First Principles Dynamics of Photoexcited DNA and RNA Bases

Hudock, Hanneli R.; Levine, Bernard B.; Thompson, Alexis L.; Martı́nez, Todd J.

doi:10.1063/1.2836045

Cited by 5 publications

(6 citation statements)

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“…The CI t12 conical intersection is located at 4.55 eV and has a planar geometry which does not differ much from the ground-state equilibrium geometry, except for some elongation of the C4−O4 and C5−C6 bond lengths (0.02 and 0.09 Å, respectively) and a reduction of the C4−C5 bond length by 0.06 Å. Similar bond length variations are found in CASSCF and CASPT2 calculations, , which however also reported out-of-plane deformations.…”

Section: Resultssupporting

confidence: 65%

“…The pyrimidine bases uracil, thymine, and cytosine are the simplest nucleobases. They have been often used as prototypes to investigate the photostability of DNA and RNA bases. − In their electronic spectra, there is a broad absorption band centered at 4−6 eV, assigned to the transition between the ground state (gs) and a ππ* state. In the same energy range, circular dichroism spectra reveal the presence of a dark excited-state of nπ* character .…”

Section: Introductionmentioning

confidence: 99%

“…However, most published theoretical studies either lack a dynamical treatment or only include a few degrees of freedom and therefore have not been able to determine the relative importance of different relaxation pathways and to predict the different decay times. These limitations have been overcome by a recent ab initio multiple spawning (AIMS) study of nonadiabatic dynamics in uracil and thymine , that directly simulated their time-resolved photoelectron spectra by computing the total photoionization probability at the CASSCF level; on the basis of 500 fs AIMS simulations, the ultrafast decay of the photoelectron signal was attributed to the relaxation to a true minimum on the S 2 potential energy surface and not to electronic quenching as in previous work. It should be noted that the existence of such an S 2 minimum has not yet been firmly established since the commonly found CASSCF minimum tends to disappear when applying higher-level ab initio methods or unconstrained optimization. ,,, Further dynamics studies thus appear desirable for a detailed mechanistic understanding of photoinduced nonradiative relaxation in the pyrimidine bases.…”

Section: Introductionmentioning

confidence: 99%

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Photoinduced Nonadiabatic Dynamics of Pyrimidine Nucleobases: On-the-Fly Surface-Hopping Study with Semiempirical Methods

2009

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The photoinduced relaxation dynamics of pyrimidine nucleobases (uracil, thymine, and cytosine) was studied using the surface-hopping approach at the semiempirical OM2/MRCI level of theory. The relevant potential energy surfaces were characterized by performing geometry optimizations of the energy minima of the lowest electronic states and of the most important conical intersections and by computing excitation energies at each configuration. Surface-hopping molecular dynamics simulations were performed to describe the nonadiabatic dynamics after excitation into the optically active state. In each of the molecules, the two lowest excited singlet states are involved in the dynamics, and there are competing relaxation paths. The dynamics is dominated by a two-step relaxation mechanism in uracil and thymine, while the direct decay to the ground state is most important in cytosine. For all three molecules, the simulations yield ultrafast S(2)-S(1) deexcitation within 50 fs and internal conversion to the ground state in less than 1 ps, consistent with recent experimental results from time-resolved photoelectron spectroscopy.

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Section: Resultssupporting

confidence: 65%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Photoinduced Nonadiabatic Dynamics of Pyrimidine Nucleobases: On-the-Fly Surface-Hopping Study with Semiempirical Methods

2009

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“…It has been shown, for instance, that while in the purine bases (Ade, Gua) a single mechanism dominates the ultrafast internal conversion, in the pyrimidine bases (Cyt, Thy, Ura), there is a strong competition between few different mechanisms. 762 Dynamics has also revealed exotic mechanisms, not predicted by steady-state studies, as the S 2 trapping of thymine 786 or the solvent-chromophore electron transfer in 7H-adenine. 782 Concerning the three-state conical intersections, according to the dynamics, they seem to be limited to a minor process occurring in cytosine.…”

Section: Singlet Oxygen Photosensitizationmentioning

confidence: 99%

Multireference Approaches for Excited States of Molecules

et al. 2018

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Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications.

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“…The full multiple spawning ͑FMS͒ method [19][20][21][22][23][24][25] meets these requirements, and has been successfully applied to photoisomerization in various hydrocarbons, 4,19 excited-state proton transfer in salicylic acid derivatives, 26,27 energy transfer in phenylacetylene dendrimers, 28,29 and photochemistry in DNA bases. 30,31 In addition, it is relatively straightforward to recast the results of a FMS simulation into forms directly comparable to time-resolved photoionization 30,32,33 and fluorescence upconversion 26,30,[34][35][36] signals.…”

Section: Introductionmentioning

confidence: 99%

An “optimal” spawning algorithm for adaptive basis set expansion in nonadiabatic dynamics

Yang¹,

Coe²,

Kaduk³

et al. 2009

The Journal of Chemical Physics

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The full multiple spawning (FMS) method has been developed to simulate quantum dynamics in the multistate electronic problem. In FMS, the nuclear wave function is represented in a basis of coupled, frozen Gaussians, and a "spawning" procedure prescribes a means of adaptively increasing the size of this basis in order to capture population transfer between electronic states. Herein we detail a new algorithm for specifying the initial conditions of newly spawned basis functions that minimizes the number of spawned basis functions needed for convergence. "Optimally" spawned basis functions are placed to maximize the coupling between parent and child trajectories at the point of spawning. The method is tested with a two-state, one-mode avoided crossing model and a two-state, two-mode conical intersection model.

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First Principles Dynamics of Photoexcited DNA and RNA Bases

Cited by 5 publications

References 0 publications

Photoinduced Nonadiabatic Dynamics of Pyrimidine Nucleobases: On-the-Fly Surface-Hopping Study with Semiempirical Methods

Photoinduced Nonadiabatic Dynamics of Pyrimidine Nucleobases: On-the-Fly Surface-Hopping Study with Semiempirical Methods

Multireference Approaches for Excited States of Molecules

An “optimal” spawning algorithm for adaptive basis set expansion in nonadiabatic dynamics

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