1
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Cadet J, Angelov D, Di Mascio P, Wagner JR. Contribution of oxidation reactions to photo-induced damage to cellular DNA. Photochem Photobiol 2024. [PMID: 38970297 DOI: 10.1111/php.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/08/2024]
Abstract
This review article is aimed at providing updated information on the contribution of immediate and delayed oxidative reactions to the photo-induced damage to cellular DNA/skin under exposure to UVB/UVA radiations and visible light. Low-intensity UVC and UVB radiations that operate predominantly through direct excitation of the nucleobases are very poor oxidizing agents giving rise to very low amounts of 8-oxo-7,8-dihydroguanine and DNA strand breaks with respect to the overwhelming bipyrimidine dimeric photoproducts. The importance of these two classes of oxidatively generated damage to DNA significantly increases together with a smaller contribution of oxidized pyrimidine bases upon UVA irradiation. This is rationalized in terms of sensitized photooxidation reactions predominantly mediated by singlet oxygen together with a small contribution of hydroxyl radical that appear to also be implicated in the photodynamic effects of the blue light component of visible light. Chemiexcitation-mediated formation of "dark" cyclobutane pyrimidine dimers in UVA-irradiated melanocytes is a recent major discovery that implicates in the initial stage, a delayed generation of reactive oxygen and nitrogen species giving rise to triplet excited carbonyl intermediate and possibly singlet oxygen. High-intensity UVC nanosecond laser radiation constitutes a suitable source of light to generate pyrimidine and purine radical cations in cellular DNA via efficient biphotonic ionization.
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Affiliation(s)
- Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LMBC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University, Balçova, Izmir, Turkey
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - J Richard Wagner
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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2
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Martínez-Fernández L, Green JA, Esposito L, Jouybari MY, Zhang Y, Santoro F, Kohler B, Improta R. The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study. Chem Sci 2024; 15:9676-9693. [PMID: 38939156 PMCID: PMC11206432 DOI: 10.1039/d4sc00910j] [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: 02/06/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024] Open
Abstract
Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - James Alexander Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main Frankfurt am Main Germany
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
| | - Martha Yaghoubi Jouybari
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
- National Research Council of Canada 100 Sussex Drive Ottawa Ontario K1A 0R6 Canada
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
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3
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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [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: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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4
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Markovitsi D. On the Use of the Intrinsic DNA Fluorescence for Monitoring Its Damage: A Contribution from Fundamental Studies. ACS OMEGA 2024; 9:26826-26837. [PMID: 38947837 PMCID: PMC11209687 DOI: 10.1021/acsomega.4c02256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024]
Abstract
The assessment of DNA damage by means of appropriate fluorescent probes is widely spread. In the specific case of UV-induced damage, it has been suggested to use the emission of dimeric photoproducts as an internal indicator for the efficacy of spermicidal lamps. However, in the light of fundamental studies on the UV-induced processes, outlined in this review, this is not straightforward. It is by now well established that, in addition to photodimers formed via an electronic excited state, photoionization also takes place with comparable or higher quantum yields, depending on the irradiation wavelength. Among the multitude of final lesions, some have been fully characterized, but others remain unknown; some of them may emit, while others go undetected upon monitoring fluorescence, the result being strongly dependent on both the irradiation and the excitation wavelength. In contrast, the fluorescence of undamaged nucleobases associated with emission from ππ* states, localized or excitonic, appearing at wavelengths shorter than 330 nm is worthy of being explored to this end. Despite its low quantum yield, it is readily detected nowadays. Its intensity decreases due to the disappearance of the reacting nucleobases and the loss of exciton coherence provoked by the presence of lesions, independently of their type. Thus, it could potentially provide valuable information about the DNA damage induced, not only by UV radiation but also by other sanitizing or therapeutic agents.
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Affiliation(s)
- Dimitra Markovitsi
- Université Paris-Saclay, CNRS,
Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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5
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Jaiswal VK, Aranda Ruiz D, Petropoulos V, Kabaciński P, Montorsi F, Uboldi L, Ugolini S, Mukamel S, Cerullo G, Garavelli M, Santoro F, Nenov A. Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state. Nat Commun 2024; 15:4900. [PMID: 38851775 PMCID: PMC11162464 DOI: 10.1038/s41467-024-48871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/15/2024] [Indexed: 06/10/2024] Open
Abstract
Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54±11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Daniel Aranda Ruiz
- ICMol, Universidad de Valencia, Catedrático José Beltrán Martínez, 2, 46980, Paterna, Spain
| | - Vasilis Petropoulos
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Francesco Montorsi
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Lorenzo Uboldi
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Simone Ugolini
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, CA, 92697, USA
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy.
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124, Pisa, Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy.
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6
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Yu D, Yang W, Chen S, Zhou CY, Guo Z. Photocatalyst-Free Visible Light-Induced C(sp 2)-H Arylation of Quinoxalin-2(1H)-ones and Coumarins. Chemistry 2024:e202401371. [PMID: 38825569 DOI: 10.1002/chem.202401371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/04/2024]
Abstract
Herein, we describe a visible light-induced C(sp2)-H arylation method for quinoxalin-2(1H)-ones and coumarins using iodonium ylides without the need for external photocatalysts. The protocol demonstrates a broad substrate scope, enabling the arylation of diverse heterocycles through a simple and mild procedure. Furthermore, the photochemical reaction showcases its applicability in the efficient synthesis of biologically active molecules. Computational investigations at the CASPT2//CASSCF/PCM level of theory revealed that the excited state of quinoxalin-2(1H)-one facilitates electron transfer from its π bond to the antibonding orbital of the C-I bond in the iodonium ylide, ultimately leading to the formation of an aryl radical, which subsequently participates in the C-H arylation process. In addition, our calculations reveal that during the single-electron transfer (SET) process, the C-I bond cleavage in iodonium ylide and new C-C bond formation between resultant aryl radical and cationic quinoxaline species take place in a concerned manner. This enables the arylation reaction to efficiently proceed along an energy-efficient route.
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Affiliation(s)
- Dingzhe Yu
- College of Materials Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China
| | - Wenjing Yang
- College of Materials Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China
| | - Shuicai Chen
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Cong-Ying Zhou
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Zhen Guo
- College of Materials Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China
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7
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Herb D, Rossini M, Ankerhold J. Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. Phys Rev E 2024; 109:064413. [PMID: 39020927 DOI: 10.1103/physreve.109.064413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/21/2024] [Indexed: 07/20/2024]
Abstract
After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.
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8
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Pham HQ, Ouyang R, Lv D. Scalable Quantum Monte Carlo with Direct-Product Trial Wave Functions. J Chem Theory Comput 2024; 20:3524-3534. [PMID: 38700513 DOI: 10.1021/acs.jctc.3c00769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
The computational demand posed by applying multi-Slater determinant trials in phaseless auxiliary-field quantum Monte Carlo methods (MSD-AFQMC) is particularly significant for molecules exhibiting strong correlations. Here, we propose using direct-product wave functions as trials for MSD-AFQMC, aiming to reduce computational overhead by leveraging the compactness of multi-Slater determinant trials in direct-product form (DP-MSD). This efficiency arises when the active space can be divided into noncoupling subspaces, a condition we term "decomposable active space". By employing localized-active space self-consistent field wave functions as an example of such trials, we demonstrate our proposed approach across a range of molecular systems, each exhibiting varying degrees of complexity in their electronic structures. Our findings indicate that the compact DP-MSD trials can reduce computational costs substantially, by up to 36 times for the C2H6N4 molecule where the two double bonds between nitrogen N=N are clearly separated by a C-C single bond, while maintaining accuracy when active spaces are decomposable. In the case of larger systems such as the benzene dimer, characterized by weak coupling between the two monomers, we observed a decrease in computational cost compared to using a complete active space trial, yet we retained the same level of accuracy. However, for systems where these active subspaces strongly couple, a scenario we refer to as "strong subspace coupling", the method's accuracy decreases compared to that achieved with a complete active space approach. We anticipate that our method will be beneficial for systems with noncoupling to weakly coupling subspaces that require local multireference treatments.
