Driving Force Dependence of Electron Transfer Dynamics in Synthetic DNA Hairpins

Lewis, Frederick D.; Kalgutkar, Rajdeep S.; Wu, Yanxia; Liu, Xiaoyang; Liu, Jian‐Qin; Hayes, Rachel M.; Miller, Scott E.; Wasielewski, Michael R.

doi:10.1021/ja0028267

Cited by 181 publications

(344 citation statements)

References 45 publications

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“…Considering the conformational distribution, we find a value for the electronic coupling of H AB = 3 meV. In comparison to previously reported values for electronic coupling 52 the presented value appears to be rather small. It became clear that the solvent controls the conformational distribution and thereby gates the charge transfer due to differences in distance and stacking.…”

Section: Discussioncontrasting

confidence: 48%

Conformational control of benzophenone-sensitized charge transfer in dinucleotides

Merz

Wenninger

Weinberger

et al. 2013

Phys. Chem. Chem. Phys.

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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.

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Section: Discussioncontrasting

confidence: 48%

Conformational control of benzophenone-sensitized charge transfer in dinucleotides

Merz

Wenninger

Weinberger

et al. 2013

Phys. Chem. Chem. Phys.

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“…[23], where for n=4 the electronic coupling is half of that for n=2. Moreover, it can explain the disagreement of the earlier theoretical results [9,17] and experiments, where the electronic coupling is usually much smaller than 0.1 eV [13]. Based on these results we conclude that the electronic coupling calcu- lated for the system of two stacked base pairs leads to the overestimation of the transfer integral for the charge transfer simulation in the DNA oligomers.…”

Section: A High Occupied Orbital Distributionsupporting

confidence: 46%

Energetics of the hole transfer in DNA duplex oligomers

Berashevich

Chakraborty

2007

Chemical Physics Letters

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We report on our calculations of the inner-sphere reorganization energy and the interaction of the π orbitals within DNA oligomers. The exponential decrease of the electronic coupling between the highest and second highest occupied base orbitals of the intrastrand nucleobases in the (A-T)n and (G-C)n oligomers have been found with an increase of the sequence number n in the DNA structure. We conclude that for realistic estimation of the electronic coupling values between the nucleobases within the DNA molecule, a DNA chain containing at least four base pairs is required. We estimate the geometry relaxation of the base pairs within the (A-T)n and (G-C)n oligomers (n = 1 − 6) due to their oxidation. The decrease of the inner-sphere reorganization energy with elongation of the oligomer structure participating in the oxidation process have been observed. The maximum degree of geometry relaxation of the nucleobase structures and correspondingly the higher charge density in the oxidized state are found to be located close to the oligomer center.

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“…The results of our calculations with these ∆G values are not affected by the fact that we chose a classical rate constant rather than a quantum mechanical rate constant. 47,48 Calculations were also performed for larger donor/acceptor radii of 2.58 and 2.95 Å for guanine and stilbene, respectively, calculated assuming 4.5 Å 3 per atom. To avoid donor/acceptor overlap for the large radii, the shortest donor/acceptor distance was ignored.…”

Section: Resultsmentioning

confidence: 99%

“…48 In their new paper, the transfer rate was measured at two distances in many Figure 7. Natural log of the rate constant vs distance for electron transfer from guanine to a stilbenedicarboxamide bridge in DNA.…”

Section: Resultsmentioning

confidence: 99%

Distance Dependence of Electron Transfer in DNA: The Role of the Reorganization Energy and Free Energy

2000

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A model of the distance dependence of photoinduced donor-acceptor electron transfer in DNA is presented that includes the distance dependence of the solvent reorganization energy and free energy in the heterogeneous DNA environment. DNA is modeled as a low dielectric region that represents the base stack and two regions with more moderate dielectric properties that represent the DNA backbone. The DNA is surrounded by a high dielectric medium, which represents water. Model calculations show the importance of including the reorganization energy and the free energy change and illustrate the differences between the inhomogeneous model and homogeneous single dielectric constant calculations using standard Marcus theory. Calculations are performed for comparison to published experimental work (Science 1997, 277, 673; 1 J. Am. Chem. Soc. 1992, 114, 3656 2 ). Fits to one set of data 2 permit the previously reported distance dependence to be separated into an electronic contribution and solvent reorganization energy and free energy contributions. For the other set of data, 1 inclusion of the solvent reorganization energy and free energy distance dependences in the analysis of the overall distance dependent data suggest that the Marcus form of the distance dependent rate constant including the Marcus reorganization energy is not consistent with the data.

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Driving Force Dependence of Electron Transfer Dynamics in Synthetic DNA Hairpins

Cited by 181 publications

References 45 publications

Conformational control of benzophenone-sensitized charge transfer in dinucleotides

Conformational control of benzophenone-sensitized charge transfer in dinucleotides

Energetics of the hole transfer in DNA duplex oligomers

Distance Dependence of Electron Transfer in DNA: The Role of the Reorganization Energy and Free Energy

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