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Khatun MN, Nandy S, Roy H, Ghosh SS, Kumar S, Iyer PK. Sulphur-atom positional engineering in perylenimide: structure-property relationships and H-aggregation directed type-I photodynamic therapy. Chem Sci 2024; 15:9298-9317. [PMID: 38903228 PMCID: PMC11186329 DOI: 10.1039/d4sc01180e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/10/2024] [Indexed: 06/22/2024] Open
Abstract
An innovative design strategy of placing sulfur (S)-atoms within the pendant functional groups and at carbonyl positions in conventional perylenimide (PNI-O) has been demonstrated to investigate the condensed state structure-property relationship and potential photodynamic therapy (PDT) application. Incorporation of simply S-atoms at the peri-functionalized perylenimide (RPNI-O) leads to an aggregation-induced enhanced emission luminogen (AIEEgen), 2-hexyl-8-(thianthren-1-yl)-1H-benzo[5,10]anthra[2,1,9-def]isoquinoline-1,3(2H)-dione (API), which achieves a remarkable photoluminescence quantum yield (Φ PL) of 0.85 in aqueous environments and established novel AIE mechanisms. Additionally, substitution of the S-atom at the carbonyl position in RPNI-O leads to thioperylenimides (RPNI-S): 2-hexyl-8-phenyl-1H-benzo[5,10]anthra[2,1,9-def]isoquinoline-1,3(2H)-dithione (PPIS), 8-([2,2'-bithiophen]-5-yl)-2-hexyl-1H-benzo[5,10]anthra[2,1,9-def]isoquinoline-1,3(2H)-dithione (THPIS), and 2-hexyl-8-(thianthren-1-yl)-1H-benzo[5,10]anthra[2,1,9-def]isoquinoline-1,3(2H)-dithion (APIS), with distinct photophysical properties (enlarged spin-orbit coupling (SOC) and Φ PL ≈ 0.00), and developed diverse potent photosensitizers (PSs). The present work provides a novel SOC enhancement mechanism via pronounced H-aggregation. Surprisingly, the lowest singlet oxygen quantum yield (Φ Δ) and theoretical calculation suggest the specific type-I PDT for RPNI-S. Interestingly, RPNI-S efficiently produces superoxide (O2˙-) due to its remarkably lower Gibbs free energy (ΔG) values (THPIS: -40.83 kcal mol-1). The non-toxic and heavy-atom free very specific thio-based PPIS and THPIS PSs showed selective and efficient PDT under normoxia, as a rare example.
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Affiliation(s)
- Mst Nasima Khatun
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-3612582349
| | - Satyendu Nandy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India
| | - Hirakjyoti Roy
- Centre for Nanotechnology, Indian Institute of Technology Guwahati Guwahati 781039 Assam India
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India
- Centre for Nanotechnology, Indian Institute of Technology Guwahati Guwahati 781039 Assam India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India
| | - Parameswar Krishnan Iyer
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-3612582349
- Centre for Nanotechnology, Indian Institute of Technology Guwahati Guwahati 781039 Assam India
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Liu S, Lee Y, Chen L, Deng J, Ma T, Barbatti M, Bai S. Unexpected longer T 1 lifetime of 6-sulfur guanine than 6-selenium guanine: the solvent effect of hydrogen bonds to brake the triplet decay. Phys Chem Chem Phys 2024; 26:13965-13972. [PMID: 38669188 PMCID: PMC11078201 DOI: 10.1039/d4cp00875h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
The decay of the T1 state to the ground state is an essential property of photosensitizers because it decides the lifetime of excited states and, thus, the time window for sensitization. The sulfur/selenium substitution of carbonyl groups can red-shift absorption spectra and enhance the triplet yield because of the large spin-orbit coupling, modifying nucleobases to potential photosensitizers for various applications. However, replacing sulfur with selenium will also cause a much shorter T1 lifetime. Experimental studies found that the triplet decay rate of 6-seleno guanine (6SeGua) is 835 times faster than that of 6-thio guanine (6tGua) in aqueous solution. In this work, we reveal the mechanism of the T1 decay difference between 6SeGua and 6tGua by computing the activation energy and spin-orbit coupling for rate calculation. The solvent effect of water is treated with explicit microsolvation and implicit solvent models. We find that the hydrogen bond between the sulfur atom of 6tGua and the water molecule can brake the triplet decay, which is weaker in 6SeGua. This difference is crucial to explain the relatively long T1 lifetime of 6tGua in an aqueous solution. This insight emphasizes the role of solvents in modulating the excited state dynamics and the efficiency of photosensitizers, particularly in aqueous environments.
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Affiliation(s)
- Shaoting Liu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China.
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yuhsuan Lee
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingfang Chen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingheng Deng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Tongmei Ma
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, 13397 Marseille, France.
- Institut Universitaire de France, Paris 75231, France
| | - Shuming Bai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Baños J, Avilés A, Colmenares F. Disruptive Model That Explains for the Long-Lived Triplet States Observed for 2-Thiocytosine upon UVA Radiation. ACS OMEGA 2024; 9:13059-13066. [PMID: 38524487 PMCID: PMC10955585 DOI: 10.1021/acsomega.3c09471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024]
Abstract
The possible role of radical species in the formation of the long-lived triplet states observed for 2-thiocytosine upon UV irradiation was theoretically investigated. It is predicted that the radical fragments arising from the homolytic rupture of the NH group of the thiobase can be yielded upon ultraviolet-A radiation. Recombination of the radicals through the most favorable singlet channel yields the lowest-lying tautomer of the 2-thiocytosine (the amino-thiol form) through a barrierless pathway. The rebounding of the radical fragments along the triplet channels that emerge from the attack of the hydrogen to the nitrogen atoms next to the C-S bond leads to stable structures for the amino-thion-N1H and amino-thion-N3H tautomers. These results allow for the rationalization of the near-unity triplet yields observed when this pure light-atom organic molecule is exposed to UV irradiation, without invoking intersystem crossings between the electronic states of different spin-multiplicities. A similar study for cytosine showed that the energy required to induce the homolytic breaking of the N-H bond of the nucleobase is not attainable under UVA radiation. This result is consistent with the experimental fact that no triplet states are observed when this molecule is exposed to that light.
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Affiliation(s)
- Jorge Baños
- Departamento de Física y Química
Teórica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX 04510, Mexico
| | | | - Fernando Colmenares
- Departamento de Física y Química
Teórica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX 04510, Mexico
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4
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Zhou Q, Hao Y, Jie J, Wang S, Xia Y, Yang C, Liu L, Fang WH, Su H. Dual Functionality of 6-Methylthioguanine: Synergistic Effects Enhancing the Photolability of DNA Nucleobases. JACS AU 2024; 4:441-453. [PMID: 38425924 PMCID: PMC10900203 DOI: 10.1021/jacsau.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/02/2024]
Abstract
A small chemical modification of the nucleobase structure can significantly enhance the photoactivity of DNA, which may incur DNA damage, thus holding promising applications in photochemotherapy treatment of cancers or pathogens. However, single substitution confers only limited phototoxicity to DNA. Herein, we combine femtosecond and nanosecond time-resolved spectroscopy with high-level ab initio calculations to disentangle the excited-state dynamics of 6-methylthioguanine (me6-TG) under variable wavelength UVA excitation (310-330 nm). We find that double substitution of nucleobases (thionation and methylation) boosts the photoactivity by introducing more reactive channels. Intriguingly, 1nNπ*, rather than 1nSπ*, acts as the doorway state engendering the formation of the long-lived reactive triplet state in me6-TG. The 1nNπ* induces a low spin-orbit coupling of 8.3 cm-1, which increases the intersystem crossing (ISC) time (2.91 ± 0.14 ns). Despite the slowed ISC, the triplet quantum yield (ΦT) still accounts for a large fraction (0.6 ± 0.1), consistent with the potential energy surface that favors excited-state bifurcation to 1nNπ*min (3.36 ± 0.15 ps) rather than 1ππ*min (5.05 ± 0.26 ps), such that the subsequent ISC to triplet via 1nNπ*min constitutes the main relaxation pathway in me6-TG. Although this ΦT is inferior to its single-substituted predecessor 6-thioguanine (6-TG, 0.8 ± 0.2), the effect of thionation in synergy with methylation opens a unique C-S bond cleavage pathway through crossing to a repulsive 1πσ* state, generating thiyl radicals as highly reactive intermediates that may invoke biological damage. This photodissociation channel is extremely difficult for conventional nucleobases. These findings demonstrate the synergistic effects of double functionality substitution in modulating excited-state dynamics and enhancing the photolabile character of DNA nucleobases, providing inspirations for the rational design of advanced photodynamic and photochemotherapy approaches.
