered. Herein, we found that the fluorescence quenching of neutral form of fluorescein derivatives in acidic medium resulted from a dark nπ* state, whereas the fluorescence of the anionic form of fluorescein derivatives in the gas phase and alkaline solutions was tuned by minimal energy conical intersection (MECI). The formation of MECI involved significant rotation of benzene ring and flip-flop motion of xanthene moiety, which would be restricted by intermolecular hydrogen bonding and lowering temperature. The energy barrier for reaching MECI depended on the substituents in the benzene moiety in accordance with experimentally observed substituent effects. These unprecedented mechanisms would lead to a recognition of fluorescein derivatives and could provide a correct and instructive design strategy for further developing new fluorescein derivatives.
Collapse
Affiliation(s)
- Panwang Zhou
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P. R. China
| | - Zhe Tang
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P. R. China
| | | | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, Liaoning China
| |
Collapse
|
103
|
Sahharova LT, Gordeev EG, Eremin DB, Ananikov VP. Computational Design of Radical Recognition Assay with the Possible Application of Cyclopropyl Vinyl Sulfides as Tunable Sensors. Int J Mol Sci 2021; 22:7637. [PMID: 34299255 PMCID: PMC8306039 DOI: 10.3390/ijms22147637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity of a radical may be assessed. The idea is to utilize a set of radical-sensitive molecules as tunable sensors, followed by insight into the studied radical species based on the observed reactivity/selectivity. We utilize this approach for selective recognition of common radicals-alkyl, phenyl, and iodine. By matching quantum chemical calculations with experimental data, we show that components of a system react differently with the studied radicals. Possible radical generation processes were studied involving model reactions under UV light and metal-catalyzed conditions.
Collapse
Affiliation(s)
| | | | | | - Valentine P. Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia; (L.T.S.); (E.G.G.); (D.B.E.)
| |
Collapse
|
104
|
Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Time Resolved Photoelectron Spectroscopy as a Test of Electronic Structure and Nonadiabatic Dynamics. J Phys Chem Lett 2021; 12:5099-5104. [PMID: 34028278 DOI: 10.1021/acs.jpclett.1c00926] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We compare different levels of theory for simulating excited state molecular dynamics and use time-resolved photoelectron spectroscopy measurements to benchmark the theory. We perform trajectory surface hopping simulations for uracil excited to the first bright state (ππ*) using three different levels of theory (CASSCF, MRCIS, and XMS-CASPT2) in order to understand the role of dynamical correlation in determining the excited state dynamics, with a focus on the coupling between different electronic states and internal conversion back to the ground state. These dynamics calculations are used to simulate the time-resolved photoelectron spectra. The comparison of the calculated and measured spectra allows us to draw conclusions regarding the relative insights and quantitative accuracy of the calculations at the three different levels of theory, demonstrating that detailed quantitative comparisons of time-resolved photoelectron spectra can be used to benchmark methodology.
Collapse
Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Samuel McClung
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
105
|
Suzuki T. Spiers Memorial Lecture: Introduction to ultrafast spectroscopy and imaging of photochemical reactions. Faraday Discuss 2021; 228:11-38. [PMID: 33876168 DOI: 10.1039/d1fd00015b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A brief overview is presented on ultrafast spectroscopy and imaging of photochemical reactions by highlighting several experimental studies reported in the last five years. A particular focus is placed on new experiments performed using high-order harmonic generation, X-ray free electron lasers, and relativistic electron beams. Exploration of fundamental chemical reaction dynamics using these advanced experimental methodologies is in an early stage, and exciting new research opportunities await in this rapidly expanding and advancing research field. At the same time, there is no experimental methodology that provides all aspects of the electronic and structural dynamics in a single experiment, and investigations using different methodologies with various perspectives need to be considered in a comprehensive manner.
Collapse
Affiliation(s)
- Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| |
Collapse
|
106
|
Theoretical Study on the Photo-Oxidation and Photoreduction of an Azetidine Derivative as a Model of DNA Repair. Molecules 2021; 26:molecules26102911. [PMID: 34068908 PMCID: PMC8157190 DOI: 10.3390/molecules26102911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
Photocycloreversion plays a central role in the study of the repair of DNA lesions, reverting them into the original pyrimidine nucleobases. Particularly, among the proposed mechanisms for the repair of DNA (6-4) photoproducts by photolyases, it has been suggested that it takes place through an intermediate characterized by a four-membered heterocyclic oxetane or azetidine ring, whose opening requires the reduction of the fused nucleobases. The specific role of this electron transfer step and its impact on the ring opening energetics remain to be understood. These processes are studied herein by means of quantum-chemical calculations on the two azetidine stereoisomers obtained from photocycloaddition between 6-azauracil and cyclohexene. First, we analyze the efficiency of the electron-transfer processes by computing the redox properties of the azetidine isomers as well as those of a series of aromatic photosensitizers acting as photoreductants and photo-oxidants. We find certain stereodifferentiation favoring oxidation of the cis-isomer, in agreement with previous experimental data. Second, we determine the reaction profiles of the ring-opening mechanism of the cationic, neutral, and anionic systems and assess their feasibility based on their energy barrier heights and the stability of the reactants and products. Results show that oxidation largely decreases the ring-opening energy barrier for both stereoisomers, even though the process is forecast as too slow to be competitive. Conversely, one-electron reduction dramatically facilitates the ring opening of the azetidine heterocycle. Considering the overall quantum-chemistry findings, N,N-dimethylaniline is proposed as an efficient photosensitizer to trigger the photoinduced cycloreversion of the DNA lesion model.
Collapse
|
107
|
Park W, Lee S, Huix-Rotllant M, Filatov M, Choi CH. Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine. J Phys Chem Lett 2021; 12:4339-4346. [PMID: 33929858 DOI: 10.1021/acs.jpclett.1c00712] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S1-trapping, S2-trapping, and S1&S2-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. We show that the previously predicted S2-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S1-trapping mechanism with two lifetimes, τ1 = 30 ± 1 fs and τ2 = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S2 (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S2→S1 internal conversion and resides around the minimum on the S1 (nOπ*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S2→S1 internal conversion is mediated by fast bond length alternation distortion, the subsequent S1→S0 occurs through several conical intersections, involving a slow puckering motion.
Collapse
Affiliation(s)
- Woojin Park
- 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
| | | | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| |
Collapse
|
108
|
Barbatti M. Velocity Adjustment in Surface Hopping: Ethylene as a Case Study of the Maximum Error Caused by Direction Choice. J Chem Theory Comput 2021; 17:3010-3018. [PMID: 33844922 DOI: 10.1021/acs.jctc.1c00012] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The most common surface hopping dynamics algorithms require velocity adjustment after hopping to ensure total-energy conservation. Based on the semiclassical analysis, this adjustment must be made parallel to the nonadiabatic coupling vector's direction. Nevertheless, this direction is not always known, and the common practice has been to adjust the velocity in either the linear momentum or velocity directions. This paper benchmarks surface hopping dynamics of photoexcited ethylene with velocity adjustment in several directions, including those of the nonadiabatic coupling vector, the momentum, and the energy gradient difference. It is shown that differences in time constants and structural evolution fall within the statistical uncertainty of the method considering up to 500 trajectories in each dynamics set, rendering the three approaches statistically equivalent. For larger ensembles beyond 1000 trajectories, significant differences between the results arise, limiting the validity of adjustment in alternative directions. Other possible adjustment directions (velocity, single-state gradients, angular momentum) are evaluated as well. Given the small size of ethylene, the results reported in this paper should be considered an upper limit for the error caused by the choice of the velocity-adjustment direction on surface hopping dynamics.
