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Bal M, Köse A, Güngör SA. Investigation of photoluminescence and DNA binding properties of benzimidazole compounds containing benzophenone group. J Biomol Struct Dyn 2024; 42:7847-7859. [PMID: 37526238 DOI: 10.1080/07391102.2023.2242496] [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: 06/02/2023] [Accepted: 07/23/2023] [Indexed: 08/02/2023]
Abstract
The synthesis of benzimidazole compounds containing benzophenone group in accordance with the literature and the investigation of DNA binding properties of these compounds by using UV-vis and photoluminescence spectroscopy methods constitute the basis of this research. The structures of the compounds were determined by methods such as FT-IR, 1H, 13C NMR, UV-vis, Photoluminescence spectroscopy, and X-ray crystallography. By using methods such as UV-vis, Photoluminescence spectroscopy, and viscosity tests, information were collected about the binding types, binding mode, and binding energies of the compounds with DNA. In addition, the binding interactions of the compounds with DNA were investigated using the molecular docking technique. Using this information, calibration equations, correlation coefficients (r2), and DNA binding constants (Kb) were calculated for their compounds. The binding constants (Kb) calculated for substances A, B, and C were found to be 3.0 × 104, 7.0 × 104, and 3.0 × 104 M-1, respectively. UV-vis, EB competitive binding, and viscosity tests showed that the compounds tended to bind to the DNA structure via the groove binding mode. At the end of molecular docking studies, it was determined that compound B showed the best DNA binding activity in in vitro studies. Compared with the studies in the literature, it is thought that the synthesized compounds can take place in cancer drug research as DNA binding agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mustafa Bal
- Department of Materials Science and Engineering, Kahramanmaras Sütcü Imam University, Kahramanmaraş, Turkey
| | - Ayşegül Köse
- Department of Property Protection and Safety, Elbistan Vocational School, Kahramanmaras Istiklal University, Kahramanmaraş, Turkey
| | - Seyit Ali Güngör
- Department of Chemistry, Faculty of Science, Kahramanmaras Sütcü Imam University, Kahramanmaraş, Turkey
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2
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Gillet N, Dumont E, Bignon E. DNA damage and repair in the nucleosome: insights from computational methods. Biophys Rev 2024; 16:345-356. [PMID: 39099841 PMCID: PMC11297232 DOI: 10.1007/s12551-024-01183-9] [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: 11/01/2023] [Accepted: 03/05/2024] [Indexed: 08/06/2024] Open
Abstract
Cellular DNA is constantly exposed to endogenous or exogenous factors that can induce lesions. Several types of lesions have been described that can result from UV/ionizing irradiations, oxidative stress, or free radicals, among others. In order to overcome the deleterious effects of such damages, i.e., mutagenicity or cytotoxicity, cells possess a highly complex DNA repair machinery, involving repair enzymes targeting specific types of lesions through dedicated cellular pathways. In addition, DNA is highly compacted in the nucleus, the first level of compaction consisting of ~ 147 DNA base pairs wrapped around a core of histones, the so-called nucleosome core particle. In this complex environment, the DNA structure is highly constrained, and fine-tuned mechanisms involving remodeling processes are required to expose the DNA to repair enzymes and to facilitate the damage removal. However, these nucleosome-specific mechanisms remain poorly understood, and computational methods emerged only recently as powerful tools to investigate DNA damages in such complex systems as the nucleosome. In this mini-review, we summarize the latest advances brought out by computational approaches in the field, opening new exciting perspectives for the study of DNA damage and repair in the nucleosome context.
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Affiliation(s)
- Natacha Gillet
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, 69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
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3
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Su Y, Song G, Shen Y, Li X, Ren H. Mechanisms and energetics for hydrogen abstraction of thymine photosensitized by benzophenone from theoretical principles. Phys Chem Chem Phys 2023; 25:6467-6472. [PMID: 36779968 DOI: 10.1039/d2cp05481g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The significant role of hydrogen abstraction in chemistry and biology has inspired many theoretical works to link its practical phenomena and mechanistic properties. Here, the photophysical processes and hydrogen abstraction mechanisms of benzophenone (BZP) photosensitized thymine damage were systematically investigated from theoretical principles. It was found that the BZP photosensitizer upon UV irradiation undergoes vertical excitation, internal conversion, vibrational relaxation and intersystem crossing into a triplet excited state. Then the triplet BZP damages thymine by a hydrogen abstraction process. However, the reverse reaction easily occurs due to the lower reaction energy, which causes a low yield of hydrogen abstraction products. We hope this comprehensive work can provide a deeper understanding of photosensitive DNA damage from hydrogen abstraction.
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Affiliation(s)
- Yingli Su
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Guanlin Song
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Yan Shen
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Xiangyuan Li
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Haisheng Ren
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
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4
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Kobets T, Smith BPC, Williams GM. Food-Borne Chemical Carcinogens and the Evidence for Human Cancer Risk. Foods 2022; 11:2828. [PMID: 36140952 PMCID: PMC9497933 DOI: 10.3390/foods11182828] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Commonly consumed foods and beverages can contain chemicals with reported carcinogenic activity in rodent models. Moreover, exposures to some of these substances have been associated with increased cancer risks in humans. Food-borne carcinogens span a range of chemical classes and can arise from natural or anthropogenic sources, as well as form endogenously. Important considerations include the mechanism(s) of action (MoA), their relevance to human biology, and the level of exposure in diet. The MoAs of carcinogens have been classified as either DNA-reactive (genotoxic), involving covalent reaction with nuclear DNA, or epigenetic, involving molecular and cellular effects other than DNA reactivity. Carcinogens are generally present in food at low levels, resulting in low daily intakes, although there are some exceptions. Carcinogens of the DNA-reactive type produce effects at lower dosages than epigenetic carcinogens. Several food-related DNA-reactive carcinogens, including aflatoxins, aristolochic acid, benzene, benzo[a]pyrene and ethylene oxide, are recognized by the International Agency for Research on Cancer (IARC) as causes of human cancer. Of the epigenetic type, the only carcinogen considered to be associated with increased cancer in humans, although not from low-level food exposure, is dioxin (TCDD). Thus, DNA-reactive carcinogens in food represent a much greater risk than epigenetic carcinogens.