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Affiliation(s)
| | | | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Shuo Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ye Xia
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lihong Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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5
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Abdelgawwad AMA, Roca-Sanjuán D, Francés-Monerris A. Electronic spectroscopy of gemcitabine and derivatives for possible dual-action photodynamic therapy applications. J Chem Phys 2023; 159:224106. [PMID: 38078522 DOI: 10.1063/5.0170949] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/12/2023] [Indexed: 12/18/2023] Open
Abstract
In this paper, we explore the molecular basis of combining photodynamic therapy (PDT), a light-triggered targeted anticancer therapy, with the traditional chemotherapeutic properties of the well-known cytotoxic agent gemcitabine. A photosensitizer prerequisite is significant absorption of biocompatible light in the visible/near IR range, ideally between 600 and 1000 nm. We use highly accurate multiconfigurational CASSCF/MS-CASPT2/MM and TD-DFT methodologies to determine the absorption properties of a series of gemcitabine derivatives with the goal of red-shifting the UV absorption band toward the visible region and facilitating triplet state population. The choice of the substitutions and, thus, the rational design is based on important biochemical criteria and on derivatives whose synthesis is reported in the literature. The modifications tackled in this paper consist of: (i) substitution of the oxygen atom at O2 position with heavier atoms (O → S and O → Se) to red shift the absorption band and increase the spin-orbit coupling, (ii) addition of a lipophilic chain at the N7 position to enhance transport into cancer cells and slow down gemcitabine metabolism, and (iii) attachment of aromatic systems at C5 position to enhance red shift further. Results indicate that the combination of these three chemical modifications markedly shifts the absorption spectrum toward the 500 nm region and beyond and drastically increases spin-orbit coupling values, two key PDT requirements. The obtained theoretical predictions encourage biological studies to further develop this anticancer approach.
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Affiliation(s)
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, 46071 València, Spain
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6
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Negi M, Dixit T, Venkatesh V. Ligand Dictated Photosensitization of Iridium(III) Dithiocarbamate Complexes for Photodynamic Therapy. Inorg Chem 2023; 62:20080-20095. [PMID: 37994001 DOI: 10.1021/acs.inorgchem.3c02942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Organelle-targeted photosensitizers (PSs) for photodynamic therapy (PDT) are considered as an effective therapeutic strategy for the development of next generation PSs with the least side effects and high therapeutic efficacy. However, multiorganelle targeted PSs eliciting PDT via both type I and type II mechanisms are scarce. Herein, a series of cyclometalated iridium(III) complexes were formulated [Ir(C∧N)2(S∧S)] (C∧N = 2-phenylpyridine (ppy) and 2-(thiophen-2-yl)pyridine (thpy); S∧S = diethyldithiocarbamate (DEDTC), morpholine-N-dithiocarbamate (MORDTC) and methoxycarbonodithioate (MEDTC)) and the newly designed complexes Ir2@DEDTC and Ir1@MEDTC were characterized by single crystal X-ray crystallography. Complexes containing thpy as C∧N ligand exhibit excellent photophysical properties such as red-shifted emission, high singlet oxygen quantum yield (ϕΔ) and longer photoluminescence lifetime when compared with complexes containing ppy ligands. Ir2@DEDTC exhibits the highest ϕΔ and photoluminescence lifetimes among the synthesized complexes. Therefore, Ir2@DEDTC was chosen to evaluate the photosensitizing ability to produce reactive oxygen species (ROS). Upon blue light irradiation (456 nm), it efficiently produces ROS, i.e., hydroxy radical (•OH) and singlet oxygen (1O2), which was confirmed by electron paramagnetic resonance (EPR) spectroscopy. In vitro photocytotoxicity toward HCT116, HeLa, and PC3 cell lines showed that out of all the synthesized complexes, Ir2@DEDTC has the highest photocytotoxic index (PI > 400) value. Ir2@DEDTC is efficiently taken up by the HCT116 cell line and accumulated mainly in the lysosome and mitochondria of the cells, and after PDT treatment, it elicits cell shrinkage, membrane blebbing, and DNA fragmentation. The phototherapeutic efficacy of Ir2@DEDTC has been investigated against 3D spheroids considering its ability to mimic some of the basic features of solid tumors. The morphology was drastically altered in the Ir2@DEDTC treated 3D spheroid after the light irradiation unleashed the potential of the Ir(III) dithiocarbamate complex as a superior PS for PDT. Hence, mitochondria and lysosome targeted photoactive cyclometalated Ir(III) dithiocarbamate complex exerting oxidative stress via both type I and type II PDT can be regarded as a dual-organelle targeted two-pronged approach for enhanced PDT.
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Affiliation(s)
- Monika Negi
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Tejal Dixit
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - V Venkatesh
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
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7
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Xie M, Ren SX, Hu D, Zhong JM, Luo J, Tan Y, Li YP, Si LP, Cao J. The impact of the chalcogen-substitution element and initial spectroscopic state on excited-state relaxation pathways in nucleobase photosensitizers: a combination of static and dynamic studies. Phys Chem Chem Phys 2023; 25:27756-27765. [PMID: 37814579 DOI: 10.1039/d3cp03730d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The substitution of oxygen with chalcogen in carbonyl group(s) of canonical nucleobases gives an impressive triplet generation, enabling their promising applications in medicine and other emerging techniques. The excited-state relaxation S2(ππ*) → S1(nπ*) → T1(ππ*) has been considered the preferred path for triplet generation in these nucleobase derivatives. Here, we demonstrate enhanced quantum efficiency of direct intersystem crossing from S2 to triplet manifold upon substitution with heavier chalcogen elements. The excited-state relaxation dynamics of sulfur/selenium substituted guanines in a vacuum is investigated using a combination of static quantum chemical calculations and on-the-fly excited-state molecular dynamics simulations. We find that in sulfur-substitution the S2 state predominantly decays to the S1 state, while upon selenium-substitution the S2 state deactivation leads to simultaneous population of the S1 and T2,3 states in the same time scale and multi-state quasi-degeneracy region S2/S1/T2,3. Interestingly, the ultrafast deactivation of the spectroscopic S3 state of both studied molecules to the S1 state occurs through a successive S3 → S2 → S1 path involving a multi-state quasi-degeneracy S3/S2/S1. The populated S1 and T2 states will cross the lowest triplet state, and the S1 → T intersystem crossing happens in a multi-state quasi-degeneracy region S1/T2,3/T1 and is accelerated by selenium-substitution. The present study reveals the influence of both the chalcogen substitution element and initial spectroscopic state on the excited-state relaxation mechanism of nucleobase photosensitizers and also highlights the important role of multi-state quasi-degeneracy in mediating the complex relaxation process. These theoretical results provide additional insights into the intrinsic photophysics of nucleobase-based photosensitizers and are helpful for designing novel photo-sensitizers for real applications.
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Affiliation(s)
- Min Xie
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Shuang-Xiao Ren
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Die Hu
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Ji-Meng Zhong
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Jie Luo
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Yin Tan
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Yan-Ping Li
- School of Medicine, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Li-Ping Si
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
| | - Jun Cao
- School of Materials Science and Hydrogen Energy & Guangdong Key Laboratory for Hydrogen Energy Technologies, Foshan University, Foshan, Guangdong, 528000, P. R. China
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou, 550018, P. R. China.