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Affiliation(s)
- Hung Q Pham
- ByteDance Research, San Jose, California 95110, United States
| | | | - Dingshun Lv
- ByteDance Research, Zhonghang Plaza, No. 43, North third Ring West Road, 100098 Beijing, China
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9
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Hennefarth MR, Hermes MR, Truhlar DG, Gagliardi L. Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory. J Chem Theory Comput 2024; 20:3637-3658. [PMID: 38639604 DOI: 10.1021/acs.jctc.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear-electronic coupling in addition to accurately predicting Franck-Condon vertical excitations. In this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.
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Affiliation(s)
- Matthew R Hennefarth
- Department of Chemistry and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew R Hermes
- Department of Chemistry and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, Illinois 60439, United States
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10
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Baweja S, Kalal B, Maity S. Spectroscopic Characterization of Hydrogen-Bonded 2,7-Diazaindole Water Complex Isolated in the Gas Phase. J Phys Chem A 2024; 128:3329-3338. [PMID: 38652167 DOI: 10.1021/acs.jpca.4c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a systematic experimental analysis of the 1:1 complex of 2,7-diazaindole (27DAI) with water in the gas phase. The complex was characterized by using two-color-resonant two-photon ionization (R2PI), laser-induced fluorescence (LIF), single vibronic level fluorescence (SVLF), and photoionization efficiency (PIE) spectroscopic methods. The 000 band of the S1←S0 electronic transition of the 27DAI-H2O complex was observed at 33,074 cm-1, largely red-shifted by 836 cm-1 compared to that of the bare 27DAI. From the R2PI spectrum, the detected modes at 141 (ν'Tx), 169 (ν'Ty), and 194 (ν'Ry) cm-1 were identified as the internal motions of the H2O molecule in the complex. However, these modes were detected at 115 (ν″Tx), 152 (ν″Ty), and 190 (ν″Ry) cm-1 in the ground state, which suggested a stronger hydrogen bonding interaction in the photo-excited state. The structural determination was aided by the detection of νNH and νOH values in the ground and excited state complexes using the FDIR and IDIR spectroscopies. The detection of νNH at 3414 and νOH at 3447 cm-1 in 27DAI-H2O has shown an excellent correlation with the most stable structure consisting of N(1)-H···O and OH···N(7) hydrogen-bonded bridging water molecule in the ground state. The structure of the complex in the electronic excited state (S1) was confirmed by the corresponding bands at 3210 (νNH) and 3265 cm-1 (νOH). The IR-UV hole-burning spectroscopy confirmed the presence of only one isomer in the molecular beam. The ionization energy (IE) of the 27DAI-H2O complex was obtained as 8.789 ± 0.002 eV, which was significantly higher than the 7AI-H2O complex. The higher IE values of N-rich molecules suggest a higher resistivity of such molecules against photodamage. The obtained structure of the 27DAI-H2O complex has explicitly shown the formation of a cyclic one-solvent bridge incorporating N(1)-H···O and O-H···N(7) hydrogen bonds upon microsolvation. The lower excitation and higher ionization energies of the 27DAI-H2O complex compared to 7AI-H2O established higher stabilization of N-rich molecules. The solvent clusters forming a linear bridge between the hydrogen/proton acceptor and donor sites in the complex can be considered as a stepping stone to investigate the photoinduced deactivation mechanisms in nitrogen containing biologically relevant molecules.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Bhavika Kalal
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Surajit Maity
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
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11
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Koga M, Kang DH, Heim ZN, Meyer P, Erickson BA, Haldar N, Baradaran N, Havenith M, Neumark DM. Extreme ultraviolet time-resolved photoelectron spectroscopy of adenine, adenosine and adenosine monophosphate in a liquid flat jet. Phys Chem Chem Phys 2024; 26:13106-13117. [PMID: 38629206 DOI: 10.1039/d4cp00856a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Time-resolved photoelectron spectroscopy using an extreme-ultraviolet (XUV) probe pulse was used to investigate the UV photoinduced dynamics of adenine (Ade), adenosine (Ado), and adenosine-5-monophosphate (AMP) in a liquid water jet. In contrast to previous studies using UV probe pulses, the XUV pulse at 21.7 eV can photoionize all excited states of a molecule, allowing for full relaxation pathways to be addressed after excitation at 4.66 eV. This work was carried out using a gas-dynamic flat liquid jet, resulting in considerably enhanced signal compared to a cylindrical jet. All three species decay on multiple time scales that are assigned based on their decay associated spectra; the fastest decay of ∼100 fs is assigned to ππ* decay to the ground state, while a smaller component with a lifetime of ∼500 fs is attributed to the nπ* state. An additional slower channel in Ade is assigned to the 7H Ade conformer, as seen previously. This work demonstrates the capability of XUV-TRPES to disentangle non-adiabatic dynamics in an aqueous solution in a state-specific manner and represents the first identification of the nπ* state in the relaxation dynamics of adenine and its derivatives.
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Affiliation(s)
- Masafumi Koga
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Do Hyung Kang
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Zachary N Heim
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Philipp Meyer
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801, Germany
| | - Blake A Erickson
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Neal Haldar
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Negar Baradaran
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801, Germany
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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12
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Hu X, Wang D, Wang Y, Wang Y, Zhang S. Ultrafast restricted intramolecular rotation in molecules with aggregation induced emission. J Chem Phys 2024; 160:154302. [PMID: 38619455 DOI: 10.1063/5.0200622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024] Open
Abstract
In this work, the ultrafast intramolecular rotation behavior of 1,1,2,3,4,5-hexaphenylsilole has been investigated in several solutions with different viscosities using femtosecond transient absorption spectroscopy combined with density functional theory and time-dependent density functional theory calculations. It is demonstrated that the nonradiative process, which competes with radiative decay, involves two main stages, namely the restricted intramolecular rotation and internal conversion processes. The intramolecular rotation depends on viscosity and presents a significant restriction. The restricted rotational rate is determined to be dozens of picoseconds. The following nonradiative process is strongly dominated by intramolecular rotation. The nonradiative decay rate will decrease with the increase in viscosity, leading to a rise in the radiative probability and photoluminous yield. These results have borne out the mechanism of ultrafast restricted intramolecular rotation of aggregation induced emission and provided a detailed photophysical picture of nonradiative processes.
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Affiliation(s)
- Xiao Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdong Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmei Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Song Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Iuzzolino G, Perrella F, Valadan M, Petrone A, Altucci C, Rega N. Photophysics of a nucleic acid-protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study. Phys Chem Chem Phys 2024; 26:11755-11769. [PMID: 38563904 DOI: 10.1039/d3cp06254f] [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: 04/04/2024]
Abstract
We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms.