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Affiliation(s)
- Tetyana Kobets
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Benjamin P. C. Smith
- Future Ready Food Safety Hub, Nanyang Technological University, Singapore 639798, Singapore
| | - Gary M. Williams
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
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5
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Volk KR, Casabianca LB. Quantum mechanical study of interactions between sunscreen ingredients and nucleotide bases. J Mol Model 2022; 28:243. [PMID: 35925497 DOI: 10.1007/s00894-022-05253-1] [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: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
Interactions between the popular sunscreen ingredients oxybenzone and homosalate and DNA bases have been studied using density functional theory and ab initio methods. Low-energy structures for each sunscreen ingredient interacting with each nucleotide base in either a pi-stacked or hydrogen-bonded fashion were found. The binding energies are comparable to those for the Watson-Crick-Franklin Ade-Thy and Cyt-Gua pairs. Pi-stacked and hydrogen-bonded structures are comparable in energy, with hydrogen-bonded structures having a more negative counterpoise-corrected binding energy, while the final pi-stacked structures are lower in energy. This is due to a geometrical rearrangement required to form the hydrogen bonds that raise the total energy of the complex. It was also found that when using the M06-2X density functional, the STO-3G basis set favors hydrogen bonding, but 6-31G(d) and 6-31 + G(s) basis sets predict similar binding geometries.
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Affiliation(s)
- Kyle R Volk
- Department of Chemistry, Clemson University, Clemson, SC, USA
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Manae MA, Hazra A. Quantum effects in photosensitization: the case of singlet oxygen generation by thiothymines. Phys Chem Chem Phys 2022; 24:13266-13274. [PMID: 35604080 DOI: 10.1039/d2cp01337a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photosensitization is the indirect electronic excitation of a molecule with the aid of a photosensitizer and is a bimolecular nonradiative energy transfer. In this study, we have attempted to elucidate its mechanism, and we do this by calculating rate constants of photosensitization of oxygen by thiothymines (2-thiothymine, 4-thiothymine and 2,4 dithiothymine). The rate constants have been calculated using two approaches: (a) a classical limit of Fermi's Golden Rule (FGR), and (b) a time-dependent variant of FGR, where the treatment is purely quantum mechanical. The former approach has previously been developed for bimolecular systems and has been applied to the photosensitization reactions studied here. The latter approach, however, has so far only been used for unimolecular reactions, and in this work, we describe how it can be adapted for bimolecular reactions. Experimentally, all three thiothymines are known to have significant singlet oxygen yields, which are indicative of similar rates. Rate constants calculated using the time-dependent variant of FGR are similar across all three thiothymines. While the classical approximation gives reasonable rate constants for 2-thiothymine, it severely underestimates them for 4-thiothymine and 2,4 dithiothymine, by several orders of magnitude. This work indicates the importance of quantum effects in driving photosensitization.
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Affiliation(s)
- Meghna A Manae
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India.
| | - Anirban Hazra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India.
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Sarkar R, Loos PF, Boggio-Pasqua M, Jacquemin D. Assessing the Performances of CASPT2 and NEVPT2 for Vertical Excitation Energies. J Chem Theory Comput 2022; 18:2418-2436. [PMID: 35333060 DOI: 10.1021/acs.jctc.1c01197] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Methods able to simultaneously account for both static and dynamic electron correlations have often been employed, not only to model photochemical events but also to provide reference values for vertical transition energies, hence allowing benchmarking of lower-order models. In this category, both the complete-active-space second-order perturbation theory (CASPT2) and the N-electron valence state second-order perturbation theory (NEVPT2) are certainly popular, the latter presenting the advantage of not requiring the application of the empirical ionization-potential-electron-affinity (IPEA) and level shifts. However, the actual accuracy of these multiconfigurational approaches is not settled yet. In this context, to assess the performances of these approaches, the present work relies on highly accurate (±0.03 eV) aug-cc-pVTZ vertical transition energies for 284 excited states of diverse character (174 singlet, 110 triplet, 206 valence, 78 Rydberg, 78 n → π*, 119 π → π*, and 9 double excitations) determined in 35 small- to medium-sized organic molecules containing from three to six non-hydrogen atoms. The CASPT2 calculations are performed with and without IPEA shift and compared to the partially contracted (PC) and strongly contracted (SC) variants of NEVPT2. We find that both CASPT2 with IPEA shift and PC-NEVPT2 provide fairly reliable vertical transition energy estimates, with slight overestimations and mean absolute errors of 0.11 and 0.13 eV, respectively. These values are found to be rather uniform for the various subgroups of transitions. The present work completes our previous benchmarks focused on single-reference wave function methods ( J. Chem. Theory Comput. 2018, 14, 4360; J. Chem. Theory Comput. 2020, 16, 1711), hence allowing for a fair comparison between various families of electronic structure methods. In particular, we show that ADC(2), CCSD, and CASPT2 deliver similar accuracies for excited states with a dominant single-excitation character.
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Affiliation(s)
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Université de Toulouse, Toulouse 31062, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Université de Toulouse, Toulouse 31062, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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8
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Visible-light-mediated metal-free decarboxylative acylation of electron-deficient quinolines using α-ketoacids under ambient air. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Abstract
Photochemical reactions are increasingly being used for chemical and materials synthesis, for example, in photoredox catalysis, and generally involve photoexcitation of molecular chromophores dissolved in a liquid solvent. The choice of solvent influences the outcomes of the photochemistry because solute-solvent interactions modify the energies of and crossings between electronic states of the chromophores, and they affect the evolving structures of the photoexcited molecules. Ultrafast laser spectroscopy methods with femtosecond to picosecond time resolution can resolve the dynamics of these photoexcited molecules as they undergo structural and electronic changes, relax back to the ground state, dissipate their excess internal energy to the surrounding solvent, or undergo photochemical reactions. In this Account, we illustrate how experimental studies using ultrafast lasers can reveal the influences that different solvents or cosolutes exert on the photoinduced nonadiabatic dynamics of internal conversion and intersystem crossing in nonradiative relaxation pathways. Although the environment surrounding a solute molecule is rapidly changing, with fluctuations in the coordination to neighboring solvent molecules occurring on femtosecond or picosecond time scales, we show that it is possible to photoexcite selectively only those molecular chromophores transiently experiencing specific solute-solvent interactions such as intermolecular hydrogen bonding.The effects of different solvation environments on the photodynamics are illustrated using four selected examples of photochemical processes in which the solvent has a marked effect on the outcomes. We first consider two aromatic carbonyl compounds, benzophenone and acetophenone, which are known to undergo fast intersystem crossing to populate the first excited triplet state on time scales of a few picoseconds. We show that the nonadiabatic excited-state dynamics are modified by transient hydrogen bonding of the carbonyl group to a protic solvent or by coordination to a metal cation cosolute. We then examine how different solvents modify the competition between two alternative relaxation pathways in a photoexcited UVA-sunscreen molecule, diethylamino hydroxybenzoyl hexyl benzoate (DHHB). This relaxation back to the ground electronic state is an essential part of the effective operation of the sunscreen compound, but the dynamics are sensitive to the surrounding environment. Finally, we consider how solvents of different polarity affect the energies and lifetimes of excited states with locally excited or charge-transfer character in heterocyclic organic compounds used as excited-state electron donors for photoredox catalysis. With these and other examples, we seek to develop a molecular level understanding of how the choice of solution environment might be used to control the outcomes of photochemical reactions.