Collapse
|
109
|
Lu C, Gutierrez-Bayona NE, Taylor JS. The effect of flanking bases on direct and triplet sensitized cyclobutane pyrimidine dimer formation in DNA depends on the dipyrimidine, wavelength and the photosensitizer. Nucleic Acids Res 2021; 49:4266-4280. [PMID: 33849058 PMCID: PMC8096240 DOI: 10.1093/nar/gkab214] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/15/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the major products of DNA produced by direct absorption of UV light, and result in C to T mutations linked to human skin cancers. Most recently a new pathway to CPDs in melanocytes has been discovered that has been proposed to arise from a chemisensitized pathway involving a triplet sensitizer that increases mutagenesis by increasing the percentage of C-containing CPDs. To investigate how triplet sensitization may differ from direct UV irradiation, CPD formation was quantified in a 129-mer DNA designed to contain all 64 possible NYYN sequences. CPD formation with UVB light varied about 2-fold between dipyrimidines and 12-fold with flanking sequence and was most frequent at YYYR and least frequent for GYYN sites in accord with a charge transfer quenching mechanism. In contrast, photosensitized CPD formation greatly favored TT over C-containing sites, more so for norfloxacin (NFX) than acetone, in accord with their differing triplet energies. While the sequence dependence for photosensitized TT CPD formation was similar to UVB light, there were significant differences, especially between NFX and acetone that could be largely explained by the ability of NFX to intercalate into DNA.
Collapse
Affiliation(s)
- Chen Lu
- Department of Chemistry, Washington University, One Brookings Dr., St. Louis, MO 63130, USA
| | | | - John-Stephen Taylor
- Department of Chemistry, Washington University, One Brookings Dr., St. Louis, MO 63130, USA
| |
Collapse
|
110
|
Castellani ME, Avagliano D, Verlet JRR. Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging. J Phys Chem A 2021; 125:3646-3652. [PMID: 33882670 DOI: 10.1021/acs.jpca.1c01646] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The excited state dynamics of the doubly deprotonated dianion of adenosine-5'-triphosphate, [ATP-H2]2-, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated 1ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the 1ππ* state is a resonance. The second is nuclear motion on the 1ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.
Collapse
Affiliation(s)
| | - Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17 1090 Vienna, Austria
| | - Jan R R Verlet
- Department of Chemistry, Durham University, DH1 3LE Durham, U.K
| |
Collapse
|
111
|
Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. Simulation of UV absorption spectra and relaxation dynamics of uracil and uracil-water clusters. Phys Chem Chem Phys 2021; 23:2594-2604. [PMID: 33475644 DOI: 10.1039/d0cp05618a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.
Collapse
Affiliation(s)
| | - Jurica Novak
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia. and Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| |
Collapse
|
112
|
Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
Collapse
Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| |
Collapse
|
113
|
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
|
114
|
Ultrafast investigation of intramolecular proton transfer dynamics and vibration relaxation in 1,8-dihydroxyanthraquinone. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
115
|
Pagacz-Kostrzewa M, Kochman M, Gul W, Wierzejewska M. Phototransformations of 2-aminonicotinic acid resolved with matrix isolation infrared spectroscopy and ab initio calculations. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
116
|
Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
Collapse
Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| |
Collapse
|
117
|
Chan RCT, Chan CTL, Ma C, Gu KY, Xie HX, Wong AKW, Xiong QW, Wang ML, Kwok WM. Long living excited state of protonated adenosine unveiled by ultrafast fluorescence spectroscopy and density functional theoretical study. Phys Chem Chem Phys 2021; 23:6472-6480. [PMID: 33729247 DOI: 10.1039/d0cp06439d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenosine (Ado) possesses ultrafast nonradiative dynamics accounting for its remarkably high photostability. The deactivation dynamics of Ado after protonation in an aqueous solution remains an elusive issue. Herein we report an investigation of the excited state dynamics of protonated Ado (AdoH+) performed using ultrafast time-resolved fluorescence spectroscopy combined with density functional theoretical calculation. The result obtained from comparison of conformers with protonation at different sites revealed that the syn-conformer with protonation occurring at the N3 position (syn-N3) is the predominant form of AdoH+ in the ground state, similar to that of Ado. In contrast, the fluorescence of AdoH+ with maximum intensity at 385 nm, significantly red-shifted from that of Ado, displaying decay dynamics composed of an ultrafast component with the lifetime of ∼0.5 ps and a slower one of ∼2.9 ns. The former is because of the decay of the syn-N3 conformer, similar to that reported for AdoH+ under the gas phase condition. The latter is due to the syn-N1 conformer formed via ultrafast proton transfer of the syn-N3. The excited state of syn-N1 has a peculiar nonplanar conformation over the purine molecule, which is responsible for the substantial Stokes shift showed in the fluorescence spectrum and correlates with a large energy barrier for nonradiative decay likely involving a reversed proton transfer. This study demonstrates the importance of protonation and solvent environment in altering dramatically the excited states of Ado, providing insight for better understanding nonradiative dynamics of both the monomeric bases and the oligomeric or polymeric DNAs.
Collapse
Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China.
| | | | | | | | | | | | | | | | | |
Collapse
|
118
|
Abstract
The intrinsic fluorescence of nucleic acids is extremely weak compared to that of the fluorescent labels used to probe their structural and functional behavior. Thus, for technical reasons, the investigation of the intrinsic DNA fluorescence was limited for a long time. But with the improvement in spectroscopic techniques, the situation started to change around the turn of the century. During the past two decades, various factors modulating the static and dynamic properties of the DNA fluorescence have been determined; it was shown that, under certain conditions, quantum yields may be up 100 times higher than what was known so far. The ensemble of these studies opened up new paths for the development of label-free DNA fluorescence for biochemical applications. In parallel, these studies have shed new light on the primary processes leading to photoreactions that damage DNA when it absorbs UV radiation.We have been studying a variety of DNA systems, ranging from the monomeric nucleobases to double-stranded and four-stranded structures using fluorescence spectroscopy. The specificity of our work resides in the quantitative association of the steady-state fluorescence spectra with time-resolved data recorded from the femtosecond to the nanosecond timescales, made possible by the development of specific methodologies.Among others, our fluorescence studies provide information on the energy and the polarization of electronic transitions. These are valuable indicators for the evolution of electronic excitations in complex systems, where the electronic coupling between chromophores plays a key role. Highlighting collective effects that originate from electronic interactions in DNA multimers is the objective of the present Account.In contrast to the monomeric chromophores, whose fluorescence decays within a few picoseconds, that of DNA multimers persists on the nanosecond timescale. Even if long-lived states represent only a small fraction of electronic excitations, they may be crucial to the DNA photoreactivity because the probability to reach reactive conformations increases over time, owing to the incessant structural dynamics of nucleic acids.Our femtosecond studies have revealed that an ultrafast excitation energy transfer takes place among the nucleobases within duplexes and G-quadruplexes. Such an ultrafast process is possible when collective states are populated directly upon photon absorption. At much longer times, we discovered an unexpected long-lived high-energy emission stemming from what was coined "HELM excitons". These collective states, whose emission increases with the duplex size, could be responsible for the delayed fluorescence of ππ* states observed for genomic DNA.Most studies dealing with excited-state relaxation in DNA were carried out with excitation in the absorption band peaking at around 260 nm. We went beyond this and also performed the first time-resolved study with excitation in the UVA spectral range, where a very weak absorption tail is present. The resulting fluorescence decays are much slower and the fluorescence quantum yields are much higher than for UVC excitation. We showed that the base pairing of DNA strands enhances the UVA fluorescence and, in parallel, increases the photoreactivity because it modifies the nature of the involved collective excited states.
