Nucleobases excited-state dynamics

Transient absorption experiments have shown that all of the major DNA and RNA nucleosides have fluorescence lifetimes of less than one picosecond [2—4], and that covalently modified bases [5], and even individual tautomers [6], differ dramatically in their excited-state dynamics. Femtosecond fluorescence up-conversion studies have also shown that the lowest singlet excited states of monomeric bases, nucleosides, and nucleotides decay by ultrafast internal conversion [7-9]. As discussed elsewhere [2], solvent effects on the fluorescence lifetimes are quite modest, and no evidence has been found to date to support excited-state proton transfer as a decay mechanism. These observations have focused attention on the possibility of internal conversion via one or more conical intersections. Recently, computational studies have succeeded in locating conical intersections on the excited state potential energy surfaces of several isolated nucleobases [10-12]. 

It is well known that ROKS systematically underestimates excitation energies, this has also been reported for other nucleobases [43 15, 47, 56], Typically, however, the shape of the ROKS potential landscape, which determines the excited state dynamics, has been found to be surprisingly accurate [16,20, 21, 56], An indication for this are the Stokes shifts obtained with ROKS. The experimental Stokes shift of 0.91 eV measured in aqueous solution [30] is much smaller than the gas phase ROKS results (Table 10-1). TDDFT calculations taking into account solvent effects through a polarizable continuum model seem to confirm that the Stokes shift is significantly reduced (by 0.4 eV) due to the solvent [30], Nieber and Doltsinis [64] have calculated the Stokes shift in explicit water solvent using ROKS/DFT we shall discuss these condensed phase simulations in detail below (see Section 10.3.1.2). 

Abstract IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computatitMial techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns. 

A critical pre-requisite to using Raman and resonance Raman spectroscopy to examine the excited-state structural dynamics of nucleic acids and their components, is the determination of the normal modes of vibration for the molecule of interest. The most definitive method for determining the normal modes is exhaustive isotopic substitution, subsequent measurement of the IR and Raman spectra, and computational analysis with the FG method of Wilson, Decius, and Cross [77], Such an analysis is rarely performed presently because of the improvements in accuracy of ab initio and semi-empirical calculations. Ab initio computations have been applied to most of the nucleobases, which will be described in more detail below, resulting in relatively consistent descriptions of the normal modes for the nucleobases. 

One of the most interesting nucleobases in which to study the excited-state structural dynamics is thymine, as thymine photoproducts account for >95% of the lesions found in DNA upon either UVB or UVC irradiation [59], Excited-state structural... 

With this normal mode description, then, it is instructive to review the resonance Raman intensity-derived excited-state structural dynamics. The first UV resonance Raman study of thymine was not done until 1994 by Lagant, et al. [113], Although Raman and IR spectra of thymine had been recorded much earlier. Most earlier studies of nucleic acid components focussed on the nucleosides and nucleotides. Indeed, much of the earlier research on nucleic acid components was done by the groups of Peticolas and Spiro, working independently. Spiro focussed more on nucleosides and larger nucleic acid structures (see below), while Peticolas examined the nucleobases initially. Peticolas s approach was to combine ab initio computations of the ground-state and excited-state structures and vibrational frequencies, with... 

UV resonance Raman spectra of chemical analogues of the pyrimidine nucleobases have been recently reported. Billinghurst et al. [142] have recently reported the UV resonance Raman intensity-derived excited-state stmctural dynamics of 5-fluorouracil, and have shown them to be essentially identical to those of thymine. In that paper, they also report the UV resonance Raman spectra of 5-chlorouracil, 5-bromouracil, and 5-iodouracil, and show that the spectra all are similar. By extension, they argue that the excited-state stmctural dynamics of the 5-halouracils are all similar to each other and to those of thymine, supporting their model that the excited-state structural dynamics of uracil and thymine nucleobases are dictated by the mass of the substituent at the 5 position. 

Very few reports of the excited-state structural dynamics of the purine nucleobases have appeared in the literature. This lack of research effort is probably due to a number of factors. The primary factor is the lack of photochemistry seen in the purines. Although adenine can form photoadducts with thymine, and this accounts for 0.2% of the photolesions found upon UVC irradiation of DNA [67], the purines appear to be relatively robust to UV irradiation. This lack of photoreactivity is probably due to the aromatic nature of the purine nucleobases. A practical issue with the purine nucleobases is their insolubility in water. While adenine enjoys reasonable solubility, it is almost an order of magnitude lower than that of thymine and uracil, the two most soluble nucleobases [143], Guanine is almost completely insoluble in water at room temperature [143],... 