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Affiliation(s)
- Ravi Kumar Venkatraman
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Andrew J. Orr-Ewing
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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10
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Allahkaram L, Monari A, Dumont E. The Behavior of Triplet Thymine in a Model B-DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations †. Photochem Photobiol 2021; 98:633-639. [PMID: 34699615 DOI: 10.1111/php.13549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/20/2021] [Indexed: 11/28/2022]
Abstract
Among the naturally occurring nucleobases, thymine presents the lowest triplet state, hence it represents a hotspot for energy transfer and photosensitization. In turn, the population of the triplet state may lead to thymine dimerization and hence to the production of toxic DNA lesions and has been the subject of intensive theoretical and experimental investigations. Relying on QM/MM molecular dynamics simulations, we have sought to situate the energy of the lowest triplet state of thymine embedded in a B-DNA environment. The energy gap varies between 305 and 329 kJ mol-1 when a single thymine is treated at the quantum chemistry level, depending on its position in the model double-stranded 16-bp oligonucleotide. The energy of triplet state decreases up to 300 kJ mol-1 , due to polarization effects, when we consider coupled stacked nucleobases up to the inclusion of four nucleobases. Our value lies in good agreement with the energy inferred experimentally by Miranda and coworkers (270 kJ mol-1 ), and our theoretical exploration opens the door to investigations toward other more complex and biologically relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semi-empirical approaches such as density functional-based tight-binding, allowing to further rationalize sequence effects.
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Affiliation(s)
- Laleh Allahkaram
- Laboratoire de Chimie, CNRS UMR 5182, ENS de Lyon, Univ Lyon, Lyon, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, Nancy, France.,Université de Paris and CNRS, Itodys, Paris, France
| | - Elise Dumont
- Laboratoire de Chimie, CNRS UMR 5182, ENS de Lyon, Univ Lyon, Lyon, France.,Institut Universitaire de France, Paris, France
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11
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Ng G, Judzewitsch P, Li M, Pester CW, Jung K, Boyer C. Synthesis of Polymer Brushes Via SI-PET-RAFT for Photodynamic Inactivation of Bacteria. Macromol Rapid Commun 2021; 42:e2100106. [PMID: 33834575 DOI: 10.1002/marc.202100106] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/11/2021] [Indexed: 12/20/2022]
Abstract
Biofilms are a persistent issue in healthcare and industry. Once formed, the eradication of biofilms is challenging as the extracellular polymeric matrix provides protection against harsh environmental conditions and physically enhances resistance to antimicrobials. The fabrication of polymer brush coatings provides a versatile approach to modify the surface to resist the formation of biofilms. Herein, the authors report a facile synthetic route for the preparation of surface-tethered polymeric brushes with antifouling and visible light activated bactericidal properties using surface-initiated photoinduced electron transfer-reversible addition-fragmentation chain transfer polymerization (SI-PET-RAFT). Bactericidal property via the generation of singlet oxygen, which can be temporally and spatially controlled, is investigated against both Gram-positive and Gram-negative bacteria. In addition, the antibacterial properties of the surface can be recycled. This work paves the way for the preparation of polymer films that can resist and kill bacterial biofilms.
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Affiliation(s)
- Gervase Ng
- School of Chemical Engineering, Australian Centre for NanoMedicine, Cluster for Advanced Macromolecular Design, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Peter Judzewitsch
- School of Chemical Engineering, Australian Centre for NanoMedicine, Cluster for Advanced Macromolecular Design, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Mingxiao Li
- Department of Chemical Engineering, Department of Chemistry, Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Christian W Pester
- Department of Chemical Engineering, Department of Chemistry, Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Kenward Jung
- School of Chemical Engineering, Australian Centre for NanoMedicine, Cluster for Advanced Macromolecular Design, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Cyrille Boyer
- School of Chemical Engineering, Australian Centre for NanoMedicine, Cluster for Advanced Macromolecular Design, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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12
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Cárdenas G, Nogueira JJ. Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States. Molecules 2020; 25:E5927. [PMID: 33333751 PMCID: PMC7765225 DOI: 10.3390/molecules25245927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022] Open
Abstract
The design of more efficient photosensitizers is a matter of great importance in the field of cancer treatment by means of photodynamic therapy. One of the main processes involved in the activation of apoptosis in cancer cells is the oxidative stress on DNA once a photosensitizer is excited by light. As a consequence, it is very relevant to investigate in detail the binding modes of the chromophore with DNA, and the nature of the electronically excited states that participate in the induction of DNA damage, for example, charge-transfer states. In this work, we investigate the electronic structure of the anthraquinone photosensitizer intercalated into a double-stranded poly(dG-dC) decamer model of DNA. First, the different geometric configurations are analyzed by means of classical molecular dynamics simulations. Then, the excited states for the most relevant poses of anthraquinone inside the binding pocket are computed by an electrostatic-embedding quantum mechanics/molecular mechanics approach, where anthraquinone and one of the nearby guanine residues are described quantum mechanically to take into account intermolecular charge-transfer states. The excited states are characterized as monomer, exciton, excimer, and charge-transfer states based on the analysis of the transition density matrix, and each of these contributions to the total density of states and absorption spectrum is discussed in terms of the stacking interactions. These results are relevant as they represent the footing for future studies on the reactivity of anthraquinone derivatives with DNA and give insights on possible geometrical configurations that potentially favor the oxidative stress of DNA.
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Affiliation(s)
- Gustavo Cárdenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain;
| | - Juan J. Nogueira
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain;
- IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain
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13
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Blasco-Brusola A, Vayá I, Miranda MA. Influence of the Linking Bridge on the Photoreactivity of Benzophenone-Thymine Conjugates. J Org Chem 2020; 85:14068-14076. [PMID: 33108203 DOI: 10.1021/acs.joc.0c02088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Benzophenone (BP) is present in a variety of bioactive molecules. This chromophore is able to photosensitize DNA damage, where one of the most relevant BP/DNA interactions occurs with thymine (Thy). In view of the complex photoreactivity previously observed for dyads containing BP covalently linked to thymidine, the aim of this work is to investigate whether appropriate changes in the nature of the spacer could modulate the intramolecular BP/Thy photoreactivity, resulting in an enhanced selectivity. Accordingly, the photobehavior of a series of dyads derived from BP and Thy, separated by linear linkers of different length, has been investigated by steady-state photolysis, as well as femtosecond and nanosecond transient absorption spectroscopy. Irradiation of the dyads led to photoproducts arising from formal hydrogen abstraction or Paterno-Büchi (PB) photoreaction, with a chemoselectivity that was clearly dependent on the nature of the linking bridge; moreover, the PB process occurred with complete regio- and stereoselectivity. The overall photoreactivity increased with the length of the spacer and correlated well with the rate constants estimated from the BP triplet lifetimes. A reaction mechanism explaining these results is proposed, where the key features are the strain associated with the reactive conformations and the participation of triplet exciplexes.
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Affiliation(s)
- Alejandro Blasco-Brusola
- Departamento de Quı́mica, Instituto de Tecnologı́a Quı́mica (UPV-CSIC), Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
| | - Ignacio Vayá
- Departamento de Quı́mica, Instituto de Tecnologı́a Quı́mica (UPV-CSIC), Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
| | - Miguel A Miranda
- Departamento de Quı́mica, Instituto de Tecnologı́a Quı́mica (UPV-CSIC), Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
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14
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Semmeq A, Badawi M, Hasnaoui A, Ouaskit S, Monari A. DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets. Chemistry 2020; 26:11340-11344. [PMID: 32511805 DOI: 10.1002/chem.202002025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/04/2020] [Indexed: 11/07/2022]
Abstract
The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.
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Affiliation(s)
- Abderrahmane Semmeq
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France.,Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Michael Badawi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Abdellatif Hasnaoui
- LS3M, Faculté Polydisicplinaire-Khouribga, University Sultan Moulay Slimane of Beni Mellal, B.P 145, 25000, Khouribga, Morocco
| | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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15
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Francés-Monerris A, Lineros-Rosa M, Miranda MA, Lhiaubet-Vallet V, Monari A. Photoinduced intersystem crossing in DNA oxidative lesions and epigenetic intermediates. Chem Commun (Camb) 2020; 56:4404-4407. [DOI: 10.1039/d0cc01132k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The propensity of 5-formyluracil and 5-formylcytosine, i.e. oxidative lesions and epigenetic intermediates, in acting as intrinsic DNA photosensitizers is unraveled by using a combination of molecular modeling, simulation and spectroscopy.
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Affiliation(s)
| | - Mauricio Lineros-Rosa
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Miguel Angel Miranda
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
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16
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Lineros-Rosa M, Francés-Monerris A, Monari A, Miranda MA, Lhiaubet-Vallet V. Experimental and theoretical studies on thymine photodimerization mediated by oxidatively generated DNA lesions and epigenetic intermediates. Phys Chem Chem Phys 2020; 22:25661-25668. [DOI: 10.1039/d0cp04557h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Combined spectroscopic and computational studies reveal that, in spite of their structural similarities, 5-formyluracil and 5-formylcytosine photosensitize cyclobutane thymine dimers through two different types of mechanisms.
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Affiliation(s)
- Mauricio Lineros-Rosa
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | | | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
| | - Miguel Angel Miranda
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
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17
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Terenzi A, Gattuso H, Spinello A, Keppler BK, Chipot C, Dehez F, Barone G, Monari A. Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy. Antioxidants (Basel) 2019; 8:antiox8100472. [PMID: 31658666 PMCID: PMC6826623 DOI: 10.3390/antiox8100472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 01/24/2023] Open
Abstract
The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.
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Affiliation(s)
- Alessio Terenzi
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, Spain.
| | - Hugo Gattuso
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Angelo Spinello
- CNR-IOM DEMOCRITOS c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
| | - Christophe Chipot
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Dehez
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
| | - Giampaolo Barone
- Dipartimento di Scienze Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy.
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
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18
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Zhao J, Zhang X, Zhu R, Su T, Phillips DL. Photophysical Properties Controlled by Substituents with Lone-Pair Electrons at the Ortho- or Para-Positions of Fluoroquinolone Antibiotics. J Phys Chem B 2019; 123:3156-3162. [PMID: 30900898 DOI: 10.1021/acs.jpcb.8b10859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ortho- or para-substituents of NH2 or N-alkyl-containing lone-pair electrons were found to change the energy levels and transition configurations of the highest occupied molecular orbital for some fluoroquinolone-based antibiotics (FQs) and can significantly influence the electronic structure, intermolecular hydrogen bonding, internal conversion, and fluorescence and intersystem crossing efficiencies of FQs in acetonitrile or aqueous solution after photoexcitation. These findings provide new insights that can help in the molecular design strategies to regulate the photophysical properties of photosensitive medicines, photodynamic therapy reagents, and energy conversion materials that contain similar aromatic carbonyl structures.
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Affiliation(s)
- Jianfeng Zhao
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong 11111 , P. R. China
| | - Xiting Zhang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong 11111 , P. R. China
| | - Ruixue Zhu
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong 11111 , P. R. China.,School of Physical Science and Technology , Shanghai Tech University , Shanghai 201210 , P. R. China
| | - Tao Su
- Department of Molten Salt Chemistry and Engineering, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , 2019, Jia Luo Road , Jiading District, Shanghai 201800 , P. R. China
| | - David Lee Phillips
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong 11111 , P. R. China
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19
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Francés-Monerris A, Hognon C, Miranda MA, Lhiaubet-Vallet V, Monari A. Triplet photosensitization mechanism of thymine by an oxidized nucleobase: from a dimeric model to DNA environment. Phys Chem Chem Phys 2018; 20:25666-25675. [PMID: 30298156 DOI: 10.1039/c8cp04866e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA. In the present contribution, we use theoretical methodologies to study the triplet photosensitization mechanism of thymine exerted by ForU in a model dimer and in DNA environment. The photochemical pathways in the former system are described combining the CASPT2 and TD-DFT methods, whereas molecular dynamics simulations and QM/MM calculations are employed for the DNA duplex. It is unambiguously shown that the 1n,π* state localised in ForU mediates the population of the triplet manifold, most likely the 3π,π* state centred in ForU, whereas the 3π,π* state localized in thymine can be populated via triplet-triplet energy transfer given the small energy barrier of <0.23 eV determined for this pathway.
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20
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Shen Y, Gu Y, Martin R. sp 3 C-H Arylation and Alkylation Enabled by the Synergy of Triplet Excited Ketones and Nickel Catalysts. J Am Chem Soc 2018; 140:12200-12209. [PMID: 30184423 DOI: 10.1021/jacs.8b07405] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Triplet ketone sensitizers are of central importance within the realm of photochemical transformations. Although the radical-type character of triplet excited states of diaryl ketones suggests the viability for triggering hydrogen-atom transfer (HAT) and single-electron transfer (SET) processes, among others, their use as multifaceted catalysts in C-C bond-formation via sp3 C-H functionalization of alkane feedstocks still remains rather unexplored. Herein, we unlock a modular photochemical platform for forging C( sp3)-C( sp2) and C( sp3)-C( sp3) linkages from abundant alkane sp3 C-H bonds as functional handles using the synergy between nickel catalysts and simple, cheap and modular diaryl ketones. This method is distinguished by its wide scope that is obtained from cheap catalysts and starting precursors, thus complementing existing inner-sphere C-H functionalization protocols or recent photoredox scenarios based on iridium polypyridyl complexes. Additionally, such a platform provides a new strategy for streamlining the synthesis of complex molecules with high levels of predictable site-selectivity and preparative utility. Mechanistic experiments suggest that sp3 C-H abstraction occurs via HAT from the ketone triplet excited state. We believe this study will contribute to a more systematic utilization of triplet excited ketones as catalysts in metallaphotoredox scenarios.
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Affiliation(s)
- Yangyang Shen
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Av. Països Catalans 16 , 43007 Tarragona , Spain.,Departament de Química Analítica i Química Orgànica , Universitat Rovira i Virgili , c/Marcel·lí Domingo 1 , 43007 Tarragona , Spain
| | - Yiting Gu
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Av. Països Catalans 16 , 43007 Tarragona , Spain.,Departament de Química Analítica i Química Orgànica , Universitat Rovira i Virgili , c/Marcel·lí Domingo 1 , 43007 Tarragona , Spain
| | - Ruben Martin
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Av. Països Catalans 16 , 43007 Tarragona , Spain.,ICREA , Passeig Lluïs Companys 23 , 08010 Barcelona , Spain
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21
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Nogueira JJ, Roßbach S, Ochsenfeld C, González L. Effect of DNA Environment on Electronically Excited States of Methylene Blue Evaluated by a Three-Layered QM/QM/MM ONIOM Scheme. J Chem Theory Comput 2018; 14:4298-4308. [DOI: 10.1021/acs.jctc.8b00185] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, A-1090 Wien, Austria
| | - Sven Roßbach
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 Munich, Germany
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, A-1090 Wien, Austria
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22
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Segarra-Martí J, Zvereva E, Marazzi M, Brazard J, Dumont E, Assfeld X, Haacke S, Garavelli M, Monari A, Léonard J, Rivalta I. Resolving the Singlet Excited State Manifold of Benzophenone by First-Principles Simulations and Ultrafast Spectroscopy. J Chem Theory Comput 2018; 14:2570-2585. [DOI: 10.1021/acs.jctc.7b01208] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Javier Segarra-Martí
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Elena Zvereva
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific CentreRussian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Marco Marazzi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Johanna Brazard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Elise Dumont
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Xavier Assfeld
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Stefan Haacke
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
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23
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De Vetta M, Menger MFSJ, Nogueira JJ, González L. Solvent Effects on Electronically Excited States: QM/Continuum Versus QM/Explicit Models. J Phys Chem B 2018; 122:2975-2984. [DOI: 10.1021/acs.jpcb.7b12560] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina De Vetta
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, A-1090 Wien, Austria
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, 28049 Cantoblanco, Madrid, Spain
| | - Maximilian F. S. J. Menger
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, A-1090 Wien, Austria
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, A-1090 Wien, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, A-1090 Wien, Austria
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24
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Cuquerella MC, Lhiaubet-Vallet V, Miranda MA, Bosca F. Drug-DNA complexation as the key factor in photosensitized thymine dimerization. Phys Chem Chem Phys 2018; 19:4951-4955. [PMID: 28149985 DOI: 10.1039/c6cp08485k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crucial role of photosensitizer@DNA complexation in the formation of cyclobutane pyrimidine dimers (CPDs) has been demonstrated using femtosecond and nanosecond transient absorption and emission measurements in combination with in vitro DNA damage assays. This finding opens the door to re-evaluate the mechanisms involved in CPDs photosensitized by other chemicals.
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Affiliation(s)
- M Consuelo Cuquerella
- Instituto Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos, s/n, 46022 Valencia, Spain.
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos, s/n, 46022 Valencia, Spain.
| | - Miguel A Miranda
- Instituto Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos, s/n, 46022 Valencia, Spain.
| | - Francisco Bosca
- Instituto Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos, s/n, 46022 Valencia, Spain.