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Affiliation(s)
- Gabriele Iuzzolino
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Fulvio Perrella
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, via Pansini 5, Napoli I-80131, Italy
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, via Pansini 5, Napoli I-80131, Italy
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti "Eduardo Caianiello", URT UNINA, via Cintia 21, Napoli I-80126, Italy
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
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14
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Avagliano D, Skreta M, Arellano-Rubach S, Aspuru-Guzik A. DELFI: a computer oracle for recommending density functionals for excited states calculations. Chem Sci 2024; 15:4489-4503. [PMID: 38516092 PMCID: PMC10952086 DOI: 10.1039/d3sc06440a] [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: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/23/2024] Open
Abstract
Density functional theory (DFT) is the workhorse of computational quantum chemistry. One of its main limitations is that choosing the right functional is a non-trivial task left for human experts. The choice is particularly hard for excited state calculations when using its time-dependent formulation (TD-DFT). This is due to the approximations of the method, but also because the photophysical properties of a molecule are defined by a manifold of states that all need to be properly described. This includes not only the relative energy of the states, but also capturing the correct character, order, and intensity of the transitions. In this work, we developed a neural network to recommend functionals to be used on molecules for TD-DFT calculations, by simultaneously considering all these properties for a manifold of states. This was possible by developing a scoring system to define the accuracy of an excited state's calculation against a higher-accuracy reference. The scoring system is generalizable to any level of theory; we here applied it to evaluate the performance of common functionals of different rungs against a higher accuracy method on a large set of organic molecules. The results are collected in a database that we released and made open, providing four million data points to the community for future applications. The scoring system assigns a value between zero and one hundred to each functional for each molecule, transforming the complicated task of learning photophysical properties into a simpler regression task. We used the dataset to train a graph attention neural network to predict the scores for unseen molecules. We call this oracle DELFI (Data-driven EvaLuation of Functionals by Inference), which can be used to quickly screen and predict the ranking of functionals to calculate the optical properties of organic molecules. We validated DELFI in two in silico experiments: choosing a common functional for a series of spiropyran-merocyanine isomers and a unique functional to screen a large dataset of over 50 000 organic photovoltaic molecules, for which an extensive benchmark would be unfeasible. A corresponding web application allows DELFI to be easily run and the results to be analyzed, alleviating the hurdle of choosing the right functional for TD-DFT calculations.
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Affiliation(s)
- Davide Avagliano
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George Street Toronto ON M5S 2E4 Canada
| | - Marta Skreta
- Department of Computer Science, University of Toronto 40 St. George Street Toronto ON M5S 2E4 Canada
- Vector Institute for Artificial Intelligence 661 University Ave. Suite 710 ON M5G 1M1 Toronto Canada
| | | | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George Street Toronto ON M5S 2E4 Canada
- Vector Institute for Artificial Intelligence 661 University Ave. Suite 710 ON M5G 1M1 Toronto Canada
- Department of Materials Science & Engineering, University of Toronto 184 College St Toronto M5S 3E4 Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto 200 College St ON M5S 3E5 Toronto Canada
- Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR) 66118 University Ave. M5G 1M1 Toronto Canada
- Acceleration Consortium 80 St George St M5S 3H6 Toronto Canada
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15
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Feng B, Wu W, Yang S, He Z, Fang B, Yang D, Wu G, Yang X. Insights into ultrafast decay dynamics of electronically excited pyridine- N-oxide. Phys Chem Chem Phys 2024; 26:8308-8317. [PMID: 38389467 DOI: 10.1039/d3cp06187f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The ultrafast decay dynamics of pyridine-N-oxide upon excitation in the near-ultraviolet range of 340.2-217.6 nm is investigated using the femtosecond time-resolved photoelectron imaging technique. The time-resolved photoelectron spectra and photoelectron angular distributions at all pump wavelengths are carefully analyzed and the following view is derived: at the longest pump wavelengths (340.2 and 325.6 nm), pyridine-N-oxide is excited to the S1(1ππ*) state with different vibrational levels. The depopulation rate of the S1 state shows a marked dependence on vibrational energy and mode, and the lifetime is in the range of 1.4-160 ps. At 289.8 and 280.5 nm, both the second 1ππ* state and the S1 state are initially prepared. The former has an extremely short lifetime of ∼60 fs, which indicates that the ultrafast deactivation pathway such as a rapid internal conversion to one close-lying state is its dominant decay channel, while the latter is at high levels of vibrational excitation and decays within the range of 380-520 fs. At the shortest pump wavelengths (227.3 and 217.6 nm), another excited state of Rydberg character is mostly excited. We assign this state to the 3s Rydberg state which has a lifetime of 0.55-2.2 ps. This study provides a comprehensive picture of the ultrafast excited-state decay dynamics of the photoexcited pyridine-N-oxide molecule.
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Affiliation(s)
- Baihui Feng
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
- Key Laboratory of Chemical Lasers, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenping Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuaikang Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhigang He
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
| | - Benjie Fang
- Key Laboratory of Chemical Lasers, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Dongyuan Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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16
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Chen Z, Wang X, Jia M, He X, Pan H, Chen J. Ribose and Deoxyribose Group Alter Excited-State Dynamics of 5-Azacytosine in Solution. Photochem Photobiol 2024; 100:291-297. [PMID: 35993879 DOI: 10.1111/php.13696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/16/2022] [Indexed: 10/15/2022]
Abstract
5-Azacytosine (5-AC) is one of the best interesting noncanonical nucleobases due to its functionalization and structural imitation of natural bases. 5-AC can be used as the scaffold of two important chemotherapeutic medicines, 5-azacytidine and 2'-deoxy-5-azacytidine. Furthermore, increased sensitivity to UV leads to the photochemical effects of 5-AC also attracted attention. Yet, no study has been reported to explore the effect of glycosyl groups on the photophysical and photochemical properties of 5-AC, which can help to reveal the photostability of related actual clinic drugs. In this study, the excited-state dynamics of 5-azacytidine and 2'-deoxy-5-azacytidine are studied by femtosecond transient absorption and quantum-chemical calculations while revisiting that of 5-AC with a wider probe spectral range. It is shown that glycosyl substitution on the N1 position leads to ultrafast excited-state relaxation within several picoseconds in both nucleosides, which is distinct compared with the 17 ps lifetime seen in 5-AC. It is proposed that these changes are due to altering the energy level of the dark nπ* state. Moreover, our results suggest that it should be cautioned to simply replace sugar groups with methyl groups when doing a theoretical calculation study on nucleobases and their derivatives.
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Affiliation(s)
- Ziwei Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
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17
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Oliveira LMF, Valverde D, Costa GJ, Borin AC. The copious photochemistry of 2,6-diaminopurine: Luminescence, triplet population, and ground state recovery. Photochem Photobiol 2024; 100:323-338. [PMID: 37403286 DOI: 10.1111/php.13833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
9H- and 7H-2,6-Diaminopurine (26DAP) photoinduced events in vacuum were studied at the MS-CASPT2/cc-pVDZ level of theory. The S1 1 (ππ* La ) state is initially populated evolving barrierless towards its minimum energy structure, from where two photochemical events can take place in both tautomers. The first is the return of the electronic population to the ground state via the C6 conical intersection (CI-C6). The second involves an internal conversion to the ground through the C2 conical intersection (CI-C2). According to our geodesic interpolated paths connecting the critical structures, the second route is less favorable in both tautomers, due to the presence of high energy barriers. Our calculations suggest a competition between fluorescence and ultrafast relaxation to the electronic ground state via internal conversion process. Based on our calculated potential energy surfaces and experimental excited state lifetimes from the literature, we can infer that the 7H- must have a greater fluorescence yield than the 9H-tautomer. We also explored the triplet state population mechanisms on the 7H-26DAP to understand their long-lived components observed experimentally.
