Theoretical Investigation of Excimer and Exciplex States of Uracil and Halogen Derivatives: Effect of Nonparallelism of Bases

Abstract

Theoretical modeling of initial steps of the photodimerization mechanism of uracil, 5-methyl-and 5-halogen derivatives was performed. The interaction energy of bases in stacked dimers in the ground and lowest excited states was calculated as a function of the distance between the base planes and of the rotation angles within the perturbation theory for the extended Hückel treatment. The existence of excimer and exciplex region on the potential surface of the excited state was revealed. The excimer (exciplex) geometry has the planes nonparallel with more close contact of the C5-C6 bonds as compared to the ground state of dimers. The results provide new information useful for understanding the photodimerization mechanism of bases and testifies that the singlet excimer state can be a precursor of the photodimerization reaction.

N1-Alkylated Pyrimidine Films as a New Potential Optical Data Storage Medium

“…The extensive work of Inaki et al has been done primarily with thymine, as the chromophore of choice, but our work with uracil has so far been quite consistent with Inaki et al and their work. Although we have not isolated and characterized the photodimerization products using X-ray crystallography, we are confident that the dimerization takes place through the C-5, C-6 bond of uracil as shown for our system in Figures and and involves the formation of a cyclobutane ring as it has been proven for thymine. , The electronic properties of the C-5 and C-6 atoms/groups and their significance regarding photodimerization efficiency was investigated previously 2a. Another significant hindrance for good photodimerization efficiency arises in dilute solutions such as ours due to the fact that the excited-state lifetime of the bases is most often small, compared to the diffusion processes in the solution .…”

Femtosecond Time- and Wavelength-Resolved Fluorescence and Absorption Spectroscopic Study of the Excited States of Adenosine and an Adenine Oligomer

“…This mechanism is supported by recent theoretical studies 12,32-34 showing there is a strong coupling between the L a and L b states and the existence of a virtually barrierless depopulation channel for the L b potential surface to convert into the ground-state surface through a conical intersection. These calculations also indicate there is an essential out-of-plane conformational change of the adenine aromatic ring to access the conical intersection so as to deactivate the excited state. ,, It is interesting to mention that the fairly large Stokes shift (∼6000 cm -1 ) displayed by the fluorescence/absorption (see Figures and ) spectra may reflect not only the large extent of solvent stabilization due to the increased excited-state dipole moment but also significant structural changes in the excited states compared to the ground state. ,,− , …”

“…From comparison of the “excimer” dynamics observed for the single-stranded and corresponding double-stranded oligomers, they concluded that the base stacking is predominant in controlling the excited-state dynamics for these systems 13a. Since the relatively long “excimer” lifetime may increase its propensity toward photochemical reaction, there has been some expectation that there is a direct link of this state to some of the important photolesions observed in living cells. ,− The “excimer” state was suggested to be formed as a result of interbase π stacking coupling with excitation delocalized among the interacting bases. , The “excimer” state has a characteristic red-shifted fluorescence (λ max at ∼380−400 nm) relative to the monomer fluorescence (λ max at ∼310 nm) and was first discovered in low-temperature emission experiments by Eisinger and co-workers in 1966 20a and has been observed later in diverse di-, oligo-, and polynucleotides. ,,,, These results are consistent with the importance of base stacking in mediating the delocalization of the energy after photoexcitation and influencing the excited-state deactivation pathway. However, there is no clear picture to describe the direct dynamics relating the stacking interaction to the excitation relaxation of UV-excited base multimers.…”

“…13a Since the relatively long "excimer" lifetime may increase its propensity toward photochemical reaction, there has been some expectation that there is a direct link of this state to some of the important photolesions observed in living cells. 13,[21][22][23] The "excimer" state was suggested to be formed as a result of interbase π stacking coupling with excitation delocalized among the interacting bases. 4,20 The "excimer" state has a characteristic red-shifted fluorescence (λ max at ∼380-400 nm) relative to the monomer fluorescence (λ max at ∼310 nm) and was first discovered in lowtemperature emission experiments by Eisinger and co-workers in 1966 20a and has been observed later in diverse di-, oligo-, and polynucleotides.…”

On the Deactivation Mechanisms of Adenine–Thymine Base Pair

“…The most striking feature of these excimers is the rising of long-lived emissive features not existent in the isolated nucleobases . Because of their long lifetimes, they are supposed to be the key for intrastrand photolesions, ,− such as those cited above. A study of the excited-state dynamics of AT base pair suggests that the excited oligo- and polynucleotides decay from a localized 1 ππ* to an excimer-like state with high quantum yield, explaining why most lesions involve stacked pairs …”