Life in the light: nucleic acid photoproperties as a legacy of chemical evolution

Physical Chemistry Chemical Physics, Journal Year: 2016, Volume and Issue: 18(35), P. 24228 - 24238

Published: Jan. 1, 2016

Nucleobases exhibit protection against UV photodamage by rapid internal conversion to the ground state. This property may have led prebiotic photochemical selection.

Language: Английский

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Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction

Science, Journal Year: 2020, Volume and Issue: 368(6493), P. 885 - 889

Published: May 21, 2020

Electronic and nuclear dynamics in one Because of the complex, ultrafast interplay between electronic degrees freedom, probing both excited states within a single time-resolved experiment is great challenge. Yang et al. used electron diffraction combination with ab initio nonadiabatic molecular simulations to study relaxation isolated pyridine molecules after photoexcitation S 1 state (see Perspective by Domcke Sobolewski). They showed that evolution structural changes can be recorded simultaneously independently tracing transient signal small-angle inelastic scattering large-angle elastic diffraction, respectively. Science , this issue p. 885 ; see also 820

Language: Английский

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Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime

Chemical Reviews, Journal Year: 2017, Volume and Issue: 117(19), P. 12165 - 12226

Published: Sept. 26, 2017

Crossings of electronic potential energy surfaces in nuclear configuration space, known as conical intersections, determine the rates and outcomes a large class photochemical molecular processes. Much theoretical progress has been made computing strongly coupled motions at different levels, but how to incorporate them spectroscopic signals approximations involved are less established. This will be focus present review. We survey wide range time-resolved techniques which span from infrared X-ray regimes can used for probing nonadiabatic dynamics vicinity intersections. Transient vibrational probes their signal calculations classified by information content. includes transient methods (transient femtosecond off-resonant stimulated Raman), resonant absorption photoelectron spectroscopy), novel Raman techniques. Along with precise definition what calculate predicting various signals, we outline toolbox protocols simulation.

Language: Английский

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The DFT/MRCI method

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2018, Volume and Issue: 9(2)

Published: Oct. 23, 2018

In the past two decades, combined density functional theory and multireference configuration interaction (DFT/MRCI) method has developed from a powerful approach for computing spectral properties of singlet triplet excited states large molecules into more general applicable to all spin multiplicities. its original formulation, it shows great efficiency in evaluation which mainly originate local one‐electron transitions. Moreover, DFT/MRCI is one few methods systems that yields correct ordering extended π ‐systems where double excitations play significant role. A recently redesigned Hamiltonian extends application range bi‐chromophores such as hydrogen‐bonded or ‐stacked dimers loosely coupled donor–acceptor systems. conjunction with restricted‐open shell Kohn–Sham optimization molecular orbitals, even electronically doublet quartet can be addressed. After short outline ideas behind this semi‐empirical brief review alternative approaches combining wavefunction theory, formulae matrix elements are presented adjustments two‐electron contributions discussed. The performance variants on excitation energies organic transition metal compounds against experimental ab initio reference data analyzed case studies show strengths limitations method. Finally, an overview over available wavefunctions further developments given. This article categorized under: Electronic Structure Theory > Density Functional Semiempirical Methods Software Quantum Chemistry

Language: Английский

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Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases,

Photochemistry and Photobiology, Journal Year: 2018, Volume and Issue: 95(1), P. 33 - 58

Published: July 6, 2018

Abstract Sulfur‐substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long‐term treatment with azathioprine, 6‐mercaptopurine 6‐thioguanine has been correlated photoinduced formation of carcinomas. Establishing an in‐depth understanding photochemical properties these prodrugs may provide a route to overcoming carcinogenic side effects, or, alternatively, basis developing effective compounds targeted phototherapy. In this review, broad examination is undertaken, surveying basic excited‐state dynamics sulfur‐substituted analogs canonical DNA RNA nucleobases. A molecular‐level how sulfur substitution so remarkably perturbs presented by combining experimental results quantum‐chemical calculations. Structure‐property relationships demonstrate impact site‐specific on properties, particularly population reactive triplet state. The value fundamental investigations driving development ultraviolet‐A chemotherapeutics showcased. most promising photodynamic agents identified thus far have investigated in various carcinoma cell lines shown decrease proliferation upon exposure radiation. Overarching principles elucidated that carbonyl oxygen

Language: Английский

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Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems

Chemical Reviews, Journal Year: 2019, Volume and Issue: 119(16), P. 9361 - 9380

Published: July 5, 2019

Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment–protein complexes to nucleic acids. The former are designed capture, harvest, efficiently transport, and transform energy sunlight for photosynthesis, while the latter should dissipate absorbed radiation as quickly possible prevent photodamages corruption of carried genetic information. Because unique electronic structural characteristics, modeling their photoinduced activity is real challenge. Numerous approaches have been devised building on theoretical development achieved single chromophores model Hamiltonians that capture essential features system. Still, question remains: general strategy accurate multichromophoric systems possible? By using quantum chemical point view, here we review advancements developed so far highlighting differences similarities chromophore treatment. Finally, outline important limitations challenges still need be tackled reach complete picture properties dynamics.