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8
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Shu Y, Zhang L, Wu D, Chen X, Sun S, Truhlar DG. New Gradient Correction Scheme for Electronically Nonadiabatic Dynamics Involving Multiple Spin States. J Chem Theory Comput 2023; 19:2419-2429. [PMID: 37079755 DOI: 10.1021/acs.jctc.2c01173] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
It has been recommended that the best representation to use for trajectory surface hopping (TSH) calculations is the fully adiabatic basis in which the Hamiltonian is diagonal. Simulations of intersystem crossing processes with conventional TSH methods require an explicit computation of nonadiabatic coupling vectors (NACs) in the molecular-Coulomb-Hamiltonian (MCH) basis, also called the spin-orbit-free basis, in order to compute the gradient in the fully adiabatic basis (also called the diagonal representation). This explicit requirement destroys some of the advantages of the overlap-based algorithms and curvature-driven algorithms that can be used for the most efficient TSH calculations. Therefore, although these algorithms allow one to perform NAC-free simulations for internal conversion processes, one still requires NACs for intersystem crossing. Here, we show that how the NAC requirement is circumvented by a new computation scheme called the time-derivative-matrix scheme.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Linyao Zhang
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Dihua Wu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Xiye Chen
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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9
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Francés-Monerris A, Carmona-García J, Trabelsi T, Saiz-Lopez A, Lyons JR, Francisco JS, Roca-Sanjuán D. Photochemical and thermochemical pathways to S 2 and polysulfur formation in the atmosphere of Venus. Nat Commun 2022; 13:4425. [PMID: 35907911 PMCID: PMC9338966 DOI: 10.1038/s41467-022-32170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Polysulfur species have been proposed to be the unknown near-UV absorber in the atmosphere of Venus. Recent work argues that photolysis of one of the (SO)2 isomers, cis-OSSO, directly yields S2 with a branching ratio of about 10%. If correct, this pathway dominates polysulfur formation by several orders of magnitude, and by addition reactions yields significant quantities of S3, S4, and S8. We report here the results of high-level ab-initio quantum-chemistry computations that demonstrate that S2 is not a product in cis-OSSO photolysis. Instead, we establish a novel mechanism in which S2 is formed in a two-step process. Firstly, the intermediate S2O is produced by the coupling between the S and Cl atmospheric chemistries (in particular, SO reaction with ClS) and in a lesser extension by O-abstraction reactions from cis-OSSO. Secondly, S2O reacts with SO. This modified chemistry yields S2 and subsequent polysulfur abundances comparable to the photolytic cis-OSSO mechanism through a more plausible pathway. Ab initio quantification of the photodissociations at play fills a critical data void in current atmospheric models of Venus. Polysulfur compounds have been ascribed as the unknown near-UV absorbers in Venusian atmosphere and play a key role in the sulfur chemical cycle of this planet. Here, authors establish their production from (SO)2 on the grounds of quantifications of photochemical and thermal pathways involved in the sulfur chemical cycle of the planet.
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Affiliation(s)
| | - Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, 28006, Madrid, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, 28006, Madrid, Spain
| | | | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain.
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10
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Valverde D, Mai S, Canuto S, Borin AC, González L. Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water. JACS AU 2022; 2:1699-1711. [PMID: 35911449 PMCID: PMC9327080 DOI: 10.1021/jacsau.2c00250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S2 state that converts internally to the dark S1 state, from which the population is transferred to the triplet T2 state via intersystem crossing and finally to the lowest T1 state. This S2 → S1 → T2 → T1 deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T1 lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T1/S0 crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ1 = 131 fs and τ2 = 191 fs) that are in excellent agreement with the experimentally reported value (τexp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.
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Affiliation(s)
- Danillo Valverde
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sylvio Canuto
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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11
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Xie BB, Jia PK, Wang KX, Chen WK, Liu XY, Cui G. Generalized Ab Initio Nonadiabatic Dynamics Simulation Methods from Molecular to Extended Systems. J Phys Chem A 2022; 126:1789-1804. [PMID: 35266391 DOI: 10.1021/acs.jpca.1c10195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonadiabatic dynamics simulation has become a powerful tool to describe nonadiabatic effects involved in photophysical processes and photochemical reactions. In the past decade, our group has developed generalized trajectory-based ab initio surface-hopping (GTSH) dynamics simulation methods, which can be used to describe a series of nonadiabatic processes, such as internal conversion, intersystem crossing, excitation energy transfer and charge transfer of molecular systems, and photoinduced nonadiabatic carrier dynamics of extended systems with and without spin-orbit couplings. In this contribution, we will first give a brief introduction to our recently developed methods and related numerical implementations at different computational levels. Later, we will present some of our latest applications in realistic systems, which cover organic molecules, biological proteins, organometallic compounds, periodic organic and inorganic materials, etc. Final discussion is given to challenges and outlooks of ab initio nonadiabatic dynamics simulations.
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Affiliation(s)
- Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Ke-Xin Wang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, Sichuan, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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12
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Dimitriev OP. Dynamics of Excitons in Conjugated Molecules and Organic Semiconductor Systems. Chem Rev 2022; 122:8487-8593. [PMID: 35298145 DOI: 10.1021/acs.chemrev.1c00648] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The exciton, an excited electron-hole pair bound by Coulomb attraction, plays a key role in photophysics of organic molecules and drives practically important phenomena such as photoinduced mechanical motions of a molecule, photochemical conversions, energy transfer, generation of free charge carriers, etc. Its behavior in extended π-conjugated molecules and disordered organic films is very different and very rich compared with exciton behavior in inorganic semiconductor crystals. Due to the high degree of variability of organic systems themselves, the exciton not only exerts changes on molecules that carry it but undergoes its own changes during all phases of its lifetime, that is, birth, conversion and transport, and decay. The goal of this review is to give a systematic and comprehensive view on exciton behavior in π-conjugated molecules and molecular assemblies at all phases of exciton evolution with emphasis on rates typical for this dynamic picture and various consequences of the above dynamics. To uncover the rich variety of exciton behavior, details of exciton formation, exciton transport, exciton energy conversion, direct and reverse intersystem crossing, and radiative and nonradiative decay are considered in different systems, where these processes lead to or are influenced by static and dynamic disorder, charge distribution symmetry breaking, photoinduced reactions, electron and proton transfer, structural rearrangements, exciton coupling with vibrations and intermediate particles, and exciton dissociation and annihilation as well.
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Affiliation(s)
- Oleg P Dimitriev
- V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, pr. Nauki 41, Kyiv 03028, Ukraine
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13
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Teles-Ferreira DC, Manzoni C, Martínez-Fernández L, Cerullo G, de Paula AM, Borrego-Varillas R. Ultrafast Excited-State Decay Mechanisms of 6-Thioguanine Followed by Sub-20 fs UV Transient Absorption Spectroscopy. Molecules 2022; 27:molecules27041200. [PMID: 35208987 PMCID: PMC8878119 DOI: 10.3390/molecules27041200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/23/2022] Open
Abstract
Understanding the primary steps following UV photoexcitation in sulphur-substituted DNA bases (thiobases) is fundamental for developing new phototherapeutic drugs. However, the investigation of the excited-state dynamics in sub-100 fs time scales has been elusive until now due to technical challenges. Here, we track the ultrafast decay mechanisms that lead to the electron trapping in the triplet manifold for 6-thioguanine in an aqueous solution, using broadband transient absorption spectroscopy with a sub-20 fs temporal resolution. We obtain experimental evidence of the fast internal conversion from the S2(ππ*) to the S1(nπ*) states, which takes place in about 80 fs and demonstrates that the S1(nπ*) state acts as a doorway to the triplet population in 522 fs. Our results are supported by MS-CASPT2 calculations, predicting a planar S2(ππ*) pseudo-minimum in agreement with the stimulated emission signal observed in the experiment.
