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Zhang Q, Shao X, Li W, Mi W, Pavanello M, Akimov AV. Nonadiabatic molecular dynamics with subsystem density functional theory: application to crystalline pentacene. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:385901. [PMID: 38866023 DOI: 10.1088/1361-648x/ad577d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 06/14/2024]
Abstract
In this work, we report the development and assessment of the nonadiabatic molecular dynamics approach with the electronic structure calculations based on the linearly scaling subsystem density functional method. The approach is implemented in an open-source embedded Quantum Espresso/Libra software specially designed for nonadiabatic dynamics simulations in extended systems. As proof of the applicability of this method to large condensed-matter systems, we examine the dynamics of nonradiative relaxation of excess excitation energy in pentacene crystals with the simulation supercells containing more than 600 atoms. We find that increased structural disorder observed in larger supercell models induces larger nonadiabatic couplings of electronic states and accelerates the relaxation dynamics of excited states. We conduct a comparative analysis of several quantum-classical trajectory surface hopping schemes, including two new methods proposed in this work (revised decoherence-induced surface hopping and instantaneous decoherence at frustrated hops). Most of the tested schemes suggest fast energy relaxation occurring with the timescales in the 0.7-2.0 ps range, but they significantly overestimate the ground state recovery rates. Only the modified simplified decay of mixing approach yields a notably slower relaxation timescales of 8-14 ps, with a significantly inhibited ground state recovery.
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Affiliation(s)
- Qingxin Zhang
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
| | - Xuecheng Shao
- Department of Physics, Rutgers University, The State University of New Jersey, Newark, NJ 07102, United States of America
| | - Wei Li
- School of Chemistry and Materials Science, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Wenhui Mi
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education, College of Physics, Jilin University, Changchun 130012, People's Republic of China
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Michele Pavanello
- Department of Physics, Rutgers University, The State University of New Jersey, Newark, NJ 07102, United States of America
| | - Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
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2
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering. Org Biomol Chem 2024; 22:3025-3034. [PMID: 38530278 DOI: 10.1039/d4ob00279b] [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: 03/27/2024]
Abstract
Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Clément Denhez
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, F-38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
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Kufner CL, Krebs S, Fischaleck M, Philippou-Massier J, Blum H, Bucher DB, Braun D, Zinth W, Mast CB. Sequence dependent UV damage of complete pools of oligonucleotides. Sci Rep 2023; 13:2638. [PMID: 36788271 PMCID: PMC9929323 DOI: 10.1038/s41598-023-29833-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.
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Affiliation(s)
- Corinna L. Kufner
- grid.38142.3c000000041936754XHarvard-Smithsonian Center for Astrophysics, Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, MA 02138 USA
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Marlis Fischaleck
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Julia Philippou-Massier
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dominik B. Bucher
- grid.6936.a0000000123222966Chemistry Department, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Dieter Braun
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Wolfgang Zinth
- grid.5252.00000 0004 1936 973XBiomolecular Optics and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
| | - Christof B. Mast
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution. Phys Chem Chem Phys 2022; 24:14836-14845. [PMID: 35697028 DOI: 10.1039/d2cp00495j] [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
UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.
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Affiliation(s)
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia.,Scientific and Educational Center "Biomedical Technologies" School of Medical Biology, South Ural State University, RU-454080, Chelyabinsk, Russia.,Center for Artificial Intelligence and Cybersecurity, University of Rijeka, 51000 Rijeka, Croatia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide. Org Biomol Chem 2022; 20:2300-2307. [PMID: 35253821 DOI: 10.1039/d2ob00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Clément Denhez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
- MaSCA, P3M, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
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Soriano-Díaz I, Ortí E, Giussani A. On the Importance of Ligand-Centered Excited States in the Emission of Cyclometalated Ir(III) Complexes. Inorg Chem 2021; 60:13222-13232. [PMID: 34492762 PMCID: PMC8424641 DOI: 10.1021/acs.inorgchem.1c01604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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The photophysical
behavior of the cyclometalating Ir(III) complexes
[Ir(ppy)2(bpy)]+, where Hppy is 2-phenylpyridine
and bpy is 2,2′-bipyridine (complex 1), and [Ir(diFppy)2(dtb-bpy)]+, where diFppy is 2-(2,4-difluorophenyl)pyridine
and dtb-bpy is 4,4′-di-tert-butyl-2,2′-bipyridine
(complex 2), has been theoretically investigated by performing
density functional theory calculations. The two complexes share the
same molecular skeleton, complex 2 being derived from
complex 1 through the addition of fluoro and tert-butyl substituents, but present notable differences
in their photophysical properties. The remarkable difference in their
emission quantum yields (0.196 for complex 1 in dichloromethane
and 0.71 for complex 2 in acetonitrile) has been evaluated
by characterizing both radiative and nonradiative decay paths. It
has emerged that the probability of decaying through the nonradiative
triplet metal-centered state, normally associated with the loss of
the emission quantum yield, does not appear to be the reason behind
the reported substantially different emission efficiency. A more critical
factor appears to be the ability of complex 2 to emit
from both the usual metal-to-ligand charge-transfer state and from
two additional ligand-centered states, as supported by the fact that
the respective minima belong to the potential energy surface of the
lowest triplet T1 state and that their phosphorescence
lifetimes are in the same order of magnitude. In contrast, the emission
of complex 1 can be originated only from the metal-to-ligand
charge-transfer state, being the only emissive T1 minimum.
The results constitute a significant case in which the emission from
ligand-centered states is the key for determining the high emission
quantum yield of a complex. The
reasons behind the significant increase in the emission
quantum yield of the [Ir(diFppy)2(dtb-bpy)]+ complex with respect to [Ir(ppy)2(bpy)]+ are
rationalized on the basis of DFT, TDDFT, and TDDFT-SOC calculations,
revealing the key role that low-lying LC states can play in the emission
properties of the complex.
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Affiliation(s)
- Iván Soriano-Díaz
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Enrique Ortí
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Angelo Giussani
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán 2, 46980 Paterna, Spain
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