Language: Английский

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Nexus between in silico and in vivo models to enhance clinical translation of nanomedicine

Nano Today, Journal Year: 2020, Volume and Issue: 36, P. 101057 - 101057

Published: Dec. 24, 2020

Language: Английский

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Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy

Journal of the American Chemical Society, Journal Year: 2017, Volume and Issue: 139(23), P. 7780 - 7791

Published: May 17, 2017

The study concerns the relaxation of electronic excited states DNA nucleoside deoxycytidine (dCyd) and its methylated analogue 5-methyldeoxycytidine (5mdCyd), known to be involved in formation UV-induced lesions genetic code. Due existence four closely lying potentially coupled states, deactivation pathways these systems are particularly complex have not been assessed so far. Here, we provide a complete mechanistic picture state dCyd/5mdCyd three solvents-water, acetonitrile, tetrahydrofuran-by combining femtosecond fluorescence experiments, addressing effect solvent proticity on dynamics dCyd 5mdCyd for first time, two complementary quantum mechanical approaches (CASPT2/MM PCM/TD-CAM-B3LYP). lowest energy ππ* is responsible sub-picosecond lifetime observed all solvents. In addition, computed absorption transient IR spectra allow one, assign tens picoseconds time constant, reported previously, dark (nOπ*) involving carbonyl lone pair. A second low-lying state, nitrogen pair (nNπ*), does significantly participate dynamics. 267 nm excitation leads non-negligible population bright which affects dynamics, acting mainly as "doorway" nOπ* state. plays key role governing interplay between different states; unexpectedly, water favors states. case 5mdCyd, an barrier present main nonradiative decay route explains 6-fold lengthening compared that dCyd, examined Moreover, C5-methylation destabilizes both nNπ* thus preventing them from being populated.

Language: Английский

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Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA

Molecules, Journal Year: 2018, Volume and Issue: 23(2), P. 228 - 228

Published: Jan. 25, 2018

DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc.), which bind through non-covalent interactions. Depending on their structure and properties, binders can associate to minor or major groove double-stranded DNA. They also intercalate between two adjacent base pairs, even replace one pairs within double helix. The subsequent biological effects are strongly dependent architecture binding motif. Discriminating different patterns paramount importance predict rationalize effect a given compound structural characterization complexes remains, however, cumbersome at experimental level. In this contribution, we employed all-atom molecular dynamics simulations determine standard free energy with netropsin, well-characterized antiviral antimicrobial drug, associates To overcome sampling limitations classical simulations, cannot capture large change in configurational entropy that accompanies binding, resort series potentials mean force calculations involving set geometrical restraints acting collective variables.

Language: Английский

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Fundamentals of the Intrinsic DNA Fluorescence

Accounts of Chemical Research, Journal Year: 2021, Volume and Issue: 54(5), P. 1226 - 1235

Published: Feb. 15, 2021

The intrinsic fluorescence of nucleic acids is extremely weak compared to that the fluorescent labels used probe their structural and functional behavior. Thus, for technical reasons, investigation DNA was limited a long time. But with improvement in spectroscopic techniques, situation started change around turn century. During past two decades, various factors modulating static dynamic properties have been determined; it shown that, under certain conditions, quantum yields may be up 100 times higher than what known so far. ensemble these studies opened new paths development label-free biochemical applications. In parallel, shed light on primary processes leading photoreactions damage when absorbs UV radiation.We studying variety systems, ranging from monomeric nucleobases double-stranded four-stranded structures using spectroscopy. specificity our work resides quantitative association steady-state spectra time-resolved data recorded femtosecond nanosecond timescales, made possible by specific methodologies.Among others, provide information energy polarization electronic transitions. These are valuable indicators evolution excitations complex where coupling between chromophores plays key role. Highlighting collective effects originate interactions multimers objective present Account.In contrast chromophores, whose decays within few picoseconds, persists timescale. Even if long-lived states represent only small fraction excitations, they crucial photoreactivity because probability reach reactive conformations increases over time, owing incessant dynamics acids.Our revealed an ultrafast excitation transfer takes place among duplexes G-quadruplexes. Such process populated directly upon photon absorption. At much longer times, we discovered unexpected high-energy emission stemming coined "HELM excitons". states, duplex size, could responsible delayed ππ* observed genomic DNA.Most dealing excited-state relaxation were carried out absorption band peaking at 260 nm. We went beyond this also performed first study UVA spectral range, very tail present. resulting slower UVC excitation. showed base pairing strands enhances and, modifies nature involved excited states.

Language: Английский

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