Conformational control of benzophenone-sensitized charge transfer in dinucleotides

Abstract

Charge transfer in DNA cannot be understood without addressing the complex conformational flexibility, which occurs on a wide range of timescales. In order to reduce this complexity four dinucleotide models 1X consisting of benzophenone linked by a phosphodiester to one of the natural nucleosides X = A, G, T, C were studied in water and methanol. The theoretical work focuses on the dynamics and electronic structure of 1G. Predominant conformations in the two solvents were obtained by molecular dynamics simulations. 1G in MeOH adopts mainly an open geometry with a distance of 12-16 Å between the two aromatic parts. In H 2 O the two parts of 1G form primarily a stacked conformation yielding a distance of 5-6 Å. The low-lying excited states were investigated by electronic structure theory in a QM/MM environment for representative snapshots of the trajectories. Photo-induced intramolecular charge transfer in the S 1 state occurs exclusively in the stacked conformation. Ultrafast transient absorption spectroscopy with 1X reveals fast charge transfer from S 1 in both solvents with varying yields. Significant charge transfer from the T 1 state is only found for the nucleobases with the lowest oxidation potential: in H 2 O, charge transfer occurs with 3.2 Â 10 9 s À1 for 1A and 6.0 Â 10 9 s À1 for 1G. The reorganization energy remains nearly unchanged going from MeOH to the more polar H 2 O. The electronic coupling is rather low even for the stacked conformation with H AB = 3 meV and explains the moderate charge transfer rates. The solvent controls the conformational distribution and therefore gates the charge transfer due to differences in distance and stacking.

Temporal and spectral correlations in bulk continua and improved use in transient spectroscopy

“…9(b)] the data are much clearer and show a good signal-to-noise ratio. The benzophenone excitedstate absorption from the S 1 state at about 580 nm changes to the persistent absorption from the T 1 state the system relaxes to in about 10 ps [37]. A fit to the 550 nm trace from Fig.…”

“…The transient signals of an artificial C-nucleoside with benzophenone as chromophore (compound 1 in [37]) are measured. This compound is only weakly solvable in H 2 O and the dynamics in H 2 O could previously not be measured [37]. The sample is excited at 310 nm with an energy of 150 nJ.…”

“…9(b) renders a first exponential time constant of 1.0 ps and a second one of 6.3 ps. Due to the 310 nm excitation, there is a first ultrafast S 2 →S 1 relaxation [38], the intersystem crossing seems to be accelerated both by water as solvent and the S 2 excitation from the typical 10 ps [37,39].…”

Synthesis of Benzophenone Nucleosides and Their Photocatalytic Evaluation for [2+2] Cycloaddition in Aqueous Media

“…It became clear that the solvent, H 2 O or MeOH, controls the conformational distribution and thereby actually gates the charge‐transfer process as a result of differences in the distance and degree of stacking between benzophenone and the second component of the dinucleotide. Our results gave a full understanding of the photophysical properties of the singlet and triplet state of the BP chromophore in the context of each of the four different DNA bases 11. Moreover, these studies clearly revealed that nucleotides that contain conventional benzophenone as the artificial DNA base are not suited to serve as a photochemically inert architecture for benzophenone‐mediated photocatalysis.…”

“…The exploration of the benzophenone dinucleotides by time‐resolved transient absorption spectroscopy and theoretical methods, including molecular dynamics, revealed charge‐transfer processes predominantly with guanosine as the second component 11. It became clear that the solvent, H 2 O or MeOH, controls the conformational distribution and thereby actually gates the charge‐transfer process as a result of differences in the distance and degree of stacking between benzophenone and the second component of the dinucleotide.…”