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Special Issue "Experimental and Computational Photochemistry of Bioorganic Molecules"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Photochemistry".

Deadline for manuscript submissions: closed (15 October 2016)

Special Issue Editor

Guest Editor
Prof. Dr. Carlos E. Crespo-Hernández

Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
Website | E-Mail
Interests: electronic and vibrational spectroscopy; femtochemistry and femtobiology; electronic and structural dynamics; bioorganic photochemistry; chemical kinetics; theoretical and computational chemistry

Special Issue Information

Dear Colleagues,

It is my great pleasure to invite you to submit an article for a high-profile Special Issue on “Experimental and Computational Photochemistry of Bioorganic Molecules” to be published in Molecules. This Special Issue aims to highlight research on light-induced processes in nucleic acids and amino acids, as well as their derivatives and analogues, in both the gas and condensed phases. This includes, but is not limited to, new experimental and theoretical methodologies in the electronic and structural dynamics of these biomolecules. Research articles focusing on electronic and vibrational relaxation mechanisms; excited-state charge, energy, hydrogen, or proton transfer phenomena; and elucidation of probable mechanisms of product formation or product repair are among topics that this Special Issue aims to address. Reviews articles and perspectives from experts in the field are also welcome.

Prof. Dr. Carlos E. Crespo-Hernández
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • DNA and RNA monomers and oligomers
  • nucleobase analogues
  • aromatic amino acids, peptides, and derivatives
  • electronic and vibrational spectroscopy
  • femtochemistry and femtobiology
  • electronic and structural dynamics
  • relaxation and reaction mechanisms
  • energy and charge transfer
  • proton and hydrogen transfer
  • ab initio calculations
  • excited states
  • molecular dynamics simulations
  • potential energy surfaces
  • conical intersections

Published Papers (12 papers)