Collapse
Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| |
Collapse
|
119
|
Fang YG, Valverde D, Mai S, Canuto S, Borin AC, Cui G, González L. Excited-State Properties and Relaxation Pathways of Selenium-Substituted Guanine Nucleobase in Aqueous Solution and DNA Duplex. J Phys Chem B 2021; 125:1778-1789. [PMID: 33570942 PMCID: PMC8023715 DOI: 10.1021/acs.jpcb.0c10855] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The excited-state properties and relaxation mechanisms after light irradiation of 6-selenoguanine (6SeG) in water and in DNA have been investigated using a quantum mechanics/molecular mechanics (QM/MM) approach with the multistate complete active space second-order perturbation theory (MS-CASPT2) method. In both environments, the S1 1(nSeπ5*) and S2 1(πSeπ5*) states are predicted to be the spectroscopically dark and bright states, respectively. Two triplet states, T1 3(πSeπ5*) and T2 3(nSeπ5*), are found energetically below the S2 state. Extending the QM region to include the 6SeG-Cyt base pair slightly stabilizes the S2 state and destabilizes the S1, due to hydrogen-bonding interactions, but it does not affect the order of the states. The optimized minima, conical intersections, and singlet-triplet crossings are very similar in water and in DNA, so that the same general mechanism is found. Additionally, for each excited state geometry optimization in DNA, three kind of structures ("up", "down", and "central") are optimized which differ from each other by the orientation of the C═Se group with respect to the surrounding guanine and thymine nucleobases. After irradiation to the S2 state, 6SeG evolves to the S2 minimum, near to a S2/S1 conical intersection that allows for internal conversion to the S1 state. Linear interpolation in internal coordinates indicate that the "central" orientation is less favorable since extra energy is needed to surmount the high barrier in order to reach the S2/S1 conical intersection. From the S1 state, 6SeG can further decay to the T1 3(πSeπ5*) state via intersystem crossing, where it will be trapped due to the existence of a sizable energy barrier between the T1 minimum and the T1/S0 crossing point. Although this general S2 → T1 mechanism takes place in both media, the presence of DNA induces a steeper S2 potential energy surface, that it is expected to accelerate the S2 → S1 internal conversion.
Collapse
Affiliation(s)
- Ye-Guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Danillo Valverde
- Institute of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, SP 05508-090, Brazil
| | - Sebastian Mai
- Photonics Institute, Vienna University of Technology, Gußhausstraße 27-29, 1040 Vienna, Austria.,Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Sylvio Canuto
- Institute of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, SP 05508-090, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP Brazil
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| |
Collapse
|
120
|
Abou-Hatab S, Carnevale V, Matsika S. Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution. J Chem Phys 2021; 154:064104. [PMID: 33588532 PMCID: PMC7878019 DOI: 10.1063/5.0038342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/20/2021] [Indexed: 11/14/2022] Open
Abstract
Modeling the optical spectra of molecules in solution presents a challenge, so it is important to understand which of the solvation effects (i.e., electrostatics, mutual polarization, and hydrogen bonding interactions between solute and solvent molecules) are crucial in reproducing the various features of the absorption and fluorescence spectra and to identify a sufficient theoretical model that accurately captures these effects with minimal computational cost. In this study, we use various implicit and explicit solvation models, such as molecular dynamics coupled with non-polarizable and polarizable force fields, as well as Car-Parrinello molecular dynamics, to model the absorption and fluorescence spectra of indole in aqueous solution. The excited states are computed using the equation of motion coupled cluster with single and double excitations combined with the effective fragment potential to represent water molecules, which we found to be a computationally efficient approach for modeling large solute-solvent clusters at a high level of quantum theory. We find that modeling mutual polarization, compared to other solvation effects, is a dominating factor for accurately reproducing the position of the peaks and spectral line shape of the absorption spectrum of indole in solution. We present an in-depth analysis of the influence that different solvation models have on the electronic excited states responsible for the features of the absorption spectra. Modeling fluorescence is more challenging since it is hard to reproduce even the correct emitting state, and force field parameters need to be re-evaluated.
Collapse
Affiliation(s)
- Salsabil Abou-Hatab
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| |
Collapse
|
121
|
Fedotov DA, Paul AC, Posocco P, Santoro F, Garavelli M, Koch H, Coriani S, Improta R. Excited-State Absorption of Uracil in the Gas Phase: Mapping the Main Decay Paths by Different Electronic Structure Methods. J Chem Theory Comput 2021; 17:1638-1652. [PMID: 33529532 DOI: 10.1021/acs.jctc.0c01150] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present a computational study of the one-photon and excited-state absorption (ESA) from the two lowest energy excited states of uracil in the gas phase: an nπ* dark state (1n) and the lowest energy bright ππ* state (1π). The predictions of six different linear response electronic structure methods, namely, TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, ADC(2), ADC(2)-x, and ADC(3) are critically compared. In general, the spectral shapes predicted by TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, and ADC(3) are fairly similar, though the quality of TD-CAM-B3LYP slightly deteriorates in the high-energy region. By computing the spectra at some key structures on different potential energy surfaces (PES), that is, the Franck-Condon point, the 1n minimum, and structures representative of different regions of the 1π PES, we obtain important insights into the shift of the ESA spectra, following the motion of the wavepacket on the excited-state PES. Though 1π has larger ESA than 1n, some spectral regions are dominated by these latter signals. Aside from its methodological interest, we thus obtain interesting indications to interpret transient absorption spectra to disentangle the photoactivated dynamics of nucleobases.
Collapse
Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
| | - Alexander C Paul
- Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Paolo Posocco
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Marco Garavelli
- Department of Industrial Chemistry "Toso Montanari", Università degli Studi di Bologna, I-40126 Bologna, Italy
| | - Henrik Koch
- Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56100 Pisa, Italy
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark.,Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
| |
Collapse
|
122
|
Fu F, Liao K, Liu Z, Hong D, Yang H, Tian Y, Wei W, Liu C, Li S, Ma J, Li W. Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO. J Phys Chem B 2021; 125:518-527. [PMID: 33426891 DOI: 10.1021/acs.jpcb.0c09611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)6. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.
Collapse
Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Kang Liao
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Ziteng Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Daocheng Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yuxi Tian
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| |
Collapse
|
123
|
Mal M, Mandal D. Molecular Rotors as Guest Fluorophores Probing the Local Environment inside Host G4 Supramolecular Hydrogels. J Phys Chem B 2021; 125:219-230. [PMID: 33370116 DOI: 10.1021/acs.jpcb.0c07954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fluorescent molecular rotors with a high binding affinity toward the guanosine quartet (G4) were incorporated as guest fluorophores into host supramolecular hydrogels based on the self-assembly of G4 units, to probe the local environment. Torsional dynamics of the rotors were severely inhibited inside the hydrogels in comparison with aqueous solutions, although the hydrogels were composed of >95% water. Moreover, even though all the gels were rigid bodies with no spontaneous deformation or flow property at room temperature, torsional dynamics in G4 borate gels was found to be consistently several orders of magnitude slower than those in the other G4 gels, irrespective of the identity of the molecular rotor probe. This clear difference in the molecular mobilities of the guest fluorophore could be attributed to systematic differences in the internal structure between the two categories of host G4 hydrogels. In specific terms, the borate groups in G4 borate hydrogels serve as bridging units between separate G4 quadruplex strands, generating additional cross-links that reinforce the network structure of the gel. The results demonstrate that molecular rotors act as efficient fluorescent probes for the quantitative assessment of the molecular-level environment and dynamics inside the hydrogels, an aspect that is missed out by most other analytical methods that are routinely employed for studying them.