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Affiliation(s)
- Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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18
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Ma C, Xiong Q, Lin J, Wong AKW, Wang M, Kwok WM. Ultrafast excited state dynamics of isocytosine unveiled by femtosecond broadband time-resolved spectroscopy combined with density functional theoretical study. Photochem Photobiol 2024; 100:355-367. [PMID: 37688287 DOI: 10.1111/php.13849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
Isocytosine, having important applications in antivirus and drug development, is among the building blocks of Hachimoji nucleic acids. In this report, we present an investigation of the excited state dynamics of isocytosine in both protic and aprotic solvents, which was conducted by a combination of methods including steady-state spectroscopy, femtosecond broadband time-resolved fluorescence, and transient absorption. These methods were coupled with density functional and time-dependent density functional theory calculations. The results of our study provide the first direct evidence for a highly efficient nonradiative mechanism achieved through internal conversion from the ππ* state of the isocytosine keto-N(3)H form occurring within subpicoseconds and picoseconds following photo-excitation. Our study also unveils a crucial role of solvent, particularly solute-solvent hydrogen bonding, in determining the tautomeric composition and regulating the pathways and dynamics of the deactivation processes. The deactivation processes of isocytosine in the solvents examined are found to be distinct from those of cytosine and the case known for isocytosine in the gas phase mainly due to different tautomeric forms involved. Overall, our findings demonstrate the high photo-stability of isocytosine in the solution and showcase the remarkable effect of covalent modification in altering the spectral character and excited state dynamics of nucleobases.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Qingwu Xiong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Jingdong Lin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mingliang Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
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19
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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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20
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Markovitsi D. Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors. Photochem Photobiol 2024; 100:262-274. [PMID: 37365765 DOI: 10.1111/php.13826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures exhibiting an important polymorphism. During the past two decades, their study by time-resolved spectroscopy, from femtoseconds to milliseconds, associated to computational methods, shed light on the primary processes occurring when they absorb UV radiation. Quite recently, their utilization in label-free and dye-free biosensors was explored by a few groups. In view of such developments, this review discusses the outcomes of the fundamental studies that could contribute to the design of future optoelectronic biosensors using fluorescence or charge carriers stemming directly from GQs, without mediation of other molecules, as it is the currently the case. It explains how the excited state relaxation influences both the fluorescence intensity and the efficiency of low-energy photoionization, occurring via a complex mechanism. The corresponding quantum yields, determined with excitation at 266/267 nm, fall in the range of (3.0-9.5) × 10-4 and (3.2-9.2) × 10-3 , respectively. These values, significantly higher than the corresponding values found for duplexes, depend strongly on certain structural factors (molecularity, metal cations, peripheral bases, number of tetrads …) which intervene in the relaxation process. Accordingly, these features can be tuned to optimize the desired signal.
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Affiliation(s)
- Dimitra Markovitsi
- CNRS, Institut de Chimie Physique, UMR8000, Université Paris-Saclay, Orsay, France
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21
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Jaiswal VK, Taddei M, Nascimento DR, Garavelli M, Conti I, Nenov A. Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA. Photochem Photobiol 2024; 100:443-452. [PMID: 38356286 DOI: 10.1111/php.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024]
Abstract
Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Mario Taddei
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | | | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
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22
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Mayer D, Lever F, Gühr M. Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs. Photochem Photobiol 2024; 100:275-290. [PMID: 38174615 DOI: 10.1111/php.13903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.
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Affiliation(s)
- Dennis Mayer
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Fabiano Lever
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Gühr
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Institute of Physical Chemistry, University of Hamburg, Hamburg, Germany
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23
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Martinez-Fernandez L, Improta R. The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study. Photochem Photobiol 2024; 100:314-322. [PMID: 37409732 DOI: 10.1111/php.13832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Naples, Italy
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24
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Chen XR, Jiang WJ, Guo QH, Liu XY, Cui G, Li L. Theoretical insights into the photophysics of an unnatural base Z: A MS-CASPT2 investigation. Photochem Photobiol 2024; 100:380-392. [PMID: 38041414 DOI: 10.1111/php.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023]
Abstract
We have employed the highly accurate multistate complete active space second-order perturbation theory (MS-CASPT2) method to investigate the photoinduced excited state relaxation properties of one unnatural base, namely Z. Upon excitation to the S2 state of Z, the internal conversion to the S1 state would be dominant. From the S1 state, two intersystem crossing paths leading to the T2 and T1 states and one internal conversion path to the S0 state are possible. However, considering the large barrier to access the S1 /S0 conical intersection and the strong spin-orbit coupling between S1 and T2 states (>40 cm-1 ), the intersystem crossing to the triplet manifolds is predicted to be more preferred. Arriving at the T2 state, the internal conversion to the T1 state and the intersystem crossing back to the S1 state are both possible considering the S1 /T2 /T1 three-state intersection near the T2 minimum. Upon arrival at the T1 state, the deactivation to S0 can be efficient after overcoming a small barrier to access T1 /S0 crossing point, where the spin-orbit coupling (SOC) is as large as 39.7 cm-1 . Our present work not only provides in-depth insights into the photoinduced process of unnatural base Z, but can also help the future design of novel unnatural bases with better photostability.
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Affiliation(s)
- Xin-Rui Chen
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Wen-Jun Jiang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Qian-Hong Guo
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Laicai Li
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
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25
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Wang C, Liu X, Wang Q, Fang WH, Chen X. Unveiling Mechanistic Insights and Photocatalytic Advancements in Intramolecular Photo-(3 + 2)-Cycloaddition: A Comparative Assessment of Two Paradigmatic Single-Electron-Transfer Models. JACS AU 2024; 4:419-431. [PMID: 38425917 PMCID: PMC10900211 DOI: 10.1021/jacsau.3c00542] [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: 09/14/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 03/02/2024]
Abstract
The synthesis of 1-aminonorbornane (1-aminoNB), a potential aniline bioisostere, through photochemistry or photoredox catalysis signifies a remarkable breakthrough with implications in organic chemistry, pharmaceutical chemistry, and sustainable chemistry. However, an understanding of the underlying mechanisms involved in these reactions remains limited and ambiguous. Herein, we employ high-precision CASPT2//CASSCF calculations to elucidate the intricate mechanisms regulating the intramolecular photo-(3 + 2)-cycloaddition reactions for the synthesis of 1-aminoNB in the presence or absence of the Ir-complex-based photocatalyst. Our investigations delve into radical cascades, stereoselectivity, particularly single-electron-transfer (SET) events, etc. Furthermore, we innovatively introduce and compare two SET models integrating Marcus electron-transfer theory and transition-state theory. These models combined with kinetic data contribute to recognizing the critical control factors in diverse photocatalysis, thereby guiding the design and manipulation of photoredox catalysis as well as the improvement and modification of photocatalysts.
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Affiliation(s)
- Chu Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Xiao Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Qian Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Xuebo Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
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26
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Asplund M, Koga M, Wu YJ, Neumark DM. Time-resolved photoelectron spectroscopy of iodide-4-thiouracil cluster: The ππ* state as a doorway for electron attachment. J Chem Phys 2024; 160:054301. [PMID: 38299627 DOI: 10.1063/5.0187557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The photophysics of thiobases-nucleobases in which one or more oxygen atoms are replaced with sulfur atoms- vary greatly depending on the location of sulfonation. Not only are direct dynamics of a neutral thiobase impacted, but also the dynamics of excess electron accommodation. In this work, time-resolved photoelectron spectroscopy is used to measure binary anionic clusters of iodide and 4-thiouracil, I- · 4TU. We investigate charge transfer dynamics driven by excitation at 3.88 eV, corresponding to the lowest ππ* transition of the thiouracil, and at 4.16 eV, near the cluster vertical detachment energy. The photoexcited state dynamics are probed by photodetachment with 1.55 and 3.14 eV pulses. Excitation at 3.88 eV leads to a signal from a valence-bound ion only, indicating a charge accommodation mechanism that does not involve a dipole-bound anion as an intermediate. Excitation at 4.16 eV rapidly gives rise to dipole-bound and valence-bound ion signals, with a second rise in the valence-bound signal corresponding to the decay of the dipole-bound signal. The dynamics associated with the low energy ππ* excitation of 4-thiouracil provide a clear experimental proof for the importance of localized excitation and electron backfilling in halide-nucleobase clusters.
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Affiliation(s)
- Megan Asplund
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Masafumi Koga
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ying Jung Wu
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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27
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Ling CCH, Chan WX, Siow JX, Loh ZH. Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment. J Phys Chem A 2024; 128:626-635. [PMID: 38207335 DOI: 10.1021/acs.jpca.3c08232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.
