UV-Excitation from an Experimental Perspective: Frequency Resolved

Vries, Mattanjah S. de

doi:10.1007/128_2014_560

Cited by 7 publications

(3 citation statements)

References 118 publications

(135 reference statements)

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“…The discrepancies between the spectral transitions calculated at the TD-DFTB level and the experimental values are relatively low and to be expected given the approximate nature of the method. The experimental π → π* lowest excitation wavelengths measured for adenine, cytosine, guanine, thymine, and uracil are 276.96, 314.12, 294.90, 277.78, and 272.48 nm, respectively, whereas from our calculations such wavelengths are 262.37, 302.16, 270.90, 262.18, and 242.47 nm. These bands were excited with a pump pulse as explained in section in order to compute the TA spectra and then the IVS of each nucleobase.…”

Section: Resultscontrasting

confidence: 47%

Simulation of Impulsive Vibrational Spectroscopy

et al. 2019

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In the present work we applied a fully atomistic electron−nuclear real-time propagation protocol to compute the impulsive vibrational spectroscopy of the five DNA/RNA nucleobases in order to study the very first steps (subpicosecond) of their energy distribution after UV excitation. We observed that after the pump pulse absorption the system is prepared in a coherent superposition of the ground and the pumped electronic excited states in the equilibrium geometry of the ground state. Furthermore, for relatively low fluency values of the pump pulse, the dominant contribution to the electronic wave function of the coherent state is of the ground state and the mean potential energy surface within the Ehrenfest approximation is similar to that of the ground state. As a consequence, the molecular displacements are better correlated with ground-state normal modes. On the other hand, when the pump fluency is increased the excited-state contribution to the electronic wave function becomes more important and the mean potential energy surface resembles more that of the excited state, producing a better correlation between the molecular displacements and the excited-state normal modes. Finally, it has been observed that the impulsive activation of several vibrational modes upon electronic excitation is triggered by the development of excited-state forces which accelerate the nuclei from their equilibrium positions causing a distribution of the absorbed electronic energy on the nuclear degrees of freedom and could be closely related to the driving force of the ultrafast nonradiative deactivation observed in these systems.

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Section: Resultscontrasting

confidence: 47%

Simulation of Impulsive Vibrational Spectroscopy

et al. 2019

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“…What distinguishes short lived, and thus UV-robust, compounds from their long lived counterparts are variations in excited state potential landscapes, resulting from structural variations. Figure 4 shows examples with three of the canonical nucleobases and hypoxanthine in the left column and some of their derivatives in the right column 5,[31][32][81][82] . When probed at energies close to the onset of absorption, all compounds in the left column have excited state lifetimes of the order of picoseconds or less, while those in the right column have lifetimes of the order of nanoseconds.…”

Section: Derivativesmentioning

confidence: 99%

How nature covers its bases

Boldissar

Vries

2018

Phys. Chem. Chem. Phys.

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The response of DNA and RNA bases to ultraviolet (UV) radiation has been receiving increasing attention for a number of important reasons: (i) the selection of the building blocks of life on an early earth may have been mediated by UV photochemistry, (ii) radiative damage of DNA depends critically on its photochemical properties, and (iii) the processes involved are quite general and play a role in more biomolecules as well as in other compounds. A growing number of groups worldwide have been studying the photochemistry of nucleobases and their derivatives. Here we focus on gas phase studies, which (i) reveal intrinsic properties distinct from effects from the molecular environment, (ii) allow for the most detailed comparison with the highest levels of computational theory, and (iii) provide isomeric selectivity. From the work so far a picture is emerging of rapid decay pathways following UV excitation. The main understanding, which is now well established, is that canonical nucleobases, when absorbing UV radiation, tend to eliminate the resulting electronic excitation by internal conversion (IC) to the electronic ground state in picoseconds or less. The availability of this rapid "safe" de-excitation pathway turns out to depend exquisitely on molecular structure. The canonical DNA and RNA bases are generally short-lived in the excited state, and thus UV protected. Many closely related compounds are longer lived, and thus more prone to other, potentially harmful, photochemical processes. It is this structure dependence that suggests a mechanism for the chemical selection of the building blocks of life on an early earth. However, the picture is far from complete and many new questions now arise.

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“…Also, up to our knowledge, no time-resolved photoelectron spectroscopy (TRPES) 27 has been reported for these molecules, even though this methodology has been extensively applied to study the excited-state dynamics of the canonical nucleobases [28][29][30] (see, e.g., Ref. 31 for a list of these experiments) and a small number of nucleobase analogous.…”

Section: Introductionmentioning

confidence: 99%

Photoelectron spectra of 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil

Ruckenbauer

Mai

Marquetand

et al. 2016

The Journal of Chemical Physics

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Ground-and excited-state UV photoelectron spectra of thiouracils (2-thiouracil, 4-thiouracil and 2,4-dithiouracil) have been simulated using multireference configuration interaction calculations and Dyson norms as measure for the photoionization intensity. Except for a constant shift, the calculated spectrum of 2-thiouracil agrees very well with experiment, while no experimental spectra are available for the two other compounds. For all three molecules, the photoelectron spectra show distinct bands due to ionization of the sulphur and oxygen lone pairs and the pyrimidine π system. The excited-state photoelectron spectra of 2-thiouracil show bands at much lower energies than in the ground state spectrum, allowing to monitor the excited-state population in time-resolved UV photoelectron spectroscopy (TRPES) experiments. However, the results also reveal that single-photon ionization probe schemes alone will not allow monitoring all photodynamic processes existing in 2-thiouracil. Especially, due to overlapping bands of singlet and triplet states the clear observation of intersystem crossing will be hampered.

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UV-Excitation from an Experimental Perspective: Frequency Resolved

Cited by 7 publications

References 118 publications

Simulation of Impulsive Vibrational Spectroscopy

Simulation of Impulsive Vibrational Spectroscopy

How nature covers its bases

Photoelectron spectra of 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil

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