Collapse
Affiliation(s)
- Madhushree Mal
- Department of Chemistry, University of Calcutta, 92, APC Road, Kolkata 700009, India
| | - Debabrata Mandal
- Department of Chemistry, University of Calcutta, 92, APC Road, Kolkata 700009, India
| |
Collapse
|
124
|
Green JA, Asha H, Santoro F, Improta R. Excitonic Model for Strongly Coupled Multichromophoric Systems: The Electronic Circular Dichroism Spectra of Guanine Quadruplexes as Test Cases. J Chem Theory Comput 2021; 17:405-415. [PMID: 33378185 DOI: 10.1021/acs.jctc.0c01100] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We here propose a general and flexible approach, based on fragment diabatization, which incorporates charge transfer states and significantly increases the reliability of excitonic Hamiltonians for systems where the chromophores are very close. This model (FrDEx) is used to compute the electronic circular dichroism and absorption spectra of two prototype guanine-rich DNA sequences folded in quadruple helices (GQs), i.e., a fragment of the human telomeric sequence (Tel21, antiparallel), and (TGGGGT)4 (TG4T, parallel). Calculations on different subsets of Tel21 and TG4T, from dimers to tetramers, show that FrDEx provides spectra close to the reference full quantum mechanical (QM) ones (obtained with time-dependent density functional theory), with significant improvements with respect to "standard" excitonic Hamiltonians. Furthermore, these tests enable the most cost-effective procedure for the whole GQ to be determined. FrDEx spectra of Tel21 and TG4T are also in good agreement with the QM and experimental ones and give access to interesting insights into the chemical-physical effects modulating the spectral signals. FrDEx could be profitably used to investigate many other biological and nanotechnological materials, from DNA to (opto)electronic polymers.
Collapse
Affiliation(s)
- James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| |
Collapse
|
125
|
Kretz B, Egger DA. Accurate Molecular Geometries in Complex Excited-State Potential Energy Surfaces from Time-Dependent Density Functional Theory. J Chem Theory Comput 2021; 17:357-366. [PMID: 33284603 DOI: 10.1021/acs.jctc.0c00858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interplay of electronic excitations and structural changes in molecules impacts nonradiative decay and charge transfer in the excited state, thus influencing excited-state lifetimes and photocatalytic reaction rates in optoelectronic and energy devices. To capture such effects requires computational methods providing an accurate description of excited-state potential energy surfaces and geometries. We suggest time-dependent density functional theory using optimally tuned range-separated hybrid (OT-RSH) functionals as an accurate approach to obtain excited-state molecular geometries. We show that OT-RSH provides accurate molecular geometries in excited-state potential energy surfaces that are complex and involve an interplay of local and charge-transfer excitations, for which conventional semilocal and hybrid functionals fail. At the same time, the nonempirical OT-RSH approach maintains the high accuracy of parametrized functionals (e.g., B3LYP) for predicting excited-state geometries of small organic molecules showing valence excited states.
Collapse
Affiliation(s)
- Bernhard Kretz
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - David A Egger
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| |
Collapse
|
126
|
Hu Y, Xu C, Ye L, Gu FL, Zhu C. Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces. Phys Chem Chem Phys 2021; 23:5236-5243. [PMID: 33629668 DOI: 10.1039/d0cp06104b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation. The present TD(DFT) simulation provides accurate calculation for conical intersections between the first-excited and ground states. Thus, simulated quantum yield and lifetime of 0.23 and 620 fs (0.15 and 600 fs) for E-to-Z (Z-to-E) isomerization are in good (relatively good) agreement with experimental observation of 0.25 and 480 fs (0.24 and 430 fs), respectively. Simulated results reveal that photoisomerization pathways are initially uphill to conical intersection zones on the S1 potential energy surface and then downhill to product zones. Three types of representative conical intersections are found for determining photoisomerization mechanisms: one is the rotation type responsible for reactive isomerization and the other two are close to E and Z configurations, respectively, only for nonreactive isomerization. The present conclusions can be held in general for similar large NAIP systems of photoinduced isomerization based on E and Z configurations.
Collapse
Affiliation(s)
- Ying Hu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Linfeng Ye
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China. and Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Chaoyuan Zhu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China. and Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan. and Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| |
Collapse
|
127
|
Chakraborty P, Liu Y, Weinacht T, Matsika S. Effect of dynamic correlation on the ultrafast relaxation of uracil in the gas phase. Faraday Discuss 2021; 228:266-285. [DOI: 10.1039/d0fd00110d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High level multi-reference non-adiabatic dynamics simulations reveal that uracil’s photoexcited S2 state decays very quickly without any significant trapping.
Collapse
Affiliation(s)
| | - Yusong Liu
- Department of Physics and Astronomy
- Stony Brook University
- New York 11794
- USA
| | - Thomas Weinacht
- Department of Physics and Astronomy
- Stony Brook University
- New York 11794
- USA
| | | |
Collapse
|
128
|
Zuluaga C, Spata VA, Matsika S. Benchmarking Quantum Mechanical Methods for the Description of Charge-Transfer States in π-Stacked Nucleobases. J Chem Theory Comput 2020; 17:376-387. [PMID: 33346637 DOI: 10.1021/acs.jctc.0c00973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge-transfer (CT) states are of special interest in photochemical research because they can facilitate chemical reactions through the rearrangement of electrons and subsequently chemical bonds in a molecular system. Of particular importance to this research is the transfer of electrons between π-stacked nucleobases in DNA because they play an important role in its photophysics and photochemistry. Computational methods are paramount for the study of CT states because of the current inability of experimental methods to easily detect such states. However, many ab-initio wavefunction-based and density functional theory (DFT) methods fail to accurately describe these CT states. Here, we benchmark how 40 different quantum mechanical methods describe the excited states of a guanine-thymine π-stacked nucleobase dimer system, both in 5'-TG-3' and 5'-GT-3' conformations. We find that the distance between the nucleobases plays a major role in the energy of the CT state and in the difference of the dipole moments between the CT and ground state. There is a larger range of values (and errors) for the energies of CT states compared to those of states localized on one nucleobase. Wavefunction-based methods have similar errors for the CT and localized valence states, while DFT methods are very sensitive to the amount of Hartree-Fock exchange. Long-range-corrected functionals with a careful balance of the Hartree-Fock exchange included can predict very accurate CT states and a balanced description with the localized states.