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Affiliation(s)
- Christine Chun Hui Ling
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Wei Xin Chan
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Jing Xuan Siow
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Zhi-Heng Loh
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
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28
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Ma C, Xiong Q, Lin J, Zeng X, Wang M, Kwok WM. Is 1-methylcytosine a faithful model compound for ultrafast deactivation dynamics of cytosine nucleosides in solution? Phys Chem Chem Phys 2024; 26:2963-2972. [PMID: 38214513 DOI: 10.1039/d3cp05509d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
1-Methylcytosine (1mCyt) is the base for nucleoside N1-methylpseudodeoxycytidine of Hachimoji nucleic acids and a frequently used model compound for theoretical studies on excited states of cytosine nucleosides. However, there is little experimental characterization of spectra and photo-dynamic properties of 1mCyt. Herein, we report a comprehensive investigation into excited state dynamics and effects of solvents on fluorescence dynamics of 1mCyt in both water and acetonitrile. The study employed femtosecond broadband time-resolved fluorescence, transient absorption, and steady-state spectroscopy, along with density functional theory and time-dependent density functional theory calculations. The results obtained provide the first experimental evidence for identifying a dark-natured ∼5.7 ps lifetime nπ* state in the ultrafast non-radiative deactivation with 1mCyt in aqueous solution. This study also demonstrates a significant effect of the solvent on 1mCyt's fluorescence emission, which highlights the crucial role of solute-solvent hydrogen bonding in altering structures and reshaping the radiative as well as nonradiative dynamics of the 1mCyt's ππ* state in the aprotic solvent compared to the protic solvent. The solvent effect exhibited by 1mCyt is distinctive from that known for deoxycytidine, indicating the need for caution in using 1mCyt for modelling the ultrafast dynamics of Cyt nucleosides in solvents with varying properties. Overall, our study unveils a deactivation mechanism that confers a high degree of photo-stability for 1mCyt in solution, shedding light on the molecular basis for solvent-induced effects on the excited state dynamics of nucleobases and derivatives.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Qingwu Xiong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
- College of Physics and optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Jingdong Lin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Xiaoyan Zeng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Mingliang Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 999077, P. R. China.
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29
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Martínez-Fernández L, Kohl FR, Zhang Y, Ghosh S, Saks AJ, Kohler B. Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs. J Am Chem Soc 2024; 146:1914-1925. [PMID: 38215466 DOI: 10.1021/jacs.3c08793] [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: 01/14/2024]
Abstract
The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Forrest R Kohl
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Supriya Ghosh
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Andrew J Saks
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
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30
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Wang X, Martínez-Fernández L, Zhang Y, Wu P, Kohler B, Improta R, Chen J. Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation. J Am Chem Soc 2024; 146:1839-1848. [PMID: 38194423 DOI: 10.1021/jacs.3c04567] [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: 01/11/2024]
Abstract
Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Peicong Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via De Amicis 95, Napoli I-80145, Italy
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, Shanxi, China
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31
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Sidat A, Ingham M, Rivera M, Misquitta AJ, Crespo-Otero R. Performance of point charge embedding schemes for excited states in molecular organic crystals. J Chem Phys 2023; 159:244108. [PMID: 38149734 DOI: 10.1063/5.0177278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023] Open
Abstract
Modeling excited state processes in molecular crystals is relevant for several applications. A popular approach for studying excited state molecular crystals is to use cluster models embedded in point charges. In this paper, we compare the performance of several embedding models in predicting excited states and S1-S0 optical gaps for a set of crystals from the X23 molecular crystal database. The performance of atomic charges based on ground or excited states was examined for cluster models, Ewald embedding, and self-consistent approaches. We investigated the impact of various factors, such as the level of theory, basis sets, embedding models, and the level of localization of the excitation. We consider different levels of theory, including time-dependent density functional theory and Tamm-Dancoff approximation (TDA) (DFT functionals: ωB97X-D and PBE0), CC2, complete active space self-consistent field, and CASPT2. We also explore the impact of selection of the QM region, charge leakage, and level of theory for the description of different kinds of excited states. We implemented three schemes based on distance thresholds to overcome overpolarization and charge leakage in molecular crystals. Our findings are compared against experimental data, G0W0-BSE, periodic TDA, and optimally tuned screened range-separated functionals.
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Affiliation(s)
- Amir Sidat
- School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Michael Ingham
- Department of Chemistry, University College London, London, United Kingdom
| | - Miguel Rivera
- Department of Chemistry, University College London, London, United Kingdom
| | - Alston J Misquitta
- School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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32
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Bezabih MS, Kaliakin DS, Blanco-González A, Barneschi L, Tarnovsky AN, Olivucci M. Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories. J Phys Chem B 2023; 127:10871-10879. [PMID: 38055701 DOI: 10.1021/acs.jpcb.3c06433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.
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Affiliation(s)
- Meseret Simachew Bezabih
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Danil S Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Leonardo Barneschi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Alexander N Tarnovsky
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
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33
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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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34
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Zielinski P, Black JA, Köhn A. Performance Tests of the Second-Order Approximate Internally Contracted Multireference Coupled-Cluster Singles and Doubles Method icMRCC2. J Chem Theory Comput 2023; 19:8671-8688. [PMID: 37991987 PMCID: PMC10720349 DOI: 10.1021/acs.jctc.3c00969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Benchmark results are presented for the second-order approximation of the internally contracted multireference coupled-cluster method with single and double excitations, icMRCC2 [Köhn, Bargholz, J. Chem. Phys. 2019, 151, 041106], which was designed as a multireference analogue of the single-reference second-order approximate coupled-cluster method CC2 [Christiansen, Koch, Jørgensen, Chem. Phys. Lett. 1995, 243, 409-418]. Vertical excitation energies of various small to medium-sized organic molecules are investigated based on established test sets from the literature. Additionally, the spectroscopic constants of ground and excited states of diatomics and the geometric parameters of excited triatomic molecules were determined and compared to the experimental data. The results show that the method clearly extends the applicability of single-reference CC2, including doubly excited states, and also artifacts of CC2 like too low Rydberg excitations and too weak multiple bonds are eliminated. The method is computationally more demanding than standard multireference second-order perturbation theories but improves significantly in accuracy, as shown by the benchmark results. In addition, it is demonstrated that small active spaces are often sufficient to obtain accurate energies with icMRCC2. Example applications like the automerization of cyclobutadiene, the deactivation pathway of ethylene, and the excited states of an iron complex with a noninnocent nitrosyl ligand demonstrate the potential of icMRCC2 in cases with strong multireference character.
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Affiliation(s)
- Patrik Zielinski
- Institute for Theoretical
Chemistry, University of Stuttgart, Paffenwaldring 55, Stuttgart D-70569, Germany
| | | | - Andreas Köhn
- Institute for Theoretical
Chemistry, University of Stuttgart, Paffenwaldring 55, Stuttgart D-70569, Germany
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35
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Cuéllar-Zuquin J, Pepino AJ, Fdez. Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size. J Chem Theory Comput 2023; 19:8258-8272. [PMID: 37882796 PMCID: PMC10851440 DOI: 10.1021/acs.jctc.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
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Affiliation(s)
- Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Ana Julieta Pepino
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Francesco Aquilante
- Theory
and Simulation of Materials (THEOS), and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
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36
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Petropoulos V, Uboldi L, Maiuri M, Cerullo G, Martinez-Fernandez L, Balanikas E, Markovitsi D. Effect of the DNA Polarity on the Relaxation of Its Electronic Excited States. J Phys Chem Lett 2023; 14:10219-10224. [PMID: 37931204 DOI: 10.1021/acs.jpclett.3c02580] [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] [Indexed: 11/08/2023]
Abstract
The DNA polarity, i.e., the order in which nucleobases are connected together via the phosphodiester backbone, is crucial for several biological processes. But, so far, there has not been experimental evidence regarding its effect on the relaxation of DNA electronic excited states. Here we examine this aspect for two dinucleotides containing adenine and guanine: 5'-dApdG-3' and 5'-dGpdA-3' in water. We used two different femtosecond transient absorption setups: one providing high temporal resolution and broad spectral coverage (330-650 nm) between 30 fs and 50 ps, and the other recording decays at selected wavelengths until 1.2 ns. The transient absorption spectra corresponding to the minima in the potential energy surface of the first excited state were computed by quantum chemistry methods. Our results show that the excited charge transfer state in 5'-dGpdA-3' is formed with a ∼75% higher quantum yield and exhibits slower decay (170 ± 10 ps vs 112 ± 12 ps) compared to 5'-dApdG-3'.