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25
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Zhang H, Gattuso H, Dumont E, Cai W, Monari A, Chipot C, Dehez F. Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA. Molecules 2018; 23:molecules23020228. [PMID: 29370096 PMCID: PMC6017086 DOI: 10.3390/molecules23020228] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/14/2018] [Accepted: 01/19/2018] [Indexed: 12/12/2022] Open
Abstract
DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc.), which bind through non-covalent interactions. Depending on their structure and their chemical properties, DNA binders can associate to the minor or to the major groove of double-stranded DNA. They can also intercalate between two adjacent base pairs, or even replace one or two base pairs within the DNA double helix. The subsequent biological effects are strongly dependent on the architecture of the binding motif. Discriminating between the different binding patterns is of paramount importance to predict and rationalize the effect of a given compound on DNA. The structural characterization of DNA complexes remains, however, cumbersome at the experimental level. In this contribution, we employed all-atom molecular dynamics simulations to determine the standard binding free energy of DNA with netropsin, a well-characterized antiviral and antimicrobial drug, which associates to the minor groove of double-stranded DNA. To overcome the sampling limitations of classical molecular dynamics simulations, which cannot capture the large change in configurational entropy that accompanies binding, we resort to a series of potentials of mean force calculations involving a set of geometrical restraints acting on collective variables.
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Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
| | - Hugo Gattuso
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
| | - Elise Dumont
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Université Claude Bernard Lyon 1, F-69342 Lyon, France.
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Antonio Monari
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
| | - Christophe Chipot
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Champaign, Illinois, 54506 Vandeouvre-lès-Nancy, France.
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Dehez
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Champaign, Illinois, 54506 Vandeouvre-lès-Nancy, France.
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26
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Zvereva E, Segarra-Martí J, Marazzi M, Brazard J, Nenov A, Weingart O, Léonard J, Garavelli M, Rivalta I, Dumont E, Assfeld X, Haacke S, Monari A. The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone. Photochem Photobiol Sci 2018; 17:323-331. [DOI: 10.1039/c7pp00439g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Modeling time-resolved spectra to unravel ultra fast solvent reorganization.
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27
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Bignon E, Marazzi M, Besancenot V, Gattuso H, Drouot G, Morell C, Eriksson LA, Grandemange S, Dumont E, Monari A. Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process. Sci Rep 2017; 7:8885. [PMID: 28827702 PMCID: PMC5566383 DOI: 10.1038/s41598-017-09406-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/25/2017] [Indexed: 11/23/2022] Open
Abstract
Nonsteroidal 2-arylproprionic acids are widely used, over-the-counter, anti-inflammatory drugs. Photosensitivity is a commonly overlooked adverse effect of these drugs. Based on the combined use of cell viability assays and molecular modeling, we prove and rationalize the photochemical pathways triggering photosensitization for two drugs, ibuprofen and ketoprofen. As its parent compound benzophenone, ketoprofen produces singlet oxygen, upon triplet manifold population. However, ibuprofen and ketoprofen photodissociate and hence may generate two highly reactive radicals. The formation of metastable aggregates between the two drugs and B-DNA is also directly probed by molecular dynamics. Our approach characterizes the coupled influence of the drug's intrinsic photochemistry and the interaction pattern with DNA. The photosensitization activity of nonsteroidal 2-arylproprionic acids, being added to gels and creams for topical use, should be crucially analyzed and rationalized to enact the proper preventive measures.
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Affiliation(s)
- Emmanuelle Bignon
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France
- Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342, Lyon, France
| | - Marco Marazzi
- Theory-Modeling-Simulation, Université de Lorraine - Nancy, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France
- Theory-Modeling-Simulation, CNRS, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France
| | - Vanessa Besancenot
- CRAN, UMR 7039 Université de Lorraine-Nancy, Vandoeuvre-lès-Nancy, Nancy, France
- CRAN, UMR 7039 CNRS, Vandoeuvre-lès-Nancy, Nancy, France
| | - Hugo Gattuso
- Theory-Modeling-Simulation, Université de Lorraine - Nancy, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France
- Theory-Modeling-Simulation, CNRS, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France
| | - Guillaume Drouot
- CRAN, UMR 7039 Université de Lorraine-Nancy, Vandoeuvre-lès-Nancy, Nancy, France
- CRAN, UMR 7039 CNRS, Vandoeuvre-lès-Nancy, Nancy, France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France
| | - Leif A Eriksson
- Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 c, 40530, Göteborg, Sweden
| | - Stephanie Grandemange
- CRAN, UMR 7039 Université de Lorraine-Nancy, Vandoeuvre-lès-Nancy, Nancy, France.
- CRAN, UMR 7039 CNRS, Vandoeuvre-lès-Nancy, Nancy, France.
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342, Lyon, France.
| | - Antonio Monari
- Theory-Modeling-Simulation, Université de Lorraine - Nancy, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France.
- Theory-Modeling-Simulation, CNRS, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France.
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28
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Nogueira JJ, Meixner M, Bittermann M, González L. Impact of Lipid Environment on Photodamage Activation of Methylene Blue. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201600062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry; University of Vienna; Währinger Str. 17 1090 Wien Austria
| | - Maximilian Meixner
- Institute of Theoretical Chemistry, Faculty of Chemistry; University of Vienna; Währinger Str. 17 1090 Wien Austria
| | - Marius Bittermann
- Institute of Theoretical Chemistry, Faculty of Chemistry; University of Vienna; Währinger Str. 17 1090 Wien Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry; University of Vienna; Währinger Str. 17 1090 Wien Austria
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Zobel JP, Nogueira JJ, González L. The IPEA dilemma in CASPT2. Chem Sci 2017; 8:1482-1499. [PMID: 28572908 PMCID: PMC5452265 DOI: 10.1039/c6sc03759c] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/23/2016] [Indexed: 12/22/2022] Open
Abstract
Multi-configurational second order perturbation theory (CASPT2) has become a very popular method for describing excited-state properties since its development in 1990. To account for systematic errors found in the calculation of dissociation energies, an empirical correction applied to the zeroth-order Hamiltonian, called the IPEA shift, was introduced in 2004. The errors were attributed to an unbalanced description of open-shell versus closed-shell electronic states and is believed to also lead to an underestimation of excitation energies. Here we show that the use of the IPEA shift is not justified and the IPEA should not be used to calculate excited states, at least for organic chromophores. This conclusion is the result of three extensive analyses. Firstly, we survey the literature for excitation energies of organic molecules that have been calculated with the unmodified CASPT2 method. We find that the excitation energies of 356 reference values are negligibly underestimated by 0.02 eV. This value is an order of magnitude smaller than the expected error based on the calculation of dissociation energies. Secondly, we perform benchmark full configuration interaction calculations on 137 states of 13 di- and triatomic molecules and compare the results with CASPT2. Also in this case, the excited states are underestimated by only 0.05 eV. Finally, we perform CASPT2 calculations with different IPEA shift values on 309 excited states of 28 organic small and medium-sized organic chromophores. We demonstrate that the size of the IPEA correction scales with the amount of dynamical correlation energy (and thus with the size of the system), and gets immoderate already for the molecules considered here, leading to an overestimation of the excitation energies. It is also found that the IPEA correction strongly depends on the size of the basis set. The dependency on both the size of the system and of the basis set, contradicts the idea of a universal IPEA shift which is able to compensate for systematic CASPT2 errors in the calculation of excited states.