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Affiliation(s)
| | - Cristian Manzoni
- Istituto di Fotonica e Nanotecnologie-Consiglio Nazionale delle Ricerche (IFN-CNR), Piazza Leonardo da Vinci 32, I-20133 Milano, Italy; (C.M.); (G.C.)
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain;
| | - Giulio Cerullo
- Istituto di Fotonica e Nanotecnologie-Consiglio Nazionale delle Ricerche (IFN-CNR), Piazza Leonardo da Vinci 32, I-20133 Milano, Italy; (C.M.); (G.C.)
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Rocío Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie-Consiglio Nazionale delle Ricerche (IFN-CNR), Piazza Leonardo da Vinci 32, I-20133 Milano, Italy; (C.M.); (G.C.)
- Correspondence:
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14
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Xie BB, Tang XF, Liu XY, Chang XP, Cui G. Mechanistic photophysics and photochemistry of unnatural bases and sunscreen molecules: insights from electronic structure calculations. Phys Chem Chem Phys 2021; 23:27124-27149. [PMID: 34849517 DOI: 10.1039/d1cp03994f] [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
Photophysics and photochemistry are basic subjects in the study of light-matter interactions and are ubiquitous in diverse fields such as biology, energy, materials, and environment. A full understanding of mechanistic photophysics and photochemistry underpins many recent advances and applications. This contribution first provides a short discussion on the theoretical calculation methods we have used in relevant studies, then we introduce our latest progress on the mechanistic photophysics and photochemistry of two classes of molecular systems, namely unnatural bases and sunscreens. For unnatural bases, we disclose the intrinsic driving forces for the ultrafast population to reactive triplet states, impacts of the position and degree of chalcogen substitutions, and the effects of complex environments. For sunscreen molecules, we reveal the photoprotection mechanisms that dissipate excess photon energy to the surroundings by ultrafast internal conversion to the ground state. Finally, relevant theoretical challenges and outlooks are discussed.
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Affiliation(s)
- Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China.
| | - Xiu-Fang Tang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China.
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan, 610068, China
| | - Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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15
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Mukherjee S, Varganov SA. Intersystem crossing and internal conversion dynamics with GAIMS-TeraChem: Excited state relaxation in 2-cyclopentenone. J Chem Phys 2021; 155:174107. [PMID: 34742200 DOI: 10.1063/5.0068040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Excited states relaxation in complex molecules often involves two types of nonradiative transitions, internal conversion (IC) and intersystem crossing (ISC). In the situations when the timescales of IC and ISC are comparable, an interplay between these two types of transitions can lead to complex nonadiabatic dynamics on multiple electronic states of different characters and spin multiplicities. We demonstrate that the generalized ab initio multiple spawning (GAIMS) method interfaced with the fast graphics processing unit-based TeraChem electronic structure code can be used to model such nonadiabatic dynamics involving both the IC and ISC transitions in molecules of moderate size. We carried out 1500 fs GAIMS simulations leading to the creation of up to 2500 trajectory basis functions to study the excited states relaxation in 2-cyclopentenone. After a vertical excitation from the ground state to the bright S2 state, the molecule quickly relaxes to the S1 state via conical intersection. The following relaxation proceeds along two competing pathways: one involves IC to the ground state, and the other is dominated by ISC to the low-lying triplet states. The time constants describing the population transfer between the six lowest singlet and triplet states predicted by the GAIMS dynamics are in good agreement with the characteristic times of IC and ISC obtained from the analysis of the time-resolved photoelectron spectrum.
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Affiliation(s)
- Saikat Mukherjee
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, USA
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, USA
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16
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Zhu YH, Tang XF, Chang XP, Zhang TS, Xie BB, Cui G. Mechanistic Photophysics of Tellurium-Substituted Uracils: Insights from Multistate Complete-Active-Space Second-Order Perturbation Calculations. J Phys Chem A 2021; 125:8816-8826. [PMID: 34606278 DOI: 10.1021/acs.jpca.1c06169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The photophysical mechanisms of tellurium-substituted uracils were studied at the multistate complete-active-space second-order perturbation level with a particular focus on how the position and number of tellurium substitutions affect their nonadiabatic relaxation processes. Electronic structure analysis reveals that the lowest several excited states are closely concerned with the n and π orbitals at the Te7-C2 [Te8-C4] moiety of 2-tellurouracil (2TeU) [4TeU and 24TeU]. Both planar and twisted minima were optimized for 2TeU, whereas only planar ones were obtained for 4TeU and 24TeU, except for a twisted T1 minimum of 4TeU. Based on intersection structures and linearly interpolated internal coordinate paths, we proposed several feasible excited-state deactivation paths. It is found that the relaxation channels for 2TeU are more complicated than those of 4TeU and 24TeU. The electronic population transfer to the T1 state for 2TeU is easier than that for 4TeU and 24TeU in consideration of the barrier heights from the S2 Franck-Condon point to the S2/S1 or S2/T2 intersections. In addition, the recovery of the ground state from the T1 state for 2TeU will be more efficient than that for the other two systems as well.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiu-Fang Tang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, P. R. China
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, P R. China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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17
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Liu J, Lan Z, Yang J. An efficient implementation of spin-orbit coupling within the framework of semiempirical orthogonalization-corrected methods for ultrafast intersystem crossing dynamics. Phys Chem Chem Phys 2021; 23:22313-22323. [PMID: 34591049 DOI: 10.1039/d1cp03477d] [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
We implement spin-orbit coupling (SOC) within the framework of semiempirical orthogonalization-corrected methods (OMx). The excited-state wavefunction is generated from configuration interaction with single excitations (CIS). The SOC Hamiltonian in terms of the one-electron Breit-Pauli operator with effective nuclear charges is adopted in this work. Benchmark calculations show that SOCs evaluated using the OMx/CIS method agree very well with those obtained from time-dependent density functional theory. As a particularly attractive application, we incorporate SOCs between singlet and triplet states into Tully's fewest switches surface hopping algorithm to enable excited-state nonadiabatic dynamics simulations, treating internal conversion and intersystem crossing on an equal footing. This semiempirical dynamics simulation approach is applied to investigate ultrafast intersystem crossing processes in core-substituted naphthalenediimides.
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Affiliation(s)
- Jie Liu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.
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18
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Ortiz-Rodríguez LA, Ortiz-Zayas G, Pollum M, Hoehn SJ, Jockusch S, Crespo-Hernández CE. Intramolecular Charge Transfer in the Azathioprine Prodrug Quenches Intersystem Crossing to the Reactive Triplet State in 6-Mercaptopurine †. Photochem Photobiol 2021; 98:617-632. [PMID: 34480764 DOI: 10.1111/php.13513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
The thiopurine prodrugs 6-mercaptopurine and azathioprine are among the world's essential medications for acute lymphoblastic leukemia, immunosuppression and several autoimmune conditions. Thiopurine prodrugs are efficient UVA absorbers and singlet oxygen generators and the long-term treatment with these prodrugs correlates with a high incidence of sunlight-induced skin cancer in patients. In this contribution, we show that the electronic relaxation mechanisms and photochemical properties of azathioprine are remarkably different from those of 6-mercaptopurine upon absorption of UVA radiation. UVA excitation of 6-mercaptopurine results in nearly 100% triplet yield and up to 30% singlet oxygen generation, whereas excitation of azathioprine with UVA leads to triplet yields of 15-3% depending on pH of the aqueous solution and <1% singlet oxygen generation. While photoexcitation of 6-mercaptopurine and other thiopurine prodrugs can facilitate oxidatively generated cell damage, azathioprine's poor photosensitization ability reveals the use of interchromophoric charge-transfer interactions for the molecular design of photostable prodrugs exhibiting a remarkable reduction in photocytotoxic side effects before drug metabolization.