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Affiliation(s)
- Vasilis Petropoulos
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lorenzo Uboldi
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Evangelos Balanikas
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva-4, Switzerland
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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37
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Vasconcelos Sanches de Araújo A, Borin AC. Water Solvated Zn(II)-Guanine Complex: Structural Aspects and Luminescence Properties. J Phys Chem A 2023; 127:8297-8306. [PMID: 37772405 DOI: 10.1021/acs.jpca.3c04132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Understanding the role of metal ions in living organisms and their interactions with biological compounds is fundamental for our health and for developing technological devices for bioinorganic applications. In this work, structural aspects and photophysical mechanisms involved in the luminescence of the Zn(II)-guanine complex in water were studied by using computational quantum chemical methods, providing molecular-level explanations for reported experimental findings. Structural aspects were investigated with def2-SVP basis sets, Density Functional Theory, Resolution of Identity Algebraic Diagrammatic Construction in Second-Order (RI-ADC(2)), Polarizable Continuum Model (PCM), and Conductor-like Screening Model (COSMO) methods. Spectroscopic properties and photophysical deactivation mechanisms were explored with the atomic natural orbital basis sets including relativistic and semicore correlation (ANO-RCC-VDZP) basis sets, Multistate Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2), and Polarizable Continuum Model (PCM) methods. Our results indicate that Zn(II) ions bind preferentially to the N7 position, and three water molecules in its coordination sphere are sufficient for describing the photophysical properties. The complexation with Zn(II) ions and solvation effects favor fluorescence because the minimum energy region of the S1 (La) (1ππ*) ((La)min) potential energy hypersurface is stabilized, the (La/GS) crossing region is destabilized, and a high energetic barrier along the pathway from the (La)min and (La/GS) regions hampers fast nonradiative return of the electronic population to the ground state, as observed for isolated 9H-guanine.
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Affiliation(s)
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, São Paulo 05508-000, Brazil
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38
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Gu B. A Discrete-Variable Local Diabatic Representation of Conical Intersection Dynamics. J Chem Theory Comput 2023; 19:6557-6563. [PMID: 37737832 DOI: 10.1021/acs.jctc.3c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Conical intersections (CIs) are ubiquitous in polyatomic molecules and are responsible for a wide range of phenomena in photochemistry and photophysics. Modeling the conical intersection dynamics with adiabatic electronic states is hindered by the divergence of the first- and second-order derivative couplings at CIs due to electronic degeneracy. We introduce and implement a novel diabatic representation for exact correlated electron-nuclear wave packet dynamics through conical intersections. It directly employs the adiabatic electronic states but avoids the singular first- and second-order derivative couplings and is robust to different gauge choices of the electronic wave function phases. The reference nuclear geometries defining the adiabatic electronic states are determined by a discrete-variable representation of the nuclear coordinates. The nonadiabatic effects are accounted for by the electronic overlap matrix instead of derivative couplings as in the adiabatic representation. Illustrated by a two-mode conical intersection model, this representation captures all nonadiabatic effects, including electronic transitions, electronic coherence, and geometric phases. Thus, this representation provides a singularity-free framework for modeling ab initio conical intersection wave packet dynamics.
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Affiliation(s)
- Bing Gu
- Department of Chemistry & Department of Physics, Westlake University, Hangzhou, Zhejiang 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
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39
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Chang XP, Fan FR, Zhang TS, Xie BB. Quantum mechanics/molecular mechanics studies on the excited-state decay mechanisms of cytidine aza-analogues: 5-azacytidine and 2'-deoxy-5-azacytidine in aqueous solution. Phys Chem Chem Phys 2023; 25:26258-26269. [PMID: 37743787 DOI: 10.1039/d3cp03628f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The excited state properties and deactivation pathways of two DNA methylation inhibitors, i.e., 5-azacytidine (5ACyd) and 2'-deoxy-5-azacytidine (5AdCyd) in aqueous solution, are comprehensively explored with the QM(CASPT2//CASSCF)/MM protocol. We systematically map the feasible decay mechanisms based on the obtained excited-state decay paths involving all the identified minimum-energy structures, conical intersections, and crossing points driving the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the 1ππ*, 1nπ*, 3ππ*, 3nπ*, and S0 states. Unlike the 1nπ* state below the 1ππ* state in 5ACyd, deoxyribose group substitution at the N1 position leads to the 1ππ* state becoming the S1 state in 5AdCyd. In 5ACyd and 5AdCyd, the initially populated 1ππ* state mainly deactivates to the S0 state through the direct 1ππ* → S0 IC or mediated by the 1nπ* state. The former nearly barrierless IC channel of 1ππ* → S0 occurs ultrafast via the nearby low-lying 1ππ*/S0 conical intersection. In the latter IC channel of 1ππ* → 1nπ* → S0, the initially photoexcited 1ππ* state first approaches the nearby S2/S1 conical section 1ππ*/1nπ* and then undergoes efficient IC to the 1nπ* state, followed by the further IC to the initial S0 state via the S1/S0 conical intersection 1nπ*/S0. The 1nπ*/S0 conical intersection is estimated to be located 6.0 and 4.9 kcal mol-1 above the 1nπ* state minimum in 5ACyd and 5AdCyd, respectively, at the QM(CASPT2)/MM level. In addition to the efficient singlet-mediated IC channels, the minor ISC routes would populate 1ππ* to T1(ππ*) through 1ππ* → T1 or 1ππ* → 1nπ* → T1. Relatively, the 1ππ* → 1nπ* → T1 route benefits from the spin-orbit coupling (SOC) of 1nπ*/3ππ* of 8.7 cm-1 in 5ACyd and 10.2 cm-1 in 5AdCyd, respectively. Subsequently, the T1 system will approach the nearby T1/S0 crossing point 3ππ*/S0 driving it back to the S0 state. Given the 3ππ*/S0 crossing point located above the T1 minimum and the small T1/S0 SOC, i.e., 8.4 kcal mol-1 and 2.1 cm-1 in 5ACyd and 6.8 kcal mol-1 and 1.9 cm-1 in 5AdCyd, respectively, the slow T1 → S0 would trap the system in the T1 state for a while. The present work could contribute to understanding the mechanistic photophysics and photochemistry of similar aza-nucleosides and their derivatives.
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Affiliation(s)
- Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China.
| | - Feng-Ran Fan
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China.
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou 311231, China
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40
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Improta R. Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations. Int J Mol Sci 2023; 24:12614. [PMID: 37628797 PMCID: PMC10454157 DOI: 10.3390/ijms241612614] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.
