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DDC: 540 × Has files: Yes × Publisher: Washington, DC : American Chemical Society × WGL Institute: MBI ×

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    Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: A computational study
    (Washington, DC : American Chemical Society, 2014) Ando, H.; Fingerhut, B.P.; Dorfman, K.E.; Biggs, J.D.; Mukamel, S.
    Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C=O and C=C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3′→5′)-thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C5-C′5 splitting and a main barrier for the C6-C′6 splitting, and identify the appearance of two C5=C6 stretch vibrations due to the C6-C′6 splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes. (Figure Presented).
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    Short-Range Cooperative Slow-down of Water Solvation Dynamics Around SO42--Mg2+ Ion Pairs
    (Washington, DC : American Chemical Society, 2022) Kundu, Achintya; Mamatkulov, Shavkat I.; Brünig, Florian N.; Bonthuis, Douwe Jan; Netz, Roland R.; Elsaesser, Thomas; Fingerhut, Benjamin P.
    The presence of ions affects the structure and dynamics of water on a multitude of length and time scales. In this context, pairs of Mg2+ and SO42- ions in water constitute a prototypical system for which conflicting pictures of hydration geometries and dynamics have been reported. Key issues are the molecular pair and solvation shell geometries, the spatial range of electric interactions, and their impact on solvation dynamics. Here, we introduce asymmetric SO42- stretching vibrations as new and most specific local probes of solvation dynamics that allow to access ion hydration dynamics at the dilute concentration (0.2 M) of a native electrolyte environment. Highly sensitive heterodyne 2D-IR spectroscopy in the fingerprint region of the SO42- ions around 1100 cm-1 reveals a specific slow-down of solvation dynamics for hydrated MgSO4 and for Na2SO4 in the presence of Mg2+ ions, which manifests as a retardation of spectral diffusion compared to aqueous Na2SO4 solutions in the absence of Mg2+ ions. Extensive molecular dynamics and density functional theory QM/MM simulations provide a microscopic view of the observed ultrafast dephasing and hydration dynamics. They suggest a molecular picture where the slow-down of hydration dynamics arises from the structural peculiarities of solvent-shared SO42--Mg2+ ion pairs.