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Affiliation(s)
| | | | - Marvin Pollum
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
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19
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Janicki M, Kufner CL, Todd ZR, Kim SC, O’Flaherty DK, Szostak JW, Šponer J, Góra RW, Sasselov DD, Szabla R. Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides. J Phys Chem Lett 2021; 12:6707-6713. [PMID: 34260253 PMCID: PMC9634911 DOI: 10.1021/acs.jpclett.1c01384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of singlet oxygen. Here, we show that the photochemistry of a thionucleobase can be considerably modified in a nucleoside, that is, by the presence of ribose. Our transient absorption spectroscopy experiments demonstrate that thiocytosine exhibits 5 times longer excited-state lifetime and different excited-state absorption features than thiocytidine. On the basis of accurate quantum chemical simulations, we assign these differences to the dominant population of a shorter-lived triplet nπ* state in the nucleoside and longer-lived triplet ππ* states in the nucleobase. This explains the distinctive photoanomerziation of thiocytidine and indicates that the nucleoside will be a less efficient phototherapeutic agent with regard to singlet oxygen generation.
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Affiliation(s)
- Mikołaj
J. Janicki
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Corinna L. Kufner
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Zoe R. Todd
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Seohyun C. Kim
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Derek K. O’Flaherty
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jiří Šponer
- Institute
of Biophysics, Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech
Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacky
University Olomouc, Slechtitelu
241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Robert W. Góra
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Dimitar D. Sasselov
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Rafał Szabla
- EaStCHEM,
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, U.K.
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20
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Carmona-García J, Francés-Monerris A, Cuevas CA, Trabelsi T, Saiz-Lopez A, Francisco JS, Roca-Sanjuán D. Photochemistry and Non-adiabatic Photodynamics of the HOSO Radical. J Am Chem Soc 2021; 143:10836-10841. [PMID: 34270223 DOI: 10.1021/jacs.1c05149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydroxysulfinyl radical (HOSO) is important due to its involvement in climate geoengineering upon SO2 injection and generation of the highly hygroscopic H2SO4. Its photochemical behavior in the upper atmosphere is, however, uncertain. Here we present the ultraviolet-visible photochemistry and photodynamics of this species by simulating the atmospheric conditions with high-level quantum chemistry methods. Photocleavage to HO + SO arises as the major solar-induced channel, with a minor contribution of H + SO2 photoproducts. The efficient generation of SO is relevant due to its reactivity with O3 and the consequent depletion of ozone in the stratosphere.
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Affiliation(s)
- Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Antonio Francés-Monerris
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain.,Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Carlos A Cuevas
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain
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21
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Zhu YH, Zhang TS, Tang XF, Xie BB, Cui G. MS-CASPT2 studies on the mechanistic photophysics of tellurium-substituted guanine and cytosine. Phys Chem Chem Phys 2021; 23:12421-12430. [PMID: 34028476 DOI: 10.1039/d1cp01142a] [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
Sulfur-substituted nucleobases are highly promising photosensitizers that are widely used in photodynamic therapy, and there are numerous studies exploring their unique photophysical behaviors. However, relevant photophysical investigations on selenium and tellurium substitutions are still rare. Herein, the high-level multistate complete-active-space second-order perturbation (MS-CASPT2) method was performed for the first time to explore the excited-state relaxation processes of tellurium-substituted guanine (TeG) and cytosine (TeC). Based on the electronic state properties in the Franck-Condon (FC) region, we found that the lowest five (S0, S1, S2, T1, and T2) and six (S0, S1, S2, T1, T2 and T3) states will participate in the nonadiabatic transition processes of TeG and TeC systems, respectively. In these electronic states, two kinds of minimum and intersection structures (i.e., planar and twisted structures) were obtained for both TeG and TeC systems. The linearly interpolated internal coordinate (LIIC) paths and spin-orbit coupling (SOC) constants revealed several possible planar and twisted excited-state decay channels, which could lead the systems to the lowest reactive triplet state of T1. Small energy barriers in the T1 state will trap the TeG and TeC systems for a while before they finally populate to the ground state. Although tellurium substitution would further redshift the absorption wavelength and enhance the intersystem crossing (ISC) rate to the T1 state compared with sulfur and selenium substitutions, the rapid ISC process of T1 → S0 may make it a less effective photosensitizer to sensitize the molecular oxygen. We believe our present work will provide important mechanistic insights into the photophysics of tellurium-substituted nucleobases.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, P. R. China
| | - Xiu-Fang Tang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China.
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China.
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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22
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Abstract
In this article, we review nonadiabatic molecular dynamics (NAMD) methods for modeling spin-crossover transitions. First, we discuss different representations of electronic states employed in the grid-based and direct NAMD simulations. The nature of interstate couplings in different representations is highlighted, with the main focus on nonadiabatic and spin-orbit couplings. Second, we describe three NAMD methods that have been used to simulate spin-crossover dynamics, including trajectory surface hopping, ab initio multiple spawning, and multiconfiguration time-dependent Hartree. Some aspects of employing different electronic structure methods to obtain information about potential energy surfaces and interstate couplings for NAMD simulations are also discussed. Third, representative applications of NAMD to spin crossovers in molecular systems of different sizes and complexities are highlighted. Finally, we pose several fundamental questions related to spin-dependent processes. These questions should be possible to address with future methodological developments in NAMD.
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Affiliation(s)
- Saikat Mukherjee
- Institut de Chimie Radicalaire, CNRS 7273, Aix-Marseille University, 13013 Marseille, France;
| | - Dmitry A Fedorov
- Oak Ridge Associated Universities, Oak Ridge, Tennessee 37830, USA;
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, USA;
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23
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Valverde D, Mai S, Sanches de Araújo AV, Canuto S, González L, Borin AC. On the population of triplet states of 2-seleno-thymine. Phys Chem Chem Phys 2021; 23:5447-5454. [PMID: 33650609 DOI: 10.1039/d1cp00041a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The population and depopulation mechanisms leading to the lowest-lying triplet states of 2-Se-Thymine were studied at the MS-CASPT2/cc-pVDZ level of theory. Several critical points on different potential energy hypersurfaces were optimized, including minima, conical intersections, and singlet-triplet crossings. The accessibility of all relevant regions on the potential energy hypersurfaces was investigated by means of minimum energy paths and linear interpolation in internal coordinates techniques. Our analysis indicates that, after the population of the bright S2 state in the Franck-Condon region, the first photochemical event is a barrierless evolution towards one of its two minima. After that, three viable photophysical deactivation paths can take place. In one of them, the population in the S2 state is transferred to the T2 state via intersystem crossing and subsequently to the T1 state by internal conversion. Alternatively, the S1 state could be accessed by internal conversion through two distinct conical intersections with S2 state followed by singlet-triplet crossing with the T2 state. The absence of a second minimum on the T1 state and a small energy barrier on pathway along the potential energy surface towards the ground state from the lowest triplet state are attributed as potential reasons to explain why the lifetime of the triplet state of 2-Se-Thymine might be reduced in comparison with its thio-analogue.
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Affiliation(s)
- Danillo Valverde
- Institute of Physics, University of São Paulo, Rua do Matão 1371. 05508-090, São Paulo, SP, Brazil
| | - Sebastian Mai
- Photonics Institute, Vienna University of Technology, Gußhausstraße 27-29, 1040 Vienna, Austria and 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. 05508-090, São Paulo, SP, Brazil
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - 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.