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Open AccessArticle Nonradiative Relaxation Mechanisms of UV Excited Phenylalanine Residues: A Comparative Computational Study
Molecules 2017, 22(3), 493; doi:10.3390/molecules22030493
Received: 6 February 2017 / Revised: 9 March 2017 / Accepted: 16 March 2017 / Published: 21 March 2017
Cited by 1 | PDF Full-text (7314 KB) | HTML Full-text | XML Full-text
Abstract
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its
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The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenylππ*to amidenπ*state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on thenπ*state is barrierless along several pathways and leads to fast deactivation to the ground electronic state. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessCommunication Excited-State Dynamics of the Thiopurine Prodrug 6-Thioguanine: Can N9-Glycosylation Affect Its Phototoxic Activity?
Molecules 2017, 22(3), 379; doi:10.3390/molecules22030379
Received: 17 January 2017 / Revised: 15 February 2017 / Accepted: 24 February 2017 / Published: 28 February 2017
Cited by 6 | PDF Full-text (1514 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
6-Thioguanine, an immunosuppressant and anticancer prodrug, has been shown to induce DNA damage and cell death following exposure to UVA radiation. Its metabolite, 6-thioguanosine, plays a major role in the prodrug’s overall photoreactivity. However, 6-thioguanine itself has proven to be cytotoxic following UVA
[...] Read more.
6-Thioguanine, an immunosuppressant and anticancer prodrug, has been shown to induce DNA damage and cell death following exposure to UVA radiation. Its metabolite, 6-thioguanosine, plays a major role in the prodrug’s overall photoreactivity. However, 6-thioguanine itself has proven to be cytotoxic following UVA irradiation, warranting further investigation into its excited-state dynamics. In this contribution, the excited-state dynamics and photochemical properties of 6-thioguanine are studied in aqueous solution following UVA excitation at 345 nm in order to provide mechanistic insight regarding its photochemical reactivity and to scrutinize whether N9-glycosylation modulates its phototoxicity in solution. The experimental results are complemented with time-dependent density functional calculations that include solvent dielectric effects by means of a reaction-field solvation model. UVA excitation results in the initial population of the S2(ππ*) state, which is followed by ultrafast internal conversion to the S1(nπ*) state and then intersystem crossing to the triplet manifold within 560 ± 60 fs. A small fraction (ca. 25%) of the population that reaches the S1(nπ*) state repopulates the ground state. The T1(ππ*) state decays to the ground state in 1.4 ± 0.2 μs under N2-purged conditions, using a 0.2 mM concentration of 6-thioguanine, or it can sensitize singlet oxygen in 0.21 ± 0.02 and 0.23 ± 0.02 yields in air- and O2-saturated solution, respectively. This demonstrates the efficacy of 6-thioguanine to act as a Type II photosensitizer. N9-glycosylation increases the rate of intersystem crossing from the singlet to triplet manifold, as well as from the T1(ππ*) state to the ground state, which lead to a ca. 40% decrease in the singlet oxygen yield under air-saturated conditions. Enhanced vibronic coupling between the singlet and triplet manifolds due to a higher density of vibrational states is proposed to be responsible for the observed increase in the rates of intersystem crossing in 6-thioguanine upon N9-glycosylation. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle Ultrafast Electronic Deactivation Dynamics of Xanthosine Monophosphate
Molecules 2017, 22(1), 160; doi:10.3390/molecules22010160
Received: 30 November 2016 / Revised: 12 January 2017 / Accepted: 13 January 2017 / Published: 18 January 2017
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Abstract
Ultrafast energy dissipation is a crucial factor for the photostability of DNA and RNA, but even some of the key electronic deactivation pathways in monomeric nucleic acid building stones are still controversial. Here, we report on the excited-state dynamics of the rare nucleotide
[...] Read more.
Ultrafast energy dissipation is a crucial factor for the photostability of DNA and RNA, but even some of the key electronic deactivation pathways in monomeric nucleic acid building stones are still controversial. Here, we report on the excited-state dynamics of the rare nucleotide xanthosine monophosphate as a function of deprotonation state (XMP vs. XMP ) and excitation wavelength ( λ pump = 278–243 nm) by femtosecond time-resolved fluorescence and absorption spectroscopy. We show that the predominating relaxation channel leads to a return of the photo-excited molecules to the electronic ground state in τ∼1 ps. The mechanism likely involves an out-of-plane deformation of the five-membered ring, different from the main electronic deactivation pathways in the canonical purine bases adenine and guanine. The results are discussed in terms of the structural and electronic differences of XMP compared to the canonical nucleotides. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs
Molecules 2017, 22(1), 135; doi:10.3390/molecules22010135
Received: 17 November 2016 / Revised: 28 December 2016 / Accepted: 10 January 2017 / Published: 14 January 2017
Cited by 1 | PDF Full-text (3688 KB) | HTML Full-text | XML Full-text
Abstract
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the
[...] Read more.
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S1/S0 conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G-A and 8-oxo-G-C base pairs are likely too short-lived to be efficient electron-transfer repair agents. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle How Does Thymine DNA Survive Ultrafast Dimerization Damage?
Molecules 2017, 22(1), 60; doi:10.3390/molecules22010060
Received: 15 October 2016 / Revised: 13 December 2016 / Accepted: 24 December 2016 / Published: 31 December 2016
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Abstract
The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction
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The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright SCT(1ππ*) state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle Stereoselective Fluorescence Quenching in the Electron Transfer Photooxidation of Nucleobase-Related Azetidines by Cyanoaromatics
Molecules 2016, 21(12), 1683; doi:10.3390/molecules21121683
Received: 15 October 2016 / Revised: 29 November 2016 / Accepted: 1 December 2016 / Published: 7 December 2016
PDF Full-text (2077 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Electron transfer involving nucleic acids and their derivatives is an important field in bioorganic chemistry, specifically in connection with its role in the photo-driven DNA damage and repair. Four-membered ring heterocyclic oxetanes and azetidines have been claimed to be the intermediates involved in
[...] Read more.
Electron transfer involving nucleic acids and their derivatives is an important field in bioorganic chemistry, specifically in connection with its role in the photo-driven DNA damage and repair. Four-membered ring heterocyclic oxetanes and azetidines have been claimed to be the intermediates involved in the repair of DNA (6-4) photoproduct by photolyase. In this context, we examine here the redox properties of the two azetidine isomers obtained from photocycloaddition between 6-aza-1,3-dimethyluracil and cyclohexene. Steady-state and time-resolved fluorescence experiments using a series of photoreductants and photooxidants have been run to evaluate the efficiency of the electron transfer process. Analysis of the obtained quenching kinetics shows that the azetidine compounds can act as electron donors. Additionally, it appears that the cis isomer is more easily oxidized than its trans counterpart. This result is in agreement with electrochemical studies performed on both azetidine derivatives. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2