Nevertheless, a few reports of UV resonance Raman spectra of the purine nucleobases and their derivatives have appeared. Peticolas s group has reported the identification of resonance Raman marker bands of guanine, 9-methylguanine and 9-ethylguanine for DNA conformation [118, 144], In the process of doing that work, very rudimentary excitation profiles were measured, which yielded preliminary structures for two of the ultraviolet excited electronic states. Tsuboi has also performed UV resonance Raman on purine nucleobases in an effort to determine the resonance enhanced vibrational structure [94], Thus far, no excited-state structural dynamics for any of the purine nucleobases have been determined. 

In contrast to the isolated nucleobases, a significant amount of work has been done on the excited-state structural dynamics and UV resonance Raman spectroscopy of the nucleotides. The excited-state structural dynamics of nucleosides have not been determined to date, although some UV resonance Raman spectra of the nucleosides have been measured [139, 145, 146], This work on the nucleosides has been primarily for the application of UV resonance Raman spectroscopy in the determination of ground-state structure, rather than excited-state structural dynamics. This emphasis on the nucleotides is no doubt driven by their greater solubility, as well as their immediate relevance to the nucleic acids. In addition, it was believed that the vast majority of the intensity observed in the UV Raman spectra arose through resonance enhancement of the nucleobase chromophore. Much of the early work on the UV resonance Raman spectra of nucleotides and nucleosides was completed by the groups of Tsuboi, Spiro and Peticolas. 

What is remarkable is that all of these early measurements of the UV resonance Raman spectra of nucleic acid components involved computational and theoretical support to their experimental findings. For example, Spiro used CINDO calculations to determine the nature of the excited electronic states of the nucleotides [157], In the early and mid 1970 s, many researchers were also attempting to understand resonance Raman spectroscopy, the types of information it could provide, and a unifying theoretical framework to the intensities [147, 159-172], UV resonance Raman spectra provided some of the first experimental evidence to test the various theoretical models. Peticolas attempted to fit the observed experimental excitation profiles of AMP [156], UMP [151, 154] and CMP [152, 153] to the sum-over-states model for the resonance Raman cross-sections. From these simulations, they were able to obtain preliminary excited-state structural dynamics of the nucleobase chromophores of the nucleotides for UMP [151, 153, 158] and CMP [153], For AMP, the experimental excitation profiles were simulated with an A-term expression, but the excited-state structural changes were not obtained. Rather, the goal of that work was to identify the electronic transitions within the lowest-energy absorption band of adenine [156],... 

In CMP, the excited-state structural dynamics were ascribed to modes at 784, 1243, 1294 and 1529 cirr1 [153], in that order, while the major excited-state structural dynamics in the isolated nucleobase chromophore occur along the 1283, 1364, 1651, 1523, 1224, and 1630 cur1 modes [137], in that order again, very minor contributions to the excited-state structural dynamics are observed from the modes below 1000 cm-1. Here, the excited-state structural dynamics of the nucleotide appear to be very different from those of the cytosine nucleobase. A resolution to those discrepancy between the excited-state structural dynamics of the nucleobase and nucleotide awaits definitive vibrational assignments of these modes in cytosine. 

The determination of excited-state structural dynamics in nucleic acids and their components is still in its infancy. Although progress has been made in understanding the excited-state structural dynamics of the nucleobases, primarily with UV resonance Raman spectroscopy, much work still remains to be done at that level to be able to extract the structural determinants of the excited-state structural dynamics and resulting photochemistry. Much less is known about the excited-state structural dynamics of nucleotides, oligonucleotides, and nucleic acids, but the static and time-resolved spectroscopic tools exist to be able to measure them. 

In the present chapter, we will focus on the simulation of the dynamics of photoexcited nucleobases, in particular on the investigation of radiationless decay dynamics and the determination of associated characteristic time constants. We use a nonadiabatic extension of ab initio molecular dynamics (AIMD) [15, 18, 21, 22] which is formulated entirely within the framework of density functional theory. This approach couples the restricted open-shell Kohn-Sham (ROKS) [26-28] first singlet excited state, Su to the Kohn-Sham ground state, S0, by means of the surface hopping method [15, 18, 94-97], The current implementation employs a plane-wave basis set in combination with periodic boundary conditions and is therefore ideally suited to condensed phase applications. Hence, in addition to gas phase reference simulations, we will also present nonadiabatic AIMD (na-AIMD) simulations of nucleobases and base pairs in aqueous solution. 

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