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Affiliation(s)
- J Patrick Zobel
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ;
| | - Juan J Nogueira
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ;
| | - Leticia González
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ;
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30
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Antusch L, Gaß N, Wagenknecht HA. Elucidation of the Dexter-Type Energy Transfer in DNA by Thymine-Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides. Angew Chem Int Ed Engl 2016; 56:1385-1389. [PMID: 28026075 DOI: 10.1002/anie.201610065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/28/2016] [Indexed: 01/26/2023]
Abstract
C-nucleosides of 4-methylbenzophenone, 4-methoxybenzophenone, and 2'-methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A-T base pairs was observed that agrees with a Dexter-type triplet-triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.
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Affiliation(s)
- Linda Antusch
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Nadine Gaß
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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31
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Antusch L, Gaß N, Wagenknecht H. Aufklärung des Dexter‐Energietransfers in DNA an der Thymin‐Thymin‐Dimerbildung mithilfe von Photosensibilisatoren als artifizielle Nucleoside. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Linda Antusch
- Institut für Organische Chemie Karlsruher Institut für Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Nadine Gaß
- Institut für Organische Chemie Karlsruher Institut für Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Hans‐Achim Wagenknecht
- Institut für Organische Chemie Karlsruher Institut für Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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32
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Baker LA, Greenough SE, Stavros VG. A Perspective on the Ultrafast Photochemistry of Solution-Phase Sunscreen Molecules. J Phys Chem Lett 2016; 7:4655-4665. [PMID: 27791379 DOI: 10.1021/acs.jpclett.6b02104] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sunscreens are one of the most common ways of providing on-demand additional photoprotection to the skin. Ultrafast transient absorption spectroscopy has recently proven to be an invaluable tool in understanding how the components of commercial sunscreen products display efficient photoprotection. Important examples of how this technique has unravelled the photodynamics of common components are given in this Perspective, and some of the remaining unanswered questions are discussed.
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Affiliation(s)
- Lewis A Baker
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Simon E Greenough
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Vasilios G Stavros
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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33
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Ferreri C, Golding BT, Jahn U, Ravanat JL. COST Action CM1201 "Biomimetic Radical Chemistry": free radical chemistry successfully meets many disciplines. Free Radic Res 2016; 50:S112-S128. [PMID: 27750460 DOI: 10.1080/10715762.2016.1248961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The COST Action CM1201 "Biomimetic Radical Chemistry" has been active since December 2012 for 4 years, developing research topics organized into four working groups: WG1 - Radical Enzymes, WG2 - Models of DNA damage and consequences, WG3 - Membrane stress, signalling and defenses, and WG4 - Bio-inspired synthetic strategies. International collaborations have been established among the participating 80 research groups with brilliant interdisciplinary achievements. Free radical research with a biomimetic approach has been realized in the COST Action and are summarized in this overview by the four WG leaders.
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Affiliation(s)
- Carla Ferreri
- a ISOF, Consiglio Nazionale delle Ricerche, BioFreeRadicals Group , Bologna , Italy
| | - Bernard T Golding
- b School of Chemistry, Bedson Building, Newcastle University , Newcastle-upon-Tyne , UK
| | - Ullrich Jahn
- c Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Prague , Czech Republic
| | - Jean-Luc Ravanat
- d INAC-SCIB & CEA, INAC-SyMMES Laboratoire des Lésions des Acides Nucléiques , Université Grenoble Alpes , Grenoble , France
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34
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Gattuso H, Besancenot V, Grandemange S, Marazzi M, Monari A. From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents. Sci Rep 2016; 6:28480. [PMID: 27329409 PMCID: PMC4916457 DOI: 10.1038/srep28480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
We report a molecular modeling study, coupled with spectroscopy experiments, on the behavior of two well known organic dyes, nile blue and nile red, when interacting with B-DNA. In particular, we evidence the presence of two competitive binding modes, for both drugs. However their subsequent photophysical behavior is different and only nile blue is able to induce DNA photosensitization via an electron transfer mechanism. Most notably, even in the case of nile blue, its sensitization capabilities strongly depend on the environment resulting in a single active binding mode: the minor groove. Fluorescence spectroscopy confirms the presence of competitive interaction modes for both sensitizers, while the sensitization via electron transfer, is possible only in the case of nile blue.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Vanessa Besancenot
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Stéphanie Grandemange
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Marco Marazzi
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
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35
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Marazzi M, Mai S, Roca-Sanjuán D, Delcey MG, Lindh R, González L, Monari A. Benzophenone Ultrafast Triplet Population: Revisiting the Kinetic Model by Surface-Hopping Dynamics. J Phys Chem Lett 2016; 7:622-6. [PMID: 26821061 PMCID: PMC4761974 DOI: 10.1021/acs.jpclett.5b02792] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The photochemistry of benzophenone, a paradigmatic organic molecule for photosensitization, was investigated by means of surface-hopping ab initio molecular dynamics. Different mechanisms were found to be relevant within the first 600 fs after excitation; the long-debated direct (S1 → T1) and indirect (S1 → T2 → T1) mechanisms for population of the low-lying triplet state are both possible, with the latter being prevalent. Moreover, we established the existence of a kinetic equilibrium between the two triplet states, never observed before. This fact implies that a significant fraction of the overall population resides in T2, eventually allowing one to revisit the usual spectroscopic assignment proposed by transient absorption spectroscopy. This finding is of particular interest for photocatalysis as well as for DNA damages studies because both T1 and T2 channels are, in principle, available for benzophenone-mediated photoinduced energy transfer toward DNA.
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Affiliation(s)
- Marco Marazzi
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54000 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation, CNRS, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France
- E-mail: (M.M.)