Molecules 2016, 21(12), 1666; doi:10.3390/molecules21121666
Received: 15 October 2016 / Revised: 30 November 2016 / Accepted: 1 December 2016 / Published: 3 December 2016
Cited by 1 | PDF Full-text (2503 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and
[...] Read more.
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle Xanthines Studied via Femtosecond Fluorescence Spectroscopy
Molecules 2016, 21(12), 1668; doi:10.3390/molecules21121668
Received: 14 October 2016 / Revised: 25 November 2016 / Accepted: 29 November 2016 / Published: 3 December 2016
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Abstract
Xanthines represent a wide class of compounds closely related to the DNA bases adenine and guanine. Ubiquitous in the human body, they are capable of replacing natural bases in double helices and give rise to four-stranded structures. Although the use of their fluorescence
[...] Read more.
Xanthines represent a wide class of compounds closely related to the DNA bases adenine and guanine. Ubiquitous in the human body, they are capable of replacing natural bases in double helices and give rise to four-stranded structures. Although the use of their fluorescence for analytical purposes was proposed, their fluorescence properties have not been properly characterized so far. The present paper reports the first fluorescence study of xanthine solutions relying on femtosecond spectroscopy. Initially, we focus on 3-methylxanthine, showing that this compound exhibits non-exponential fluorescence decays with no significant dependence on the emission wavelength. The fluorescence quantum yield (3 × 10−4) and average decay time (0.9 ps) are slightly larger than those found for the DNA bases. Subsequently, we compare the dynamical fluorescence properties of seven mono-, di- and tri-methylated derivatives. Both the fluorescence decays and fluorescence anisotropies vary only weakly with the site and the degree of methylation. These findings are in line with theoretical predictions suggesting the involvement of several conical intersections in the relaxation of the lowest singlet excited state. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessCommunication Excited-State Dynamics of Melamine and Its Lysine Derivative Investigated by Femtosecond Transient Absorption Spectroscopy
Molecules 2016, 21(12), 1645; doi:10.3390/molecules21121645
Received: 1 November 2016 / Revised: 24 November 2016 / Accepted: 24 November 2016 / Published: 30 November 2016
Cited by 1 | PDF Full-text (2196 KB) | HTML Full-text | XML Full-text
Abstract
Melamine may have been an important prebiotic information carrier, but its excited-state dynamics, which determine its stability under UV radiation, have never been characterized. The ability of melamine to withstand the strong UV radiation present on the surface of the early Earth is
[...] Read more.
Melamine may have been an important prebiotic information carrier, but its excited-state dynamics, which determine its stability under UV radiation, have never been characterized. The ability of melamine to withstand the strong UV radiation present on the surface of the early Earth is likely to have affected its abundance in the primordial soup. Here, we studied the excited-state dynamics of melamine (a proto-nucleobase) and its lysine derivative (a proto-nucleoside) using the transient absorption technique with a UV pump, and UV and infrared probe pulses. For melamine, the excited-state population decays by internal conversion with a lifetime of 13 ps without coupling significantly to any photochemical channels. The excited-state lifetime of the lysine derivative is slightly longer (18 ps), but the dominant deactivation pathway is otherwise the same as for melamine. In both cases, the vast majority of excited molecules return to the electronic ground state on the aforementioned time scales, but a minor population is trapped in a long-lived triplet state. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessArticle New Insights into the State Trapping of UV-Excited Thymine
Molecules 2016, 21(11), 1603; doi:10.3390/molecules21111603
Received: 12 October 2016 / Revised: 15 November 2016 / Accepted: 17 November 2016 / Published: 23 November 2016
Cited by 2 | PDF Full-text (3301 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
After UV excitation, gas phase thymine returns to a ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the
[...] Read more.
After UV excitation, gas phase thymine returns to a ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the first (S1) or in the second (S2) excited states. In the present study, a nonadiabatic dynamics simulation of thymine is performed on the basis of ADC(2) surfaces, to understand the role of dynamic electron correlation on the deactivation pathways. The results show that trapping in S2 is strongly reduced in comparison to previous simulations considering only non-dynamic electron correlation on CASSCF surfaces. The reason for the difference is traced back to the energetic cost for formation of a CO π bond in S2. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessPerspective Photophysics and Photochemistry of Canonical Nucleobases’ Thioanalogs: From Quantum Mechanical Studies to Time Resolved Experiments
Molecules 2017, 22(6), 998; doi:10.3390/molecules22060998
Received: 7 May 2017 / Revised: 10 June 2017 / Accepted: 12 June 2017 / Published: 18 June 2017
Cited by 1 | PDF Full-text (3378 KB) | HTML Full-text | XML Full-text
Abstract
Interest in understanding the photophysics and photochemistry of thiated nucleobases has been awakened because of their possible involvement in primordial RNA or their potential use as photosensitizers in medicinal chemistry. The interpretation of the photodynamics of these systems, conditioned by their intricate potential
[...] Read more.
Interest in understanding the photophysics and photochemistry of thiated nucleobases has been awakened because of their possible involvement in primordial RNA or their potential use as photosensitizers in medicinal chemistry. The interpretation of the photodynamics of these systems, conditioned by their intricate potential energy surfaces, requires the powerful interplay between experimental measurements and state of the art molecular simulations. In this review, we provide an overview on the photophysics of natural nucleobases’ thioanalogs, which covers the last 30 years and both experimental and computational contributions. For all the canonical nucleobase’s thioanalogs, we have compiled the main steady state absorption and emission features and their interpretation in terms of theoretical calculations. Then, we revise the main topographical features, including stationary points and interstate crossings, of their potential energy surfaces based on quantum mechanical calculations and we conclude, by combining the outcome of different spectroscopic techniques and molecular dynamics simulations, with the mechanism by which these nucleobase analogs populate their triplet excited states, which are at the origin of their photosensitizing properties. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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Open AccessPerspective Challenges in Simulating Light-Induced Processes in DNA
Molecules 2017, 22(1), 49; doi:10.3390/molecules22010049
Received: 18 November 2016 / Revised: 14 December 2016 / Accepted: 21 December 2016 / Published: 29 December 2016
Cited by 2 | PDF Full-text (416 KB) | HTML Full-text | XML Full-text
Abstract
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject
[...] Read more.
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments. Full article
(This article belongs to the Special Issue Experimental and Computational Photochemistry of Bioorganic Molecules)
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