Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA

An ab initio multiple cloning approach for the simulation of photoinduced dynamics in conjugated molecules

Multidimensional wave function: a superposition of Gaussian coherent states guided by Ehrenfest trajectories suited to clone and swap their electronic amplitudes.

Sub-50 fs excited state dynamics of 6-chloroguanine upon deep ultraviolet excitation

The photophysical properties of natural nucleobases and their respective nucleotides are ascribed to the sub-picosecond lifetime of their first singlet states in the UV-B region (260-350 nm). Electronic transitions of the ππ* type, which are stronger than those in the UV-B region, lie at the red edge of the UV-C range (100-260 nm) in all isolated nucleobases. The lowest energetic excited states in the UV-B region of nucleobases have been investigated using a plethora of experimental and theoretical methods in gas and solution phases. The sub-picosecond lifetime of these molecules is not a general attribute of all nucleobases but specific to the five primary nucleobases and a few xanthine and methylated derivatives. To determine the overall UV photostability, we aim to understand the effect of more energetic photons lying in the UV-C region on nucleobases. To determine the UV-C initiated photophysics of a nucleobase system, we chose a halogen substituted purine, 6-chloroguanine (6-ClG), that we had investigated previously using resonance Raman spectroscopy. We have performed quantitative measurements of the resonance Raman cross-section across the Bb absorption band (210-230 nm) and constructed the Raman excitation profiles. We modeled the excitation profiles using Lee and Heller's time-dependent theory of resonance Raman intensities to extract the initial excited state dynamics of 6-ClG within 30-50 fs after photoexcitation. We found that imidazole and pyrimidine rings of 6-ClG undergo expansion and contraction, respectively, following photoexcitation to the Bb state. The amount of distortions of the excited state structure from that of the ground state structure is reflected by the total internal reorganization energy that is determined at 112 cm(-1). The contribution of the inertial component of the solvent response towards the total reorganization energy was obtained at 1220 cm(-1). In addition, our simulation also yields an instantaneous response of the first solvation shell within an ultrafast timescale of less than 30 fs following photoexcitation.

Geometric and energetic consequences of prototropy for adenine and its structural models – a review

Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.

Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases

Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids' structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.

Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment

The nonadiabatic photodynamics of the all-trans-2,4-pentadiene-iminium cation (protonated Schiff base 3, PSB3) and the all-trans-3-methyl-2,4-pentadiene-iminium cation (MePSB3) were investigated in the gas phase and in polar (aqueous) and nonpolar (n-hexane) solutions by means of surface hopping using a multireference configuration-interaction (MRCI) quantum mechanical/molecular mechanics (QM/MM) level. Spectra, lifetimes for radiationless deactivation to the ground state, and structural and electronic parameters are compared. A strong influence of the polar solvent on the location of the crossing seam, in particular in the bond length alternation (BLA) coordinate, is found. Additionally, inclusion of the polar solvent changes the orientation of the intersection cone from sloped in the gas phase to peaked, thus enhancing considerably its efficiency for deactivation of the molecular system to the ground state. These factors cause, especially for MePSB3, a substantial decrease in the lifetime of the excited state despite the steric inhibition by the solvent.