Initial Excited-State Structural Dynamics of Thymine Are Coincident with the Expected Photochemical Dynamics

Ng, Susan; Yarasi, Soujanya; Brost, Philip; Loppnow, Glen R.

doi:10.1021/jp806433h

Cited by 8 publications

(8 citation statements)

References 2 publications

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“…From Table 1, it can be seen that both homogeneous and inhomogeneous line widths used need to be fairly large in order to reproduce both absolute Raman intensities and absorption band shape. The homogeneous line width is fairly consistent with previously reported values for thymine and uracil, 54,55 but higher than for cytosine and 5-fluorouracil (5-FU). 22,23 The inhomogeneous line width is however consistent with the values previously reported for all four nucleobases.…”

Section: ' Resultssupporting

confidence: 91%

“…22,23 The inhomogeneous line width is however consistent with the values previously reported for all four nucleobases. 22,23,54,55 In the condensed phase, solvent dynamics may contribute significantly to the breadth of the absorption spectrum, either through homogeneous or inhomogeneous mechanisms. 21À23 These two factors affect the absorption spectrum and the resonance Raman excitation profiles differently.…”

Section: ' Resultsmentioning

confidence: 99%

“…Our group has previously reported on the excited-state structural dynamics of cytosine, 5-fluorouracil (5-FU), thymine, and uracil. ,,, In all these reports, the differences in the resonance Raman spectral intensities between these similar nucleobases were highlighted, as well as the implication on their structural dynamics and photochemistry. For example, thymine only differs from uracil by the presence of a methyl group at the C5 position.…”

Section: Discussionmentioning

confidence: 99%

“…It was found that in thymine, the dynamics lie primarily along the C5C6 bond lengthening coordinate, while in uracil, most of the structural dynamics occur along a carbon pyramidalization coordinate. These differences in initial excited-state structural dynamics are one factor responsible for the different photoproducts observed for these two similar nucleobases. ,, It was therefore suggested that the observed differences in the excited-state structural dynamics of thymine and uracil arises from the methyl group in thymine acting as a mass barrier, thereby localizing the vibrations at the photochemically active site. The resonance Raman spectra obtained for the related analogue of these two, 5-FU, shows intensity that are more similar to thymine than uracil, thereby supporting the mass barrier hypothesis …”

Section: Discussionmentioning

confidence: 99%

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Initial Excited-State Structural Dynamics of 9-Methyladenine from UV Resonance Raman Spectroscopy

Oladepo

Loppnow

2011

J. Phys. Chem. B

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The photophysics and photochemistry of nucleobases are the factors governing the photostability of DNA and RNA, since they are the UV chromophores in nucleic acids. Because the formation of photoproducts involves structural changes in the excited electronic state, we study here the initial excited-state structural dynamics of 9-methyladenine (9-MeA) by using UV resonance Raman (UVRR) spectroscopy. UV resonance Raman intensities are sensitive to the initial excited-state structural dynamics of molecules. Therefore, information about the initial structural changes in the excited-state of a given molecule can be obtained from its UVRR intensities. The resonance Raman spectra of 9-MeA at wavelengths throughout its 262 nm absorption band were measured, and a self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum was performed using a time-dependent wave packet formalism. We found that the initial structural dynamics of this molecule primarily lie along the N3C4, C4C5, C5C6, C5N7, N7C8, and C8N9 stretching vibrations and CH(3) deformation vibrations. These results are discussed in the context of photochemistry and other deactivation processes.

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Section: ' Resultssupporting

confidence: 91%

Section: ' Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Initial Excited-State Structural Dynamics of 9-Methyladenine from UV Resonance Raman Spectroscopy

Oladepo

Loppnow

2011

J. Phys. Chem. B

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“…The initial excited-state structural dynamics of the nucleobases are also of great interest because they initiate the long-time photodynamics. Experimentally the initial dynamics for the nucleobases on the excited electronic state can be probed by resonance Raman spectroscopy. − By tuning the incident excitation wavelength to be resonant with the electronic transition of the nucleobase studied, the intensity of the Raman spectrum is strongly enhanced. The frequencies and intensities of the peaks in the resonance Raman spectrum provide crucial information on how the normal modes of the nucleobases are driven by the forces in the electronically excited state.…”

Section: Introductionmentioning

confidence: 99%

Simulation of the Resonance Raman Spectrum for Uracil

Sun

Brown

2014

J. Phys. Chem. A

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The resonance Raman spectrum of uracil is simulated using the Herzberg-Teller short-time dynamics formalism. The ground-state geometry is optimized at the levels of PBE0/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ, respectively. The gradient of the bright excited state is computed using time-dependent density functional theory and spin-flip time-dependent density functional theory. The excited-state calculations are carried out in both the gas phase and implicit water using the conductor-like polarizable continuum model. The ground-state equilibrium structure is found to impact the resulting resonance Raman spectrum significantly. The simulated resonance Raman spectrum using the long-range corrected functionals, that is, CAMB3LYP and LC-BLYP, and based on the PBE0/aug-cc-pVTZ optimized ground-state structure shows better agreement with the experimental spectrum than using standard hybrid functionals, that is, PBE0 and B3LYP. The solvation effect leads to a change in the energetic order of the n → π* and π → π* excited states, and it improves the agreement with the experimental spectrum, especially with regard to the relative intensities of the peaks with frequencies greater than 1600 cm(-1).

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Interaction of β‐cyclodextrin‐capped CdