Ab initio studies on the photophysics of the guanine–cytosine base pair

Sobolewski, Andrzej L.; Domcke, Wolfgang

doi:10.1039/b314419d

Cited by 295 publications

(407 citation statements)

References 51 publications

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“…Therefore, the population decay through ( 1 ππ*/gs) CI is expected to occur preferentially in the deactivation process of keto cytosine. Our calculated barrier height agrees well with previous theoretical results of 0.1 ~ 0.14 eV 24,27,30,31,64 .…”

Section: Deactivation Pathway To ( 1 ππ*/Gs) CIsupporting

confidence: 92%

“…64 We performed a MECI search between the ground and 1 ππ* states at the MS(2)-CASPT2 (8,7) level, where the active space is the same as that used in the geometry optimization of the 1 ππ* minimum. As seen in Figure 3(b), the MECI geometry exhibits a significant puckering of the C6 atom, and the amino group possesses an almost planar structure.…”

Section: S 1 /S 0 Meci Structuresmentioning

confidence: 99%

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Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

Nakayama

Harabuchi

Yamazaki

et al. 2013

Phys. Chem. Chem. Phys.

111

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A comprehensive picture of the ultrafast nonradiative decay mechanisms of three cytosine tautomers (amino-keto, imino-keto, and amino-enol forms) is revealed by high-level ab initio potential energy calculations using the multistate (MS) CASPT2 method and also by on-the-fly excited-state molecular dynamics simulations employing the CASSCF method. To obtain a reliable potential energy profile along the deactivation pathways, the MS-CASPT2 method is employed even for the optimization of minimum energy structures in the excited state and conical intersection (CI) structures between the ground and excited states. In the imino (imino-keto) form, we locate a new CI structure involving the twisting of the imino group, and the decay pathway leading to this CI is found to be barrierless, suggesting a remarkably efficient deactivation of imino cytosine. In the keto (amino-keto) form, the MS-CASPT2 calculations exhibit an efficient decay path to the ethylene-like CI involving the twisting of C-C double bond in the six-membered ring, with a barrier of ~0.08 eV from the minimum of the 1 ππ* state. In the enol (amino-enol) form, three types of CIs are identified for the first time. Among them, the ethylene-like CI with a similar molecular structure to the keto form provides the most preferred deactivation pathway of enol cytosine. This pathway exhibits a higher barrier of ~0.22 eV and a higher energy of CI than those of keto cytosine. Nonadiabatic molecular dynamics simulations provide a time-dependent picture of the deactivation processes, including the excited-state lifetime of each tautomer. In particular, the decay time of the imino tautomer is predicted to be only ~100 fs. Our computational results are in remarkably good agreement with the experimental findings in recent femtosecond pump-probe photoionization spectroscopy [J. Am. Chem. Soc. 131, 16939 (2009); J. Phys. Chem. A 115, 8406 (2011)], supporting the coexistence of more than one tautomer in the photophysics of isolated cytosine and that each tautomer exhibits a different excited-state lifetime.1

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Section: Deactivation Pathway To ( 1 ππ*/Gs) CIsupporting

confidence: 92%

Section: S 1 /S 0 Meci Structuresmentioning

confidence: 99%

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

Nakayama

Harabuchi

Yamazaki

et al. 2013

Phys. Chem. Chem. Phys.

111

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“…The former exhibits broad UV absorption features; this is in contrast with the sharp UV spectra exhibited by non-WC structures. The broad absorption can be explained by recent theoretical results, predicting a pathway for rapid internal conversion (10). If the difference is solely due to lifetime broadening, these results correspond to a lifetime for the WC structures that is at least 2 orders of magnitude shorter than those of observed non-WC structures.…”

mentioning

confidence: 83%

“…A similar process can play a role in base pairs, albeit possibly involving different excited states. Recently, Sobolewski and Domcke (27) have reported detailed computations for the GC base pair in the WC configuration, identifying two doorway states that can mediate the internal conversion. One of those is a 1 * state that can be thought of as a proton transfer state (10).…”

Section: Discussionmentioning

confidence: 99%

Photochemical selectivity in guanine–cytosine base-pair structures

Abo-Riziq

Grace

Nir

et al. 2004

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

248

284

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Prebiotic chemistry presumably took place before formation of an oxygen-rich atmosphere and thus under conditions of intense short wavelength UV irradiation. Therefore, the UV photochemical stability of the molecular building blocks of life may have been an important selective factor in determining the eventual chemical makeup of critical biomolecules. To investigate the role of UV irradiation in base-pairing we have studied guanine (G) and cytosine (C) base pairs in the absence of the RNA backbone. We distinguished base-pair structures by IR-UV hole-burning spectroscopy as well as by high-level correlated ab initio calculations. The Watson-Crick structure exhibits broad UV absorption, in stark contrast to other GC structures and other base-pair structures. This broad absorption may be explained by a rapid internal conversion that makes this specific base pair arrangement uniquely photochemically stable.ab initio computation ͉ DNA base pairs ͉ IR-UV spectroscopy ͉ jet cooling ͉ photochemistry T he DNA bases involved in reproduction have short S 1 excited state lifetimes, of the order of 1 ps or less (1-7). It has been argued that this phenomenon serves to protect these bases against photochemical damage, because after excitation they do not cross to the reactive triplet state; instead, they rapidly internally convert to the electronic ground state (8). This mechanism may have been particularly significant under the conditions of the early earth, when purines and pyrimidines presumably were assembled into the first macromolecular structures, producing RNA. At that time, the earth was exposed to shorter wavelength UV radiation than it is today. For an analysis of possible prebiotic chemistry, it is necessary not only to consider the individual bases but also to study them as they interact and to do so without the RNA backbone (9). We achieve such an analysis by studying clusters of guanine (G) and cytosine (C) in the gas phase by using double resonant laser spectroscopy techniques. The experimental studies are accompanied by stateof-the-art quantum chemical and molecular dynamics calculations of the pairing of G and C. These two bases can form many different hydrogen-bonded structures, of which at least 20 are within 12 kcal͞mol of the global minimum. Thus, the familiar Watson-Crick (WC) structure may not be unique, based on energies alone. Here, we report a remarkable difference in excited state properties among the WC structure and other structures. The former exhibits broad UV absorption features; this is in contrast with the sharp UV spectra exhibited by non-WC structures. The broad absorption can be explained by recent theoretical results, predicting a pathway for rapid internal conversion (10). If the difference is solely due to lifetime broadening, these results correspond to a lifetime for the WC structures that is at least 2 orders of magnitude shorter than those of observed non-WC structures. Thus, it appears possible that the WC recognition mechanism involves a structure that was significantly more stab...

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“…The ultrashort lifetime of DNA may be associated with base-pairing and base-stacking interaction, genuine electronic property of DNA bases, and the solvation. [1][2][3][4][5][6][7][8][9][10] However, it is difficult to identify the exact mechanism due to the complexity of DNA structures. In this context, the 2-AP dimer was used as a simplified model for DNA base pairs by Schultz et al 1 and Sobolewski and Domcke.…”

Section: Introductionmentioning

confidence: 99%

Nonradiative decay of the lowest excited singlet state of 2-aminopyridine is considerably faster than the radiative decay

Zhang

Luo

et al. 2009

The Journal of Chemical Physics

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Ab initio calculations reveal that radiative lifetime of the lowest excited singlet state of 2-aminopyridine molecule should be around 20 ns, consistent with the molecules of the same type but is about one order of magnitude larger than the claimed experimental fluorescent lifetime in recent years. An S 1 / S 0 conical intersection close to the S 1 state has been located, which could be the possible nonradiative channel that is responsible for the fast decay observed in the experiment.

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Ab initio studies on the photophysics of the guanine–cytosine base pair

Cited by 295 publications

References 51 publications

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

Photochemical selectivity in guanine–cytosine base-pair structures

Nonradiative decay of the lowest excited singlet state of 2-aminopyridine is considerably faster than the radiative decay

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