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24
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Euceda N, Jahnke J, Espinal A, Louis MF, Bashkin E, Roccanova P, Espaillat A, Fuentes GV, Nieto F, Gao R. Thioguanine restoration through type I photosensitization-superoxide oxidation-glutathione reduction cycles. Phys Chem Chem Phys 2021; 23:5069-5073. [PMID: 33655288 DOI: 10.1039/d1cp00101a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UVA-induced deleterious effect of thiopurine prodrugs including azathioprine, 6-mercaptopurine and 6-thioguanine (6-TG) increases the risk of cancer development due to the incorporation of 6-TG in patients' DNA. The catalytic mechanism by which thiobases act as a sustained oxidant producer has yet to be explored, especially through the Type I electron transfer pathway that produces superoxide radicals (O2˙-). Under Fenton-like conditions O2˙- radicals convert to extremely reactive hydroxyl radicals (˙OH), thus carrying even higher risk of biological damage than that induced by the well-studied type II reaction. By monitoring 6-TG/UVA-induced photochemistry in mass spectra and superoxide radicals (O2˙-) via nitro blue tetrazolium (NBT) reduction, this work provides two new findings: (1) in the presence of reduced glutathione (GSH), the production of O2˙-via the type I reaction is enhanced 10-fold. 6-TG thiyl radicals are identified as the primary intermediate formed in the reaction of 6-TG with O2˙-. The restoration of 6-TG and concurrent generation of O2˙- occur via a 3-step-cycle: 6-TG type I photosensitization, O2˙- oxidation and GSH reduction. (2) In the absence of GSH, 6-TG thiyl radicals undergo oxygen addition and sulfur dioxide removal to form carbon radicals (C6) which further convert to thioether by reacting with 6-TG molecules. These findings help explain not only thiol-regulation in a biological system but chemoprevention of cancer.
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Affiliation(s)
- Nelson Euceda
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Joyce Jahnke
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Aileen Espinal
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Monique F Louis
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Edan Bashkin
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Patricia Roccanova
- Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA
| | - Abraham Espaillat
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - German V Fuentes
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - Fernando Nieto
- Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA
| | - Ruomei Gao
- Chemistry and Physics Department, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
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25
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Moitra T, Karak P, Chakraborty S, Ruud K, Chakrabarti S. Behind the scenes of spin-forbidden decay pathways in transition metal complexes. Phys Chem Chem Phys 2021; 23:59-81. [PMID: 33319894 DOI: 10.1039/d0cp05108j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The interpretation of the ultrafast photophysics of transition metal complexes following photo-absorption is quite involved as the heavy metal center leads to a complicated and entangled singlet-triplet manifold. This opens up multiple pathways for deactivation, often with competitive rates. As a result, intersystem crossing (ISC) and phosphorescence are commonly observed in transition metal complexes. A detailed understanding of such an excited-state structure and dynamics calls for state-of-the-art experimental and theoretical methodologies. In this review, we delve into the inability of non-relativistic quantum theory to describe spin-forbidden transitions, which can be overcome by taking into account spin-orbit coupling, whose importance grows with increasing atomic number. We present the quantum chemical theory of phosphorescence and ISC together with illustrative examples. Finally, a few applications are highlighted, bridging the gap between theoretical studies and experimental applications, such as photofunctional materials.
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Affiliation(s)
- Torsha Moitra
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
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26
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Talotta F, Morisset S, Rougeau N, Lauvergnat D, Agostini F. Internal Conversion and Intersystem Crossing with the Exact Factorization. J Chem Theory Comput 2020; 16:4833-4848. [PMID: 32633509 DOI: 10.1021/acs.jctc.0c00493] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a detailed derivation of the generalized coupled-trajectory mixed quantum-classical (G-CT-MQC) algorithm based on the exact-factorization equations. The ultimate goal is to propose an algorithm that can be employed for molecular dynamics simulations of nonradiative phenomena, as the spin-allowed internal conversions and the spin-forbidden intersystem crossings. Internal conversions are nonadiabatic processes driven by the kinetic coupling between electronic states, whereas intersystem crossings are mediated by the spin-orbit coupling. In this paper, we discuss computational issues related to the suitable representation for electronic dynamics and the different natures of kinetic and spin-orbit coupling. Numerical studies on model systems allow us to test the performance of the G-CT-MQC algorithm in different situations.
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Affiliation(s)
- Francesco Talotta
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405 Orsay, France.,Institut des Sciences Moléculaires d'Orsay, CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Sabine Morisset
- Institut des Sciences Moléculaires d'Orsay, CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Nathalie Rougeau
- Institut des Sciences Moléculaires d'Orsay, CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - David Lauvergnat
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Federica Agostini
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405 Orsay, France
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27
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Tang J, Wang L, Loredo A, Cole C, Xiao H. Single-atom replacement as a general approach towards visible-light/near-infrared heavy-atom-free photosensitizers for photodynamic therapy. Chem Sci 2020; 11:6701-6708. [PMID: 32953031 PMCID: PMC7473402 DOI: 10.1039/d0sc02286a] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/30/2020] [Indexed: 12/31/2022] Open
Abstract
Photodynamic therapy has become an emerging strategy for the treatment of cancer. This technology relies on the development of photosensitizers (PSs) that convert molecular oxygen to cytotoxic reactive oxygen species upon exposure to light. In this study, we have developed a facile and general strategy for obtaining visible light/near-infrared-absorbing PSs by performing a simple sulfur-for-oxygen replacement within existing fluorophores. Thionation of carbonyl groups within existing fluorophore cores leads to an improvement of the singlet oxygen quantum yield and molar absorption coefficient at longer wavelengths (deep to 600-800 nm). Additionally, these thio-based PSs lack dark cytotoxicity but exhibit significant phototoxicity against monolayer cancer cells and 3D multicellular tumor spheroids with IC50 in the micromolar range. To achieve tumor-specific delivery, we have conjugated these thio-based PSs to an antibody and demonstrated their tumor-specific therapeutic activity.
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Affiliation(s)
- Juan Tang
- Department of Chemistry , Rice University , 6100 Main Street , Houston , Texas 77005 , USA .
| | - Lushun Wang
- Department of Chemistry , Rice University , 6100 Main Street , Houston , Texas 77005 , USA .
| | - Axel Loredo
- Department of Chemistry , Rice University , 6100 Main Street , Houston , Texas 77005 , USA .
| | - Carson Cole
- Department of Chemistry , Rice University , 6100 Main Street , Houston , Texas 77005 , USA .
| | - Han Xiao
- Department of Chemistry , Rice University , 6100 Main Street , Houston , Texas 77005 , USA .
- Department of Biosciences , Rice University , 6100 Main Street , Houston , Texas 77005 , USA
- Department of Bioengineering , Rice University , 6100 Main Street , Houston , Texas 77005 , USA
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28
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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.
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Affiliation(s)
- Qin Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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29
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Kochman MA, Durbeej B. Simulating the Nonadiabatic Relaxation Dynamics of 4-( N, N-Dimethylamino)benzonitrile (DMABN) in Polar Solution. J Phys Chem A 2020; 124:2193-2206. [PMID: 32083861 DOI: 10.1021/acs.jpca.9b10588] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The compound 4-(N,N-dimethylamino)benzonitrile (DMABN) represents the archetypal system for dual fluorescence, a rare photophysical phenomenon in which a given fluorophore shows two distinct emission bands. Despite extensive studies, the underlying mechanism remains the subject of debate. In the present contribution, we address this issue by simulating the excited-state relaxation process of DMABN as it occurs in polar solution. The potential energy surfaces for the system are constructed with the use of the additive quantum mechanics/molecular mechanics (QM/MM) method, and the coupled dynamics of the electronic wave function and the nuclei is propagated with the semiclassical fewest switches surface hopping method. The DMABN molecule, which comprises the QM subsystem, is treated with the use of the second-order algebraic diagrammatic construction (ADC(2)) method with the imposition of spin-opposite scaling (SOS). It is verified that this level of theory achieves a realistic description of the excited-state potential energy surfaces of DMABN. The simulation results qualitatively reproduce the main features of the experimentally observed fluorescence spectrum, thus allowing the unambiguous assignment of the two fluorescence bands: the normal band is due to the near-planar locally excited (LE) structure of DMABN, while the so-called "anomalous" second band arises from the twisted intramolecular charge transfer (TICT) structure. The transformation of the LE structure into the TICT structure takes place directly via intramolecular rotation, and is not mediated by another excited-state structure. In particular, the oft-discussed rehybridized intramolecular charge transfer (RICT) structure, which is characterized by a bent nitrile group, does not play a role in the relaxation process.