Collapse
Affiliation(s)
- Camilo Zuluaga
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania, United States
| | - Vincent A Spata
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania, United States
| |
Collapse
|
129
|
Tang Z, Li P, Liu J, Zhou P. Carbonyl Stretch as a Franck-Condon Active Mode and Driving Force for Excited-State Decay of 8-Methoxy-4-methyl-2 H-benzo[ g]chromen-2-one from nπ* State. J Phys Chem B 2020; 124:11472-11480. [PMID: 33264022 DOI: 10.1021/acs.jpcb.0c08207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The fluorescence of most organic chromophore is emitted from the ππ* state, whereas the nπ* state, as a dark state, plays an important role in quenching the fluorescence when its energy is close to the ππ* state. Herein, we report a theoretical study on the fluorescence quenching of 8-methoxy-4-methyl-2H-benzo[g]chromen-2-one by the nπ* state and propose a new mechanism for describing the vibronic coupling between the ππ* and nπ* states. By applying extended multistate complete-active-space second-order perturbation theory (XMS-CASPT2) to optimize the geometries, the geometry distortion of the ππ* state along the out-of-plane mode is observed. This geometry distortion causes the stretching vibration of the carbonyl group to be coupled with the C-C bonds of the pyran ring, which become a Franck-Condon active mode upon photoexcitation and provides a driving force for nonradiative decay from the nπ* state, even if it is energetically unfavorable. This mechanism is significantly different from the previously proposed "proximity effect" and cannot be captured by the popularly used time-dependent density functional theory (TDDFT) and complete-active-space self-consistent field (CASSCF) methods.
Collapse
Affiliation(s)
- Zhe Tang
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266235, P. R. China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023 Liaoning, P. R. China
| | - Peng Li
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266235, P. R. China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023 Liaoning, P. R. China
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266235, P. R. China
| |
Collapse
|
130
|
Tölle J, Cupellini L, Mennucci B, Neugebauer J. Electronic couplings for photo-induced processes from subsystem time-dependent density-functional theory: The role of the diabatization. J Chem Phys 2020; 153:184113. [PMID: 33187428 DOI: 10.1063/5.0022677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Subsystem time-dependent density-functional theory (sTDDFT) making use of approximate non-additive kinetic energy (NAKE) functionals is known to be capable of describing excitation energy transfer processes in a variety of applications. Here, we show that sTDDFT, especially when combined with projection-based embedding (PbE), can be employed for the entire range of photo-induced electronic couplings essential for modeling photophysical properties of complex chemical and biological systems and therefore represents a complete toolbox for this class of problems. This means that it is capable of capturing the interaction/coupling associated with local- and charge-transfer (CT) excitons. However, this requires the choice of a reasonable diabatic basis. We therefore propose different diabatization strategies of the virtual orbital space in PbE-sTDDFT and show how CT excitations can be included in sTDDFT using NAKE functionals via a phenomenological approach. Finally, these electronic couplings are compared to couplings from a multistate fragment excitation difference (FED)-fragment charge difference (FCD) diabatization procedure. We show that both procedures, multistate FED-FCD and sTDDFT (with the right diabatization procedure chosen), lead to an overall good agreement for the electronic couplings, despite differences in their general diabatization strategy. We conclude that the entire range of photo-induced electronic couplings can be obtained using sTDDFT (with the right diabatization procedure chosen) in a black-box manner.
Collapse
Affiliation(s)
- Johannes Tölle
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster Corrensstraße 40, 48149 Münster, Germany
| | - Lorenzo Cupellini
- Università di Pisa, Dipartimento di Chimica e Chimica Industriale, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Università di Pisa, Dipartimento di Chimica e Chimica Industriale, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster Corrensstraße 40, 48149 Münster, Germany
| |
Collapse
|
131
|
Yang G, Chen K, Jin X, Yang D. Photo‐excited intramolecular charge transfer and excited state intramolecular proton transfer behaviors for
HPIBT
system: A theoretical investigation. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Guang Yang
- Basic Teaching Department Jiaozuo University Jiaozuo People's Republic of China
| | - Kaifeng Chen
- Basic Teaching Department Jiaozuo University Jiaozuo People's Republic of China
| | - Xiaofeng Jin
- Basic Teaching Department Jiaozuo University Jiaozuo People's Republic of China
| | - Dapeng Yang
- Group 1101, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian People's Republic of China
| |
Collapse
|
132
|
Piccinni V, Reiter S, Keefer D, de Vivie-Riedle R. Multiscale Conformational Sampling Reveals Excited-State Locality in DNA Self-Repair Mechanism. J Phys Chem A 2020; 124:9133-9140. [PMID: 33089694 DOI: 10.1021/acs.jpca.0c07207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet (UV) irradiation is known to be responsible for DNA damage. However, experimental studies in DNA oligonucleotides have shown that UV light can also induce sequence-specific self-repair. Following charge transfer from a guanine adenine sequence adjacent to a cyclobutane pyrimidine dimer (CPD), the covalent bond between the two thymines could be cleaved, recovering the intact base sequence. Mechanistic details promoting the self-repair remained unclear, however. In our theoretical study, we investigated whether optical excitation could directly lead to a charge-transfer state, thereby initiating the repair, or whether the initial excited state remains localized on a single nucleobase. We performed conformational sampling of 200 geometries of the damaged DNA double strand solvated in water and used a hybrid quantum and molecular mechanics approach to compute excited states at the complete active space perturbation level of theory. Analysis of the conformational data set clearly revealed that the excited-state properties are uniformly distributed across the fluctuations of the nucleotide in its natural environment. From the electronic wavefunction, we learned that the electronic transitions remained predominantly local on either adenine or guanine, and no direct charge transfer occurred in the experimentally accessed energy range. The investigated base sequence is not only specific to the CPD repair mechanism but ubiquitously occurs in nucleic acids. Our results therefore give a very general insight into the charge locality of UV-excited DNA, a property that is regarded to have determining relevance in the structural consequences following absorption of UV photons.
Collapse
Affiliation(s)
- Viviana Piccinni
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | - Sebastian Reiter
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | - Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | | |
Collapse
|
133
|
Lee W, Matsika S. Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA. Chemistry 2020; 26:14181-14186. [PMID: 32809239 DOI: 10.1002/chem.202002834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/01/2020] [Indexed: 11/08/2022]
Abstract
Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.
Collapse
Affiliation(s)
- Wook Lee
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, South Korea
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| |
Collapse
|
134
|
Kuchlyan J, Martinez-Fernandez L, Mori M, Gavvala K, Ciaco S, Boudier C, Richert L, Didier P, Tor Y, Improta R, Mély Y. What Makes Thienoguanosine an Outstanding Fluorescent DNA Probe? J Am Chem Soc 2020; 142:16999-17014. [PMID: 32915558 DOI: 10.1021/jacs.0c06165] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thienoguanosine (thG) is an isomorphic guanosine (G) surrogate that almost perfectly mimics G in nucleic acids. To exploit its full potential and lay the foundation for future applications, 20 DNA duplexes, where the bases facing and neighboring thG were systematically varied, were thoroughly studied using fluorescence spectroscopy, molecular dynamics simulations, and mixed quantum mechanical/molecular mechanics calculations, yielding a comprehensive understanding of its photophysics in DNA. In matched duplexes, thG's hypochromism was larger for flanking G/C residues but its fluorescence quantum yield (QY) and lifetime values were almost independent of the flanking bases. This was attributed to high duplex stability, which maintains a steady orientation and distance between nucleobases, so that a similar charge transfer (CT) mechanism governs the photophysics of thG independently of its flanking nucleobases. thG can therefore replace any G residue in matched duplexes, while always maintaining similar photophysical features. In contrast, the local destabilization induced by a mismatch or an abasic site restores a strong dependence of thG's QY and lifetime values on its environmental context, depending on the CT route efficiency and solvent exposure of thG. Due to this exquisite sensitivity, thG appears ideal for monitoring local structural changes and single nucleotide polymorphism. Moreover, thG's dominant fluorescence lifetime in DNA is unusually long (9-29 ns), facilitating its selective measurement in complex media using a lifetime-based or a time-gated detection scheme. Taken together, our data highlight thG as an outstanding emissive substitute for G with good QY, long fluorescence lifetimes, and exquisite sensitivity to local structural changes.