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Affiliation(s)
- Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
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41
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Jiang G, Liu J, Zhou P. Unraveling the Mechanism of ACQ-to-AIE Transformation of Fluorescein Derivatives. J Phys Chem A 2023. [PMID: 37294934 DOI: 10.1021/acs.jpca.3c02244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although fluorescein derivatives have excellent properties and strong practicability, they are typical aggregation-induced quenching (ACQ) molecules, which are not conducive to working in the solid state. Recently, the fluorescein derivative Fl-Me with aggregation-induced emission (AIE) property was synthesized, which brought a new dawn for the research and development of fluorescein-based materials. In this study, the AIE mechanism of Fl-Me was investigated based on time-dependent density functional theory and the ONIOM method. The results revealed that an effective dark-state deactivation pathway leads to the fluorescence quenching of Fl-Me in a solution environment. Accordingly, the AIE phenomenon originates from the closure of the dark-state quenching channel. It is worth emphasizing that we found that the carbonyl group of molecular Fl-Me has intermolecular hydrogen bonding interaction with the adjacent molecules, which caused the increase of the dark-state energy in the crystalline state. Moreover, the restriction of the rotational motion and the nonexistence of the π-π stacking interaction are beneficial to the enhancement of fluorescence upon aggregation. Finally, the ACQ-to-AIE transformation mechanisms of fluorescein derivatives have been discussed. This work provides deeper insight into the photophysical mechanism for the fluorescein derivatives Fl-Me with AIE feature and eventually is expected to help researchers to develop more fluorescein-based AIE materials with remarkable properties for various fields.
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Affiliation(s)
- Gaoshang Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, P. R. China
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, P. R. China
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
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42
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Yang W, Chen Y, Mei M, Li W, Wang C, Yang Y, Liang J, Guo Z, Wu L, Chen X. Synergetic argentophilic and through space electronic interactions in a single-crystal-to-single-crystal photocycloaddition reaction: a mechanistic study. Phys Chem Chem Phys 2023; 25:12783-12790. [PMID: 37128988 DOI: 10.1039/d3cp00838j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ag(I) is able to mediate single-crystal-to-single-crystal transformation through [2+2] photocycloaddition to prepare high-conductivity materials. However, the intrinsic mechanism of Ag(I) mediation, the detailed photophysical and photochemical processes as well as the origin of the enhanced conductivity of nanocrystals are still unclear. In this work, the comprehensive kinetic scheme and regulation mechanism are established by the accurate QM/MM calculations at the CASPT2//CASSCF/AMBER level of theory with consideration of the crystal environment. We find that the argentophilic interaction and through space electronic interaction are the key factors that promote Ag(I)-mediated [2+2] PCA reactions and may account for the enhancement of conductivity. These mechanistic insights into the Ag(I)-regulated photo-dimerization in the crystal surrounding are beneficial for the design of the structurally and electrically favorable skeletons of a metal-organic coordination polymer.
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Affiliation(s)
- Wenjing Yang
- College of Materials Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Taiyuan, Shanxi, 030024, P. R. China.
| | - Yonglin Chen
- College of Materials Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Taiyuan, Shanxi, 030024, P. R. China.
| | - Min Mei
- College of Science, Hunan College for Preschool Education, Changde, Hunan, 415000, P. R. China
| | - Weijia Li
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, P. R. China.
| | - Chu Wang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, P. R. China.
| | - Yanting Yang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, P. R. China.
| | - Jing Liang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, P. R. China.
| | - Zhen Guo
- College of Materials Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Taiyuan, Shanxi, 030024, P. R. China.
| | - Liangliang Wu
- Laboratory of Beam Technology and Energy Materials, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, P. R. China.
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, P. R. China.
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43
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Reiner M, Bachmair B, Tiefenbacher MX, Mai S, González L, Marquetand P, Dellago C. Nonadiabatic Forward Flux Sampling for Excited-State Rare Events. J Chem Theory Comput 2023; 19:1657-1671. [PMID: 36856706 PMCID: PMC10061683 DOI: 10.1021/acs.jctc.2c01088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Indexed: 03/02/2023]
Abstract
We present a rare event sampling scheme applicable to coupled electronic excited states. In particular, we extend the forward flux sampling (FFS) method for rare event sampling to a nonadiabatic version (NAFFS) that uses the trajectory surface hopping (TSH) method for nonadiabatic dynamics. NAFFS is applied to two dynamically relevant excited-state models that feature an avoided crossing and a conical intersection with tunable parameters. We investigate how nonadiabatic couplings, temperature, and reaction barriers affect transition rate constants in regimes that cannot be otherwise obtained with plain, traditional TSH. The comparison with reference brute-force TSH simulations for limiting cases of rareness shows that NAFFS can be several orders of magnitude cheaper than conventional TSH and thus represents a conceptually novel tool to extend excited-state dynamics to time scales that are able to capture rare nonadiabatic events.
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Affiliation(s)
- Madlen
Maria Reiner
- Research
Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Doctoral School in Physics, University of
Vienna, Boltzmanngasse
5, 1090 Vienna, Austria
| | - Brigitta Bachmair
- Research
Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry, University
of Vienna, Währinger
Strasse 42, 1090 Vienna, Austria
| | - Maximilian Xaver Tiefenbacher
- Research
Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry, University
of Vienna, Währinger
Strasse 42, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Leticia González
- Research
Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Research
Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Christoph Dellago
- Research
Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Faculty
of Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria
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44
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Orimo N, Yamamoto YI, Karashima S, Boyer A, Suzuki T. Ultrafast Electronic Relaxation in 6-Methyluracil and 5-Fluorouracil in Isolated and Aqueous Conditions: Substituent and Solvent Effects. J Phys Chem Lett 2023; 14:2758-2763. [PMID: 36897645 DOI: 10.1021/acs.jpclett.3c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report ultrafast extreme ultraviolet photoelectron spectroscopy of 6-methyluracil (6mUra) and 5-fluorouracil (5FUra) in the gas phase and 6mUra and 5-fluorouridine in an aqueous environment. In the gas phase, internal conversion (IC) occurs from 1ππ* to 1nπ* states in tens of femtoseconds, followed by intersystem crossing to the 3ππ* state in several picoseconds. In an aqueous solution, 6mUra undergoes IC almost exclusively to the ground state (S0) in about 100 fs, which is essentially the same process as that for unsubstituted uracil, but much faster than that for thymine (5-methyluracil). The different dynamics for C5 and C6 methylation suggest that IC from 1ππ* to S0 is facilitated by out-of-plane (OOP) motion of the C5 substituent. The slow IC for C5-substituted molecules in an aqueous environment is ascribed to the solvent reorganization that is required for this OOP motion to occur. The slow rate for 5FUrd may arise in part from an increased barrier height due to C5 fluorination.
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Affiliation(s)
- Natsumi Orimo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Yo-Ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Shutaro Karashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Alexie Boyer
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
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45
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Chang XP, Zhao G, Zhang TS, Xie BB. Quantum mechanics/molecular mechanics studies on mechanistic photophysics of cytosine aza-analogues: 2,4-diamino-1,3,5-triazine and 2-amino-1,3,5-triazine in aqueous solution. Phys Chem Chem Phys 2023; 25:7669-7680. [PMID: 36857660 DOI: 10.1039/d2cp05639a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The excited-state properties and photophysics of cytosine aza-analogues, i.e., 2,4-diamino-1,3,5-triazine (2,4-DT) and 2-amino-1,3,5-triazine (2-AT) in solution have been systematically explored using the QM(MS-CASPT2//CASSCF)/MM approach. The excited-state nonradiative relaxation mechanisms for the initially photoexcited S1(ππ*) state decay back to the S0 state are proposed in terms of the present computed minima, surface crossings (conical intersections and singlet-triplet crossings), and excited-state decay paths in the S1, S2, T1, T2, and S0 states. Upon photoexcitation to the bright S1(ππ*) state, 2,4-DT quickly relaxes to its S1 minimum and then overcomes a small energy barrier of 5.1 kcal mol-1 to approach a S1/S0 conical intersection, where the S1 system hops to the S0 state through S1 → S0 internal conversion (IC). In addition, at the S1 minimum, the system could partially undergo intersystem crossing (ISC) to the T1 state, followed by further ISC to the S0 state via the T1/S0 crossing point. In the T1 state, an energy barrier of 7.9 kcal mol-1 will trap 2,4-DT for a while. In parallel, for 2-AT, the system first relaxes to the S1 minimum and then S1 → S0 IC or S1 → T1 → S0 ISCs take place to the S0 state by surmounting a large barrier of 15.3 kcal mol-1 or 11.9 kcal mol-1, respectively, which heavily suppress electronic transition to the S0 state. Different from 2,4-DT, upon photoexcitation in the Franck-Condon region, 2-AT can quickly evolve in an essentially barrierless manner to nearby S2/S1 conical intersection, where the S2 and T1 states can be populated. Once it hops to the S2 state, the system will overcome a relatively small barrier (6.6 kcal mol-1vs. 15.3 kcal mol-1) through IC to the S0 state. Similarly, an energy barrier of 11.9 kcal mol-1 heavily suppresses the T1 state transformation to the S0 state. The present work manifests that the amination/deamination of the triazine rings can affect some degree of different vertical and adiabatic excitation energies and nonradiative decay pathways in solution. It not only rationalizes excited-state decay dynamics of 2,4-DT and 2-AT in aqueous solution but could also provide insights into the understanding of the photophysics of aza-nucleobases.