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Affiliation(s)
- Michał Andrzej Kochman
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden.,Department of Chemistry, University College London (UCL), 20 Gordon Street, London WC1H 0A, United Kingdom
| | - Bo Durbeej
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
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30
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Norell J, Odelius M, Vacher M. Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024101. [PMID: 32206689 PMCID: PMC7078009 DOI: 10.1063/1.5143228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S 2 ( π , π * ) state is found to promptly relax to S 1 ( n , π * ) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both complex population transfers among all the available states and intersystem crossing predominantly through the "El-Sayed forbidden" S 1 ( n , π * ) to T 2 ( n , π * ) channel, through significant mixing of electronic excitation characters. Despite this complexity, the femto- to picosecond triplet population, expected from several spectroscopic measurements, is well described as a simple exponential decay of the singlet state manifold. No proton transfer is found in the reported trajectories, but two mechanisms for its possible mediation in previously reported experiments are proposed based on the observed structural dynamics: (i) ultrafast intra-molecular transfer driven by the initially coherent in-plane motion and (ii) inter-molecular solvent-mediated transfer driven by the out-of-plane modes that dominate the later motion.
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Affiliation(s)
- Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
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31
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Brister MM, Gustavsson T, Crespo-Hernández CE. Excited State Lifetimes of Sulfur-Substituted DNA and RNA Monomers Probed Using the Femtosecond Fluorescence Up-Conversion Technique. Molecules 2020; 25:E584. [PMID: 32013184 PMCID: PMC7037914 DOI: 10.3390/molecules25030584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 11/16/2022] Open
Abstract
Sulfur-substituted DNA and RNA nucleobase derivatives (a.k.a., thiobases) are an important family of biomolecules. They are used as prodrugs and as chemotherapeutic agents in medical settings, and as photocrosslinker molecules in structural-biology applications. Remarkably, excitation of thiobases with ultraviolet to near-visible light results in the population of long-lived and reactive triplet states on a time scale of hundreds of femtoseconds and with near-unity yields. This efficient nonradiative decay pathway explains the vanishingly small fluorescence yields reported for the thiobases and the scarcity of fluorescence lifetimes in the literature. In this study, we report fluorescence lifetimes for twelve thiobase derivatives, both in aqueous solution at physiological pH and in acetonitrile. Excitation is performed at 267 and 362 nm, while fluorescence emission is detected at 380, 425, 450, 525, or 532 nm. All the investigated thiobases reveal fluorescence lifetimes that decay in a few hundreds of femtoseconds and with magnitudes that depend and are sensitive to the position and degree of sulfur-atom substitution and on the solvent environment. Interestingly, however, three thiopyrimidine derivatives (i.e., 2-thiocytidine, 2-thiouridine, and 4-thiothymidine) also exhibit a small amplitude fluorescence component of a few picoseconds in aqueous solution. Furthermore, the N-glycosylation of thiobases to form DNA or RNA nucleoside analogues is demonstrated as affecting their fluorescence lifetimes. In aqueous solution, the fluorescence decay signals exciting at 267 nm are equal or slower than those collected exciting at 362 nm. In acetonitrile, however, the fluorescence decay signals recorded upon 267 nm excitation are, in all cases, faster than those measured exciting at 362 nm. A comparison to the literature values show that, while both the DNA and RNA nucleobase and thiobase derivatives exhibit sub-picosecond fluorescence lifetimes, the 1ππ* excited-state population in the nucleobase monomers primarily decay back to the ground state, whereas it predominantly populates long-lived and reactive triplet states in thiobase monomers.
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Affiliation(s)
- Matthew M. Brister
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA;
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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32
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Talotta F, Morisset S, Rougeau N, Lauvergnat D, Agostini F. Spin-Orbit Interactions in Ultrafast Molecular Processes. PHYSICAL REVIEW LETTERS 2020; 124:033001. [PMID: 32031839 DOI: 10.1103/physrevlett.124.033001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Indexed: 06/10/2023]
Abstract
We investigate spin-orbit interactions in ultrafast molecular processes employing the exact factorization of the electron-nuclear wave function. We revisit the original derivation by including spin-orbit coupling, and show how the dynamics driven by the time-dependent potential energy surface alleviates inconsistencies arising from different electronic representations. We propose a novel trajectory-based scheme to simulate spin-forbidden non-radiative processes, and we show its performance in the treatment of excited-state dynamics where spin-orbit effects couple different spin multiplets.
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Affiliation(s)
- Francesco Talotta
- Laboratoire de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
- Institut de Sciences Moléculaires d'Orsay, UMR 8214 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Sabine Morisset
- Institut de Sciences Moléculaires d'Orsay, UMR 8214 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Nathalie Rougeau
- Institut de Sciences Moléculaires d'Orsay, UMR 8214 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - David Lauvergnat
- Laboratoire de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Federica Agostini
- Laboratoire de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
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33
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Francés‐Monerris A, Carmona‐García J, Acuña AU, Dávalos JZ, Cuevas CA, Kinnison DE, Francisco JS, Saiz‐Lopez A, Roca‐Sanjuán D. Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Antonio Francés‐Monerris
- Université de LorraineCNRS, LPCT 54000 Nancy France
- Departamento de Química FísicaUniversitat de València 46100 Burjassot Spain
| | | | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | | | - Joseph S. Francisco
- Department of Earth and Environmental Sciences and Department of ChemistryUniversity of Pennsylvania Philadelphia PA 19104 USA
| | - Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
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34
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Francés‐Monerris A, Carmona‐García J, Acuña AU, Dávalos JZ, Cuevas CA, Kinnison DE, Francisco JS, Saiz‐Lopez A, Roca‐Sanjuán D. Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury. Angew Chem Int Ed Engl 2020; 59:7605-7610. [DOI: 10.1002/anie.201915656] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Antonio Francés‐Monerris
- Université de LorraineCNRS, LPCT 54000 Nancy France
- Departamento de Química FísicaUniversitat de València 46100 Burjassot Spain
| | | | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | | | - Joseph S. Francisco
- Department of Earth and Environmental Sciences and Department of ChemistryUniversity of Pennsylvania Philadelphia PA 19104 USA
| | - Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
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35
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Lykhin AO, Varganov SA. Intersystem crossing in tunneling regime: T 1 → S 0 relaxation in thiophosgene. Phys Chem Chem Phys 2020; 22:5500-5508. [PMID: 32101195 DOI: 10.1039/c9cp06956a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The T1 excited state relaxation in thiophosgene has attracted much attention as a relatively simple model for the intersystem crossing (ISC) transitions in polyatomic molecules. The very short (20-40 ps) T1 lifetime predicted in several theoretical studies strongly disagrees with the experimental values (∼20 ns) indicating that the kinetics of T1 → S0 ISC is not well understood. We use the nonadiabatic transition state theory (NA-TST) with the Zhu-Nakamura transition probability and the multireference perturbation theory (CASPT2) to show that the T1 → S0 ISC occurs in the quantum tunneling regime. We also introduce a new zero-point vibrational energy correction scheme that improves the accuracy of the predicted ISC rate constants at low internal energies. The predicted lifetimes of the T1 vibrational states are between one and two orders of magnitude larger than the experimental values. This overestimation is attributed to the multidimensional nature of quantum tunneling that facilitates ISC transitions along the non-minimum energy path and is not accounted for in the one-dimensional NA-TST.
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Affiliation(s)
- Aleksandr O Lykhin
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557-0216, USA.
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557-0216, USA.