Collapse
Affiliation(s)
- Jagannath Kuchlyan
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Mattia Mori
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France.,Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| |
Collapse
|
135
|
Lamas I, Montero R, Martínez-Martínez V, Longarte A, Blancafort L. An nπ* gated decay mediates excited-state lifetimes of isolated azaindoles. Phys Chem Chem Phys 2020; 22:18639-18645. [PMID: 32789383 DOI: 10.1039/d0cp02635b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aiming to serve as a guide to understand the relaxation mechanisms of more complex aza-aromatic compounds, such as purine bases, we have studied the non-radiative channels of a set of azaindole structural isomers: 4-, 5-, 6- and 7-azaindole (AI). The relaxation of the isolated molecules, after excitation at the low energy portion of their spectra, has been tracked by femtosecond time-resolved ionization, and the decay paths have been obtained with MS-CASPT2//TD-DFT calculations. Although the ultrashort measured lifetimes for 5- and 6-AI are in contrast to the long-living excited state found in 7-AI, the calculations describe a common relaxation pathway. Along it, the initially excited ππ* states decay to the ground state through a conical intersection accessed through an nπ* state that functions as a gate state. The work reveals that the position of the nitrogen atoms in the purine ring determines the barrier to access the gate state and therefore, the rate of the non-radiative relaxation.
Collapse
Affiliation(s)
- Iker Lamas
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apart. 644, 48080 Bilbao, Spain.
| | | | | | | | | |
Collapse
|
136
|
Blase X, Duchemin I, Jacquemin D, Loos PF. The Bethe-Salpeter Equation Formalism: From Physics to Chemistry. J Phys Chem Lett 2020; 11:7371-7382. [PMID: 32787315 DOI: 10.1021/acs.jpclett.0c01875] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Bethe-Salpeter equation (BSE) formalism is steadily asserting itself as a new efficient and accurate tool in the ensemble of computational methods available to chemists in order to predict optical excitations in molecular systems. In particular, the combination of the so-called GW approximation, giving access to reliable ionization energies and electron affinities, and the BSE formalism, able to model UV/vis spectra, has shown to provide accurate singlet excitation energies with a typical error of 0.1-0.3 eV. With a similar computational cost as time-dependent density-functional theory (TD-DFT), BSE is able to provide an accuracy on par with the most accurate global and range-separated hybrid functionals without the unsettling choice of the exchange-correlation functional, resolving further known issues (e.g., charge-transfer excitations). In this Perspective, we provide a historical overview of BSE, with a particular focus on its condensed-matter roots. We also propose a critical review of its strengths and weaknesses in different chemical situations.
Collapse
Affiliation(s)
- Xavier Blase
- Université Grenoble Alpes, CNRS, Institut NEEL, F-38042 Grenoble, France
| | - Ivan Duchemin
- Université Grenoble Alpes, CEA, IRIG-MEM-L Sim, 38054 Grenoble, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
137
|
Ricardi N, Ernst M, Macchi P, Wesolowski TA. Embedding-theory-based simulations using experimental electron densities for the environment. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2020; 76:571-579. [PMID: 32869754 PMCID: PMC7459768 DOI: 10.1107/s2053273320008062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/16/2020] [Indexed: 11/26/2022]
Abstract
For the first time, the use of experimentally derived molecular electron densities as ρB(r) in calculations based on frozen-density embedding theory (FDET) of environment-induced shifts of electronic excitations for chromophores in clusters is demonstrated. ρB(r) was derived from X-ray restrained molecular wavefunctions of glycylglycine to obtain environment densities for simulating electronic excitations in clusters. The basic idea of frozen-density embedding theory (FDET) is the constrained minimization of the Hohenberg–Kohn density functional EHK[ρ] performed using the auxiliary functional , where ΨA is the embedded NA-electron wavefunction and ρB(r) is a non-negative function in real space integrating to a given number of electrons NB. This choice of independent variables in the total energy functional makes it possible to treat the corresponding two components of the total density using different methods in multi-level simulations. The application of FDET using ρB(r) reconstructed from X-ray diffraction data for a molecular crystal is demonstrated for the first time. For eight hydrogen-bonded clusters involving a chromophore (represented as ΨA) and the glycylglycine molecule [represented as ρB(r)], FDET is used to derive excitation energies. It is shown that experimental densities are suitable for use as ρB(r) in FDET-based simulations.
Collapse
Affiliation(s)
- Niccolò Ricardi
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Michelle Ernst
- University of Bern, Freiestraße 3, 3012 Bern, Switzerland
| | - Piero Macchi
- Department of Chemistry, Materials and Chemical Engineering, Polytechnic of Milan, via Mancinelli 7, Milano 20131, Italy
| | - Tomasz Adam Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| |
Collapse
|
138
|
Sanches de Araújo AV, Valverde D, Canuto S, Borin AC. Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tzA, tzG, and tzI. J Phys Chem A 2020; 124:6834-6844. [PMID: 32786984 DOI: 10.1021/acs.jpca.0c03398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The photophysical relaxation pathways of tzA, tzG, and tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying 1(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the 1(ππ*)min region, the conical intersection with the ground state ((ππ*/GS)CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.
Collapse
Affiliation(s)
| | - Danillo Valverde
- Institute of Physics, University of São Paulo, Rua do Matão 1371, 05508-090 São Paulo, SP, Brazil
| | - Sylvio Canuto
- Institute of Physics, University of São Paulo, Rua do Matão 1371, 05508-090 São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| |
Collapse
|
139
|
Yaghoubi Jouybari M, Liu Y, Improta R, Santoro F. Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study. J Chem Theory Comput 2020; 16:5792-5808. [PMID: 32687360 DOI: 10.1021/acs.jctc.0c00455] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The nonadiabatic quantum dynamics (QD) of cytosine and 1-methylcytosine in the gas phase is simulated for 250 fs after a photoexcitation to one of the first two bright states. The nuclear wavepacket is propagated on the coupled diabatic potential energy surfaces of the lowest seven excited states, including ππ*, nπ*, and Rydberg states along all the vibrational degrees of freedom. We focus in particular on the interplay between the bright and the dark nπ* states, not considering the decay to the ground electronic state. To run these simulations, we implemented an automatic general procedure to parametrize linear vibronic coupling (LVC) models with time-dependent density functional theory (DFT) computations and interfaced it with Gaussian package. The wavepacket was propagated with the multilayer version of the multiconfigurational time dependent Hartree method. Two different density functionals, PBE0 and CAM-B3LYP, which provide a different description of the relative stability of the lowest energy dark states, were used to parametrize the LVC Hamiltonian. Part of the photoexcited population on lowest HOMO-LUMO transition (πHπL*) decays within less than 100 fs to a nπ* state which mainly involves a promotion of an electron from the oxygen lone pair to the LUMO (nOπL*). The population of the second ππ* state decays almost completely, in <100 fs, not only to πHπL* and to nOπL* states but also to another nπL* state involving the nitrogen lone pair. The efficiency of the adopted protocol allowed us to check the accuracy of the predictions by repeating the QD simulations with different LVC Hamiltonians parametrized either at the ground-state minimum or at stationary structures of different relevant excited states.