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Affiliation(s)
- Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China.
| | - Geng Zhao
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China.
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou 311231, China
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46
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Karak P, Moitra T, Ruud K, Chakrabarti S. Photophysics of uracil: an explicit time-dependent generating function-based method combining both nonadiabatic and spin-orbit coupling effects. Phys Chem Chem Phys 2023; 25:8209-8219. [PMID: 36881024 DOI: 10.1039/d2cp05955j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results. Next, we investigate the photophysics associated with the complex photodynamics of the uracil molecule. Interestingly, our simulated rates corroborate experimental observations. Detailed analyses using Duschinsky rotation matrices, displacement vectors and NAC matrix elements are presented to interpret the findings alongside testing the suitability of the approach for such molecular systems. The suitability of the Fermi's golden rule based method is explained qualitatively in terms of single-mode potential energy surfaces.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
| | - Torsha Moitra
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway. .,Norwegian Defence Research Establishment, P.O.Box 25, 2027 Kjeller, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
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47
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Gustavsson T, Markovitsi D. The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes. J Phys Chem Lett 2023; 14:2141-2147. [PMID: 36802626 DOI: 10.1021/acs.jpclett.2c03884] [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: 06/18/2023]
Abstract
During the past few years, several studies reported that a significant part of the intrinsic fluorescence of DNA duplexes decays with surprisingly long lifetimes (1-3 ns) at wavelengths shorter than the ππ* emission of their monomeric constituents. This high-energy nanosecond emission (HENE), hardly discernible in the steady-state fluorescence spectra of most duplexes, was investigated by time-correlated single-photon counting. The ubiquity of HENE contrasts with the paradigm that the longest-lived excited states correspond to low-energy excimers/exciplexes. Interestingly, the latter were found to decay faster than the HENE. So far, the excited states responsible for HENE remain elusive. In order to foster future studies for their characterization, this Perspective presents a critical summary of the experimental observations and the first theoretical approaches. Moreover, some new directions for further work are outlined. Finally, the obvious need for computations of the fluorescence anisotropy considering the dynamic conformational landscape of duplexes is stressed.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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Xu Q, Liu Y, Wang M, Cerezo J, Improta R, Santoro F. The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Non-Adiabatic Couplings. Molecules 2023; 28:molecules28052286. [PMID: 36903532 PMCID: PMC10005559 DOI: 10.3390/molecules28052286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected. In this way, we compute the vRR spectra, considering the quasi-resonance with the eight lowest-energy excited states, disentangling the role of their inter-state couplings from the mere interference of their different contributions to the transition polarizability. We show that these effects are only moderate in the excitation energy range explored by experiments, where the spectral patterns can be rationalized from the simple analysis of displacements of the equilibrium positions along the different states. Conversely, at higher energies, interference and inter-state couplings play a major role, and the adoption of a fully non-adiabatic approach is strongly recommended. We also investigate the effect of specific solute-solvent interactions on the vRR spectra, by considering a cluster of cytosine, hydrogen-bonded by six water molecules, and embedded in a polarizable continuum. We show that their inclusion remarkably improves the agreement with the experiments, mainly altering the composition of the normal modes, in terms of internal valence coordinates. We also document cases, mostly for low-frequency modes, in which a cluster model is not sufficient, and more elaborate mixed quantum classical approaches, in explicit solvent models, need to be applied.
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Affiliation(s)
- Qiushuang Xu
- School of Physics Engineering, Qufu Normal University, Qufu 273165, China
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, China
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Yanli Liu
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics Engineering, Qufu Normal University, Qufu 273165, China
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, China
| | - Javier Cerezo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
- Correspondence: (R.I.); (F.S.)
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Correspondence: (R.I.); (F.S.)
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Brash DE, Goncalves LCP. Chemiexcitation: Mammalian Photochemistry in the Dark †. Photochem Photobiol 2023; 99:251-276. [PMID: 36681894 PMCID: PMC10065968 DOI: 10.1111/php.13781] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/18/2023] [Indexed: 01/23/2023]
Abstract
Light is one way to excite an electron in biology. Another is chemiexcitation, birthing a reaction product in an electronically excited state rather than exciting from the ground state. Chemiexcited molecules, as in bioluminescence, can release more energy than ATP. Excited states also allow bond rearrangements forbidden in ground states. Molecules with low-lying unoccupied orbitals, abundant in biology, are particularly susceptible. In mammals, chemiexcitation was discovered to transfer energy from excited melanin, neurotransmitters, or hormones to DNA, creating the lethal and carcinogenic cyclobutane pyrimidine dimer. That process was initiated by nitric oxide and superoxide, radicals triggered by ultraviolet light or inflammation. Several poorly understood chronic diseases share two properties: inflammation generates those radicals across the tissue, and cells that die are those containing melanin or neuromelanin. Chemiexcitation may therefore be a pathogenic event in noise- and drug-induced deafness, Parkinson's disease, and Alzheimer's; it may prevent macular degeneration early in life but turn pathogenic later. Beneficial evolutionary selection for excitable biomolecules may thus have conferred an Achilles heel. This review of recent findings on chemiexcitation in mammalian cells also describes the underlying physics, biochemistry, and potential pathogenesis, with the goal of making this interdisciplinary phenomenon accessible to researchers within each field.
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Affiliation(s)
- Douglas E. Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520-8028, USA
| | - Leticia C. P. Goncalves
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
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Zhou Z, Della Sala F, Parker SM. Minimal Auxiliary Basis Set Approach for the Electronic Excitation Spectra of Organic Molecules. J Phys Chem Lett 2023; 14:1968-1976. [PMID: 36787711 DOI: 10.1021/acs.jpclett.2c03698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report a minimal auxiliary basis model for time-dependent density functional theory (TDDFT) with hybrid density functionals that can accurately reproduce excitation energies and absorption spectra from TDDFT while reducing cost by about 2 orders of magnitude. Our method, dubbed TDDFT-ris, employs the resolution-of-the-identity technique with just one s-type auxiliary basis function per atom for the linear response operator, where the Gaussian exponents are parametrized across the periodic table using tabulated atomic radii with a single global scaling factor. By tuning on a small test set, we determine a single functional-independent scale factor that balances errors in excitation energies and absorption spectra. Benchmarked on organic molecules and compared to standard TDDFT, TDDFT-ris has an average energy error of only 0.06 eV and yields absorption spectra in close agreement with TDDFT. Thus, TDDFT-ris enables simulation of realistic absorption spectra in large molecules that would be inaccessible from standard TDDFT.
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Affiliation(s)
- Zehao Zhou
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Fabio Della Sala
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, 73010 Arnesano (LE), Italy
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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