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Straße 17, A-1090 Vienna, Austria
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 València, Spain
| | - Mickaël G. Delcey
- Department of Chemistry−Ångstrom Laboratory and Uppsala Center of Computational
Chemistry - UC3, Uppsala University, Uppsala 751 05, Sweden
| | - Roland Lindh
- Department of Chemistry−Ångstrom Laboratory and Uppsala Center of Computational
Chemistry - UC3, Uppsala University, Uppsala 751 05, Sweden
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Straße 17, A-1090 Vienna, Austria
| | - Antonio Monari
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54000 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation, CNRS, SRSMC, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, Nancy, France
- E-mail: (A.M.)
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36
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Theoretical study on the excited-state π-stacking versus intermolecular hydrogen-transfer processes in the guanine–cytosine/cytosine trimer. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1762-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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37
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Liu L, Pilles BM, Gontcharov J, Bucher DB, Zinth W. Quantum Yield of Cyclobutane Pyrimidine Dimer Formation Via the Triplet Channel Determined by Photosensitization. J Phys Chem B 2016; 120:292-8. [DOI: 10.1021/acs.jpcb.5b08568] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lizhe Liu
- Lehrstuhl
für BioMolekulare
Optik, Fakultät für Physik and Center for Integrated
Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse
67, 80538 München, Germany
| | - Bert M. Pilles
- Lehrstuhl
für BioMolekulare
Optik, Fakultät für Physik and Center for Integrated
Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse
67, 80538 München, Germany
| | - Julia Gontcharov
- Lehrstuhl
für BioMolekulare
Optik, Fakultät für Physik and Center for Integrated
Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse
67, 80538 München, Germany
| | - Dominik B. Bucher
- Lehrstuhl
für BioMolekulare
Optik, Fakultät für Physik and Center for Integrated
Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse
67, 80538 München, Germany
| | - Wolfgang Zinth
- Lehrstuhl
für BioMolekulare
Optik, Fakultät für Physik and Center for Integrated
Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse
67, 80538 München, Germany
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38
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Gattuso H, Dumont E, Chipot C, Monari A, Dehez F. Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations. Phys Chem Chem Phys 2016; 18:33180-33186. [DOI: 10.1039/c6cp06078a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the investigation of the thermochemical properties of benzophenone interacting with B-DNA studied by all-atom molecular dynamic simulations.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
| | - Elise Dumont
- Laboratoire de Chimie
- UMR 5182
- Ecole Normale Supérieure de Lyon
- Lyon
- France
| | - Christophe Chipot
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
| | - Antonio Monari
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
| | - François Dehez
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
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39
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Favero L, Granucci G, Persico M. Surface hopping investigation of benzophenone excited state dynamics. Phys Chem Chem Phys 2016; 18:10499-506. [DOI: 10.1039/c6cp00328a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A mechanism of S1 decay in benzophenone: S1 → T1 is the main pathway, although transitions to T2 and higher triplets play a relevant role.
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Affiliation(s)
- Lucilla Favero
- Università di Pisa
- Dipartimento di Farmacia
- 56126 Pisa
- Italy
| | - Giovanni Granucci
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale
- 56124 Pisa
- Italy
| | - Maurizio Persico
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale
- 56124 Pisa
- Italy
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40
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Marazzi M, Wibowo M, Gattuso H, Dumont E, Roca-Sanjuán D, Monari A. Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization. Phys Chem Chem Phys 2016; 18:7829-36. [DOI: 10.1039/c5cp07938a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (3BP) on thymine nucleobase and backbone sugar.
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Affiliation(s)
- Marco Marazzi
- Université de Lorraine - Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Meilani Wibowo
- Instituto de Ciencia Molecular
- Universitat de Valencia
- Valencia
- Spain
| | - Hugo Gattuso
- Université de Lorraine - Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Elise Dumont
- Ecole Normale Supérieure de Lyon and CNRS
- Laboratoire de Chimie
- Lyon
- France
| | | | - Antonio Monari
- Université de Lorraine - Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
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41
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Liu L, Pilles BM, Reiner AM, Gontcharov J, Zinth W. 2'-Methoxyacetophenone: An Efficient Photosensitizer for Cyclobutane Pyrimidine Dimer Formation. Chemphyschem 2015; 16:3483-7. [PMID: 26377612 DOI: 10.1002/cphc.201500582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/20/2015] [Indexed: 01/08/2023]
Abstract
Stationary and time-resolved experiments show that 2'-methoxyacetophenone (2-M) is an interesting compound for the investigation of triplet states in thymine samples. Time-resolved emission experiments show that the fluorescence lifetime of 2-M is 660 ps. A similar time constant of 680 ps is found in transient IR experiments. The data indicate efficient intersystem crossing (≈97%) from the fluorescent singlet state to the triplet state. The lifetime of the triplet state of 2-M dissolved in D2O at room temperature and ambient oxygen concentration is 400 ns. 2-M has a strong absorption in the UV-A range and can photosensitize the triplet state of a thymidine dinucleotide with light at a wavelength of 320 nm. The experiments show that 2-M is well-suited for time-resolved experiments on the triplet-sensitizing process.
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Affiliation(s)
- Lizhe Liu
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Bert M Pilles
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Anne M Reiner
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Julia Gontcharov
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Wolfgang Zinth
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany.
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42
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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43
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Bignon E, Gattuso H, Morell C, Dumont E, Monari A. DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5‐Methyl‐2‐pyrimidone Deoxyribonucleoside. Chemistry 2015; 21:11509-16. [DOI: 10.1002/chem.201501212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Emmanuelle Bignon
- Laboratoire de Chimie, UMR 5182, CNRS Ecole Normale Supérieure de Lyon, Lyon (France)
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, Lyon (France)
| | - Hugo Gattuso
- Université de Lorraine, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
- CNRS, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, Lyon (France)
| | - Elise Dumont
- Laboratoire de Chimie, UMR 5182, CNRS Ecole Normale Supérieure de Lyon, Lyon (France)
| | - Antonio Monari
- Université de Lorraine, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
- CNRS, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
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44
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Gattuso H, Assfeld X, Monari A. Modeling DNA electronic circular dichroism by QM/MM methods and Frenkel Hamiltonian. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1640-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Rivail JL, Monari A, Assfeld X. The Non Empirical Local Self Consistent Field Method: Application to Quantum Mechanics/Molecular Mechanics (QM/MM) Modeling of Large Biomolecular Systems. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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