Collapse
Affiliation(s)
- Martha Yaghoubi Jouybari
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Yanli Liu
- School of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|
140
|
Suchan J, Janoš J, Slavíček P. Pragmatic Approach to Photodynamics: Mixed Landau–Zener Surface Hopping with Intersystem Crossing. J Chem Theory Comput 2020; 16:5809-5820. [DOI: 10.1021/acs.jctc.0c00512] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jiří Suchan
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Jiří Janoš
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| |
Collapse
|
141
|
Observation of Enhanced Dissociative Photochemistry in the Non-Native Nucleobase 2-Thiouracil. Molecules 2020; 25:molecules25143157. [PMID: 32664261 PMCID: PMC7397253 DOI: 10.3390/molecules25143157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022] Open
Abstract
We present the first study to measure the dissociative photochemistry of 2-thiouracil (2-TU), an important nucleobase analogue with applications in molecular biology and pharmacology. Laser photodissociation spectroscopy is applied to the deprotonated and protonated forms of 2-TU, which are produced in the gas-phase using electrospray ionization mass spectrometry. Our results show that the deprotonated form of 2-thiouracil ([2-TU-H]−) decays predominantly by electron ejection and hence concomitant production of the [2-TU-H]· free-radical species, following photoexcitation across the UVA-UVC region. Thiocyanate (SCN−) and a m/z 93 fragment ion are also observed as photodecay products of [2-TU-H]− but at very low intensities. Photoexcitation of protonated 2-thiouracil ([2-TU·H]+) across the same UVA-UVC spectral region produces the m/z 96 cationic fragment as the major photofragment. This ion corresponds to ejection of an HS· radical from the precursor ion and is determined to be a product of direct excited state decay. Fragment ions associated with decay of the hot ground state (i.e., the ions we would expect to observe if 2-thiouracil was behaving like UV-dissipating uracil) are observed as much more minor products. This behaviour is consistent with enhanced intersystem crossing to triplet excited states compared to internal conversion back to the ground state. These are the first experiments to probe the effect of protonation/deprotonation on thionucleobase photochemistry, and hence explore the effect of pH at a molecular level on their photophysical properties.
Collapse
|
142
|
Scott TR, Hermes MR, Sand AM, Oakley MS, Truhlar DG, Gagliardi L. Analytic gradients for state-averaged multiconfiguration pair-density functional theory. J Chem Phys 2020; 153:014106. [PMID: 32640800 DOI: 10.1063/5.0007040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Analytic gradients are important for efficient calculations of stationary points on potential energy surfaces, for interpreting spectroscopic observations, and for efficient direct dynamics simulations. For excited electronic states, as are involved in UV-Vis spectroscopy and photochemistry, analytic gradients are readily available and often affordable for calculations using a state-averaged complete active space self-consistent-field (SA-CASSCF) wave function. However, in most cases, a post-SA-CASSCF step is necessary for quantitative accuracy, and such calculations are often too expensive if carried out by perturbation theory or configuration interaction. In this work, we present the analytic gradients for multiconfiguration pair-density functional theory based on SA-CASSCF wave functions, which is a more affordable alternative. A test set of molecules has been studied with this method, and the stationary geometries and energetics are compared to values in the literature as obtained by other methods. Excited-state geometries computed with state-averaged pair-density functional theory have similar accuracy to those from complete active space perturbation theory at the second-order.
Collapse
Affiliation(s)
- Thais R Scott
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Matthew R Hermes
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Andrew M Sand
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, USA
| | - Meagan S Oakley
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
143
|
Brash DE. Rethinking Causation for Data-intensive Biology: Constraints, Cancellations, and Quantized Organisms: Causality in complex organisms is sculpted by constraints rather than instigators, with outcomes perhaps better described by quantized patterns than rectilinear pathways. Bioessays 2020; 42:e1900135. [PMID: 32484248 PMCID: PMC7518294 DOI: 10.1002/bies.201900135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/19/2020] [Indexed: 12/22/2022]
Abstract
Complex organisms thwart the simple rectilinear causality paradigm of "necessary and sufficient," with its experimental strategy of "knock down and overexpress." This Essay organizes the eccentricities of biology into four categories that call for new mathematical approaches; recaps for the biologist the philosopher's recent refinements to the causation concept and the mathematician's computational tools that handle some but not all of the biological eccentricities; and describes overlooked insights that make causal properties of physical hierarchies such as emergence and downward causation straightforward. Reviewing and extrapolating from similar situations in physics, it is suggested that new mathematical tools for causation analysis incorporating feedback, signal cancellation, nonlinear dependencies, physical hierarchies, and fixed constraints rather than instigative changes will reveal unconventional biological behaviors. These include "eigenisms," organisms that are limited to quantized states; trajectories that steer a system such as an evolving species toward optimal states; and medical control via distributed "sheets" rather than single control points.
Collapse
Affiliation(s)
- Douglas E Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06520-8040, USA
| |
Collapse
|
144
|
|
145
|
Yang J, Zhu X, F Nunes JP, Yu JK, Parrish RM, Wolf TJA, Centurion M, Gühr M, Li R, Liu Y, Moore B, Niebuhr M, Park S, Shen X, Weathersby S, Weinacht T, Martinez TJ, Wang X. Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction. Science 2020; 368:885-889. [PMID: 32439793 DOI: 10.1126/science.abb2235] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/03/2020] [Indexed: 01/02/2023]
Abstract
Simultaneous observation of nuclear and electronic motion is crucial for a complete understanding of molecular dynamics in excited electronic states. It is challenging for a single experiment to independently follow both electronic and nuclear dynamics at the same time. Here we show that ultrafast electron diffraction can be used to simultaneously record both electronic and nuclear dynamics in isolated pyridine molecules, naturally disentangling the two components. Electronic state changes (S1→S0 internal conversion) were reflected by a strong transient signal in small-angle inelastic scattering, and nuclear structural changes (ring puckering) were monitored by large-angle elastic diffraction. Supported by ab initio nonadiabatic molecular dynamics and diffraction simulations, our experiment provides a clear view of the interplay between electronic and nuclear dynamics of the photoexcited pyridine molecule.
Collapse
Affiliation(s)
- Jie Yang
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA. .,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Xiaolei Zhu
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - J Pedro F Nunes
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jimmy K Yu
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA.,Biophysics Program, Stanford University, Stanford, CA, USA
| | - Robert M Parrish
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Thomas J A Wolf
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Martin Centurion
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Markus Gühr
- Institut für Physik und Astronomie, Universität Potsdam, Potsdam, Germany
| | - Renkai Li
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA
| | - Bryan Moore
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Mario Niebuhr
- Institut für Physik und Astronomie, Universität Potsdam, Potsdam, Germany
| | - Suji Park
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Xiaozhe Shen
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA
| | - Todd J Martinez
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA. .,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Xijie Wang
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| |
Collapse
|
146
|
Peng Q, Zhu YH, Zhang TS, Liu XY, Fang WH, Cui G. Selenium substitution effects on excited-state properties and photophysics of uracil: a MS-CASPT2 study. Phys Chem Chem Phys 2020; 22:12120-12128. [PMID: 32440669 DOI: 10.1039/d0cp01369b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photophysics of selenium-substituted nucleobases has attracted recent experimental attention because they could serve as potential photosensitizers in photodynamic therapy. Herein, we present a comprehensive MS-CASPT2 study on the spectroscopic and excited-state properties, and photophysics of 2-selenouracil (2SeU), 4-selenouracil (4SeU), and 2,4-selenouracil (24SeU). Relevant minima, conical intersections, crossing points, and excited-state relaxation paths in the lowest five electronic states (i.e., S0, S1, S2, T2, and T1) are explored. On the basis of these results, their photophysical mechanisms are proposed. Upon photoirradiation to the bright S2 state, 2SeU quickly relaxes to its S2 minimum and then moves in an essentially barrierless way to a nearby S2/S1 conical intersection near which the S1 state is populated. Next, the S1 system arrives at an S1/T2/T1 intersection where a large S1/T1 spin-orbit coupling of 430.8 cm-1 makes the T1 state populated. In this state, a barrier of 6.8 kcal mol-1 will trap 2SeU for a while. In parallel, for 4SeU or 24SeU, the system first relaxes to the S2 minimum and then overcomes a small barrier to approach an S2/S1 conical intersection. Once hopping to the S1 state, there exists an extended region with very close S1, T2, and T1 energies. Similarly, a large S1/T1 spin-orbit coupling of 426.8 cm-1 drives the S1→ T1 intersystem crossing process thereby making the T1 state populated. Similarly, an energy barrier heavily suppresses electronic transition to the S0 state. The present work manifests that different selenium substitutions on uracil can lead to a certain extent of different vertical and adiabatic excitation energies, excited-state properties, and relaxation pathways. These insights could help understand the photophysics of selenium-substituted nucleobases.
Collapse
Affiliation(s)
- Qin Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | | | | | | | | | | |
Collapse
|
147
|
Balasubramani SG, Chen GP, Coriani S, Diedenhofen M, Frank MS, Franzke YJ, Furche F, Grotjahn R, Harding ME, Hättig C, Hellweg A, Helmich-Paris B, Holzer C, Huniar U, Kaupp M, Marefat Khah A, Karbalaei Khani S, Müller T, Mack F, Nguyen BD, Parker SM, Perlt E, Rappoport D, Reiter K, Roy S, Rückert M, Schmitz G, Sierka M, Tapavicza E, Tew DP, van Wüllen C, Voora VK, Weigend F, Wodyński A, Yu JM. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J Chem Phys 2020; 152:184107. [PMID: 32414256 PMCID: PMC7228783 DOI: 10.1063/5.0004635] [Citation(s) in RCA: 523] [Impact Index Per Article: 130.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.
Collapse
Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Guo P Chen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Michael Diedenhofen
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Marius S Frank
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Yannick J Franzke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Robin Grotjahn
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Arnim Hellweg
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Uwe Huniar
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | | | - Thomas Müller
- Forschungszentrum Jülich, Jülich Supercomputer Centre, Wilhelm-Jonen Straße, 52425 Jülich, Germany
| | - Fabian Mack
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Brian D Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Eva Perlt
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kevin Reiter
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Saswata Roy
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Matthias Rückert
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gunnar Schmitz
- Department of Chemistry, Aarhus Universitet, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Marek Sierka
- TURBOMOLE GmbH, Litzenhardtstraße 19, 76135 Karlsruhe, Germany
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, California 90840, USA
| | - David P Tew
- Max Planck Institute for Solid State Research, Heisenbergstaße 1, 70569 Stuttgart, Germany
| | - Christoph van Wüllen
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Staße 52, 67663 Kaiserslautern, Germany
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Florian Weigend
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Artur Wodyński
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jason M Yu
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| |
Collapse
|
148
|
Huet L, Perfetto A, Muniz-Miranda F, Campetella M, Adamo C, Ciofini I. General Density-Based Index to Analyze Charge Transfer Phenomena: From Models to Butterfly Molecules. J Chem Theory Comput 2020; 16:4543-4553. [DOI: 10.1021/acs.jctc.0c00296] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Léon Huet
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005 Paris, France
| | - Anna Perfetto
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005 Paris, France
| | - Francesco Muniz-Miranda
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005 Paris, France
| | - Marco Campetella
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005 Paris, France
| | - Carlo Adamo
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005 Paris, France
- France and Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| | - Ilaria Ciofini
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005 Paris, France
| |
Collapse
|
149
|
Trachsel MA, Blaser S, Lobsiger S, Siffert L, Frey HM, Blancafort L, Leutwyler S. Locating Cytosine Conical Intersections by Laser Experiments and Ab Initio Calculations. J Phys Chem Lett 2020; 11:3203-3210. [PMID: 32251591 DOI: 10.1021/acs.jpclett.0c00779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The decay mechanism of S0 → S1 excited cytosine (Cyt) and the effect of substitution are studied combining jet-cooled spectroscopy (nanosecond resonant two-photon ionization (R2PI) and picosecond lifetime measurements) with CASPT2//CASSCF computations for eight derivatives. For Cyt and five derivatives substituted at N1, C5, and C6, rapid internal conversion sets in at 250-1200 cm-1 above the 000 bands. The break-off in the spectra correlates with the calculated barriers toward the "C5-C6 twist" conical intersection, which unambiguously establishes the decay mechanism at low S1 state vibrational energies. The barriers increase with substituents that stabilize the charge shifts at C4, C5, and C6 following (1ππ*) excitation. The R2PI spectra of the clamped derivatives 5,6-trimethyleneCyt (TMCyt) and 1-methyl-TMCyt (1M-TMCyt), which decay along an N3 out-of-plane coordinate, extend up to +3500 and +4500 cm-1.
Collapse
Affiliation(s)
- Maria A Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Susan Blaser
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Luca Siffert
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Lluís Blancafort
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, C/M.A. Capmany 69, 17003 Girona, Spain
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| |
Collapse
|
150
|
Anand N, Nag P, Kanaparthi RK, Vennapusa SR. O-H vibrational motions promote sub-50 fs nonadiabatic dynamics in 3-hydroxypyran-4-one: interplay between internal conversion and ESIPT. Phys Chem Chem Phys 2020; 22:8745-8756. [PMID: 32282004 DOI: 10.1039/d0cp00741b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical study is used to explore the involvement of O-H vibrational motions in the S0 → S2 photoinduced dynamics of 3-hydroxypyran-4-one (3-HOX). Two transitions, S0 → S1 and S0 → S2, are attributed to the experimentally observed electronic absorption spectral features in the range of 3.5-5.5 eV. We compute model potential energy surfaces of vibronically coupled S1 (nπ*) and S2 (ππ*) states with the aid of extensive electronic structure calculations. The S1-S2 conical intersection is characterized in the O-H bend and O-H stretch vibrational coordinate space. Quantum wavepacket dynamics simulations reveal an ultrafast S2 → S1 internal conversion decay, where about 90% of the S2 population disappears within the first 50 fs of the propagation time. The participation of O-H vibrational motions in the early events of nonadiabatic dynamics is analyzed based on the time evolution of nuclear densities on S2. We discuss the implications of these observations to provide fundamental insights into the nonadiabatic excited-state intramolecular proton transfer in 3-HOX and its derivatives.
Collapse
Affiliation(s)
- Neethu Anand
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O, Vithura, Thiruvananthapuram-695551, Kerala, India.
| | - Probal Nag
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O, Vithura, Thiruvananthapuram-695551, Kerala, India.
| | - Ravi Kumar Kanaparthi
- Department Of Chemistry, School Of Physical Sciences, Central University of Kerala, Tejaswini Hills, Periya, Kerala - 671320, India.
| | - Sivaranjana Reddy Vennapusa
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O, Vithura, Thiruvananthapuram-695551, Kerala, India.
| |
Collapse
|