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36
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Mai S, González L. Identification of important normal modes in nonadiabatic dynamics simulations by coherence, correlation, and frequency analyses. J Chem Phys 2019; 151:244115. [DOI: 10.1063/1.5129335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
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37
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Nguyen VN, Qi S, Kim S, Kwon N, Kim G, Yim Y, Park S, Yoon J. An Emerging Molecular Design Approach to Heavy-Atom-Free Photosensitizers for Enhanced Photodynamic Therapy under Hypoxia. J Am Chem Soc 2019; 141:16243-16248. [DOI: 10.1021/jacs.9b09220] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Van-Nghia Nguyen
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sujie Qi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sangin Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Nahyun Kwon
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Gyoungmi Kim
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yubin Yim
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sungnam Park
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Juyoung Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
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38
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Kochman MA, Durbeej B. Theoretical Study of Ground- and Excited-State Charge Transfer in Fulvene-Based Donor–Acceptor Systems. J Phys Chem A 2019; 123:6660-6673. [DOI: 10.1021/acs.jpca.9b02962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michał Andrzej Kochman
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Bo Durbeej
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
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39
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Fang YG, Peng Q, Fang Q, Fang W, Cui G. MS-CASPT2 Studies on the Photophysics of Selenium-Substituted Guanine Nucleobase. ACS OMEGA 2019; 4:9769-9777. [PMID: 31460068 PMCID: PMC6649137 DOI: 10.1021/acsomega.9b01276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 05/30/2023]
Abstract
The MS-CASPT2 method has been employed to optimize minimum-energy structures of 6-selenoguanine (6SeGua) and related two- and three-state intersection structures in and between the lowest five electronic states, i.e., S2(1ππ*), S1(1 nπ*), T2(3 nπ*), T1(3ππ*), and S0. In combination with MS-CASPT2 calculated linearly interpolated internal coordinate paths, the photophysical mechanism of 6SeGua has been proposed. The initially populated S2(1ππ*) state decays to either S1(1 nπ*) or T2(3 nπ*) states through a three-state S2/S1/T2 intersection point. The large S2/T2 spin-orbit coupling of 435 cm-1, according to the classical El-Sayed rule, benefits the S2 → T2 intersystem crossing process. The S1(1 nπ*) state that stems from the S2 → S1 internal conversion process at the S2/S1/T2 intersection point can further jump to the T2(3 nπ*) state through the S1 → T2 intersystem crossing process. This process does not comply with the El-Sayed rule, but it is still related to a comparatively large spin-orbit coupling of 39 cm-1 and is expected to occur relatively fast. Finally, the T2(3 nπ*) state, which is populated from the above S2 → T2 and S1 → T2 intersystem crossing processes, decays to the T1(3ππ*) state via an internal conversion process. Because there is merely a small energy barrier of 0.11 eV separating the T1(3ππ*) minimum and an energetically allowed two-state T1/S0 intersection point, the T1(3ππ*) state still can decay to the S0 state quickly, which is also enhanced by a large T1/S0 spin-orbit coupling of 252 cm-1. Our proposed mechanism explains experimentally observed ultrafast intersystem crossing processes in 6SeGua and its 835-fold acceleration of the T1 state decay to the S0 state compared with 6tGua. Finally, we have found that the ground-state electronic structure of 6SeGua has more apparent multireference character.
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Zhang TS, Li ZW, Fang Q, Barbatti M, Fang WH, Cui G. Stereoselective Excited-State Isomerization and Decay Paths in cis-Cyclobiazobenzene. J Phys Chem A 2019; 123:6144-6151. [DOI: 10.1021/acs.jpca.9b04372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Zi-Wen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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Martinez-Fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Martì J, Mori M, Mely Y, Improta R. Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine. Chemistry 2019; 25:7375-7386. [PMID: 30882930 DOI: 10.1002/chem.201900677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias, Modúlo13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Rajhans Sharma
- 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
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Javier Segarra Martì
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134, Napoli, Italy
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42
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Aguilera-Porta N, Granucci G, Munoz-Muriedas J, Corral I. Unveiling the photophysics of thiourea from CASPT2/CASSCF potential energy surfaces and singlet/triplet excited state molecular dynamics simulations. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Aguilera-Porta N, Corral I, Munoz-Muriedas J, Granucci G. Excited state dynamics of some nonsteroidal anti-inflammatory drugs: A surface-hopping investigation. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Xia Y, Wang F, Wang RN, Liu KH, Su HM. Reaction kinetics between thiobases and singlet oxygen studied by direct detection of the 1O2 luminescence decay. CHINESE J CHEM PHYS 2019. [DOI: 10.1063/1674-0068/cjcp1811268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ye Xia
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Fei Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ren-nian Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Kun-hui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hong-mei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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45
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Janicki MJ, Roberts SJ, Šponer J, Powner MW, Góra RW, Szabla R. Photostability of oxazoline RNA-precursors in UV-rich prebiotic environments. Chem Commun (Camb) 2018; 54:13407-13410. [PMID: 30426980 DOI: 10.1039/c8cc07343k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pentose aminooxazolines and oxazolidinone thiones are considered as the key precursors which could have enabled the formation of RNA nucleotides under the conditions of early Earth. UV-irradiation experiments and quantum-chemical calculations demonstrate that these compounds are remarkably photostable and could accumulate over long periods of time in UV-rich prebiotic environments to undergo stereoisomeric purification.
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Affiliation(s)
- Mikołaj J Janicki
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Faculty of Chemistry, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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Dsouza R, Cheng X, Li Z, Miller RJD, Kochman MA. Oscillatory Photoelectron Signal of N-Methylmorpholine as a Test Case for the Algebraic-Diagrammatic Construction Method of Second Order. J Phys Chem A 2018; 122:9688-9700. [DOI: 10.1021/acs.jpca.8b10241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raison Dsouza
- Max Planck Institute for the Structure and Dynamics of Matter, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Xinxin Cheng
- Max Planck Institute for the Structure and Dynamics of Matter, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Zheng Li
- Max Planck Institute for the Structure and Dynamics of Matter, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Michał Andrzej Kochman
- Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
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47
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Janicki MJ, Szabla R, Šponer J, Góra RW. Solvation effects alter the photochemistry of 2-thiocytosine. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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48
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Mai S, Marquetand P, González L. Nonadiabatic dynamics: The SHARC approach. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2018; 8:e1370. [PMID: 30450129 PMCID: PMC6220962 DOI: 10.1002/wcms.1370] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022]
Abstract
We review the Surface Hopping including ARbitrary Couplings (SHARC) approach for excited-state nonadiabatic dynamics simulations. As a generalization of the popular surface hopping method, SHARC allows simulating the full-dimensional dynamics of molecules including any type of coupling terms beyond nonadiabatic couplings. Examples of these arbitrary couplings include spin-orbit couplings or dipole moment-laser field couplings, such that SHARC can describe ultrafast internal conversion, intersystem crossing, and radiative processes. The key step of the SHARC approach consists of a diagonalization of the Hamiltonian including these couplings, such that the nuclear dynamics is carried out on potential energy surfaces including the effects of the couplings-this is critical in any applications considering, for example, transition metal complexes or strong laser fields. We also give an overview over the new SHARC2.0 dynamics software package, released under the GNU General Public License, which implements the SHARC approach and several analysis tools. The review closes with a brief survey of applications where SHARC was employed to study the nonadiabatic dynamics of a wide range of molecular systems. This article is categorized under: Theoretical and Physical Chemistry > Reaction Dynamics and KineticsSoftware > Simulation MethodsSoftware > Quantum Chemistry.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry University of Vienna Vienna Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry University of Vienna Vienna Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry University of Vienna Vienna Austria
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49
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Nenov A, Conti I, Borrego-Varillas R, Cerullo G, Garavelli M. Linear absorption spectra of solvated thiouracils resolved at the hybrid RASPT2/MM level. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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50
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Borrego-Varillas R, Teles-Ferreira DC, Nenov A, Conti I, Ganzer L, Manzoni C, Garavelli M, Maria de Paula A, Cerullo G. Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing. J Am Chem Soc 2018; 140:16087-16093. [DOI: 10.1021/jacs.8b07057] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rocío Borrego-Varillas
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | | | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Lucia Ganzer
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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