Ultrafast Deactivation of an Excited Cytosine−Guanine Base Pair in DNA

Groenhof, Gerrit; Schaefer, L.; Boggio‐Pasqua, Martial; Goette, Maik; Grubmueller, Helmut; Robb, Michael A.

doi:10.1021/ja069176c

Cited by 173 publications

(188 citation statements)

References 31 publications

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“…From this point, the ultrafast decay path through the CI localized in the G monomer can be expected. 37 This decay pathway has not been found in the trajectories performed by Groenhof et al, 85 due to the fact that all the simulations were started in the CT state, as a result of the lower level of theory employed. Simulation 2 (Sim2) includes additionally an initial velocity component in the direction of the N' 3 …H 1 N 1 hydrogen bond, favoring also the radiationless energy decay towards the TAU1 species or the restored WC base pair, via the SDHT mechanism ( Figure 6).…”

Section: Concerted Double Proton-transfer (Cdpt) Mechanism Sdpt and mentioning

confidence: 88%

“…Groenhof et al obtained a recovery of the WC configuration in 75% of 20 simulations. 85 In five out of 20 runs, the TAU1 configuration was found. Simulation 3 (Sim3) points to the ground-state formation of TAU2, instead of TAU1, via the SDHT mechanism ( Figure 7).…”

Section: Concerted Double Proton-transfer (Cdpt) Mechanism Sdpt and mentioning

confidence: 94%

“…Previous works on the dynamics of the system has been reported, although at levels of theory not able to describe the overall photochemistry of the GC base pair. 85,93 The subsequent parts of the paper are structured as follows: methods, results and discussion, and summary and concluding remarks.…”

Section: Introductionmentioning

confidence: 99%

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Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

Sauri

Gobbo

Serrano-Pérez

et al. 2012

J. Chem. Theory Comput.

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Proton/hydrogen-transfer processes have been broadly studied in the last fifty years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine-cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson-Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.

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Section: Concerted Double Proton-transfer (Cdpt) Mechanism Sdpt and mentioning

confidence: 88%

Section: Concerted Double Proton-transfer (Cdpt) Mechanism Sdpt and mentioning

confidence: 94%

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Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

Sauri

Gobbo

Serrano-Pérez

et al. 2012

J. Chem. Theory Comput.

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“…Such calculations are challenging because of the large number of nuclear degrees of freedom, the large excess energy provided by UV photons, and extremely strong nonBorn-Oppenheimer effects at conical intersections (8). Very recently, a few ab initio on-the-fly trajectory simulations have been performed on hydrogen-detachment and hydrogentransfer processes in biomolecular systems (13,14). Although such simulations can provide useful mechanistic insight, they have limitations because of the rather significant de Broglie wavelength of the proton, the approximate treatment of the nonadiabatic dynamics at the conical intersections, the inevitable compromises with respect to the accuracy of the ab initio methods, and the very limited number of trajectories that can be calculated.…”

mentioning

confidence: 99%

Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole–pyridine complex

Lan

Frutos

Sobolewski

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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The photochemical dynamics of the pyrrole-pyridine hydrogenbonded complex has been investigated with computational methods. In this system, a highly polar charge-transfer state of 1 * character drives the proton transfer from pyrrole to pyridine, leading to a conical intersection of S 1 and S0 energy surfaces. A two-sheeted potential-energy surface including 39 in-plane nuclear degrees of freedom has been constructed on the basis of ab initio multiconfiguration electronic-structure data. The non-BornOppenheimer nuclear dynamics has been treated with time-dependent quantum wave-packet methods, including the two or three most relevant nuclear degrees of freedom. The effect of the numerous weakly coupled vibrational modes has been taken into account with reduced-density-matrix methods (multilevel Redfield theory). The results provide insight into the mechanisms of excitedstate deactivation of hydrogen-bonded aromatic systems via the electron-driven proton-transfer process. This process is believed to be of relevance for the ultrafast excited-state deactivation of DNA base pairs and may contribute to the photostability of the molecular encoding of the genetic information.conical intersection ͉ excited-state hydrogen transfer ͉ nonadiabatic transition A s is well known, hydrogen bonds are of universal importance in chemistry and biochemistry. Although the structure and the functionality of hydrogen bonds in the electronic ground state have been investigated with powerful experimental and computational methods for decades and are thus quite well understood (1), much less is known about the role of hydrogenbond dynamics in excited electronic states of chemical or biochemical systems. Fluorescence quenching of aromatic chromophores by protic solvents and fluorescence quenching in intermolecularly or intramolecularly hydrogen-bonded aromatic systems are well known phenomena, but are still poorly understood at the atomistic level (2-4). One reason for our limited knowledge of excited-state hydrogen-bond dynamics is the extremely short time scale of some of these processes (presumably of the order of 10 fs or less). Another reason is the difficulty of performing accurate ab initio electronic-structure calculations for excited states of complex polyatomic systems.It has recently been proposed that electron-driven protontransfer processes along hydrogen bonds could play a decisive role for the ultrafast excited-state deactivation of biological molecules and supermolecular structures, such as DNA base pairs, peptides, or UV-protecting pigments (5-7). The computational studies suggest that proton-transfer processes driven by charge-transfer (CT) states of 1 *, 1 n*, or 1 * character provide barrierless access to conical intersections (8) of the excited-state and ground-state potential-energy surfaces, where ultrafast internal conversions take place. This particularly efficient mechanism of energy dissipation could be essential for photostability of the molecular encoding of the genetic information of life (9). Recent experimen...

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“…(12). We also introduce the Fock matrix F, which has dependence on both the MO coefficients and the nuclear position, but we do not need to enforce that ∂M var /∂F = 0.…”

Section: B Assembling a Matrix Element/coupling Derivativementioning

confidence: 99%

Analytic energy gradients for constrained DFT-configuration interaction

Kaduk¹,

Tsuchimochi²,

Voorhis³

2014

The Journal of Chemical Physics

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The constrained density functional theory-configuration interaction (CDFT-CI) method has previously been used to calculate ground-state energies and barrier heights, and to describe electronic excited states, in particular conical intersections. However, the method has been limited to evaluating the electronic energy at just a single nuclear configuration, with the gradient of the energy being available only via finite difference. In this paper, we present analytic gradients of the CDFT-CI energy with respect to nuclear coordinates, which gives the potential for accurate geometry optimization and molecular dynamics on both the ground and excited electronic states, a realm which is currently quite challenging for electronic structure theory. We report the performance of CDFT-CI geometry optimization for representative reaction transition states as well as molecules in an excited state. The overall accuracy of CDFT-CI for computing barrier heights is essentially unchanged whether the energies are evaluated at geometries obtained from QCISD or CDFT-CI, indicating that CDFT-CI produces very good reaction transition states. These results open up tantalizing possibilities for future work on excited states. * tvan@mit.edu 1

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Ultrafast Deactivation of an Excited Cytosine−Guanine Base Pair in DNA

Cited by 173 publications

References 31 publications

Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole–pyridine complex

Analytic energy gradients for constrained DFT-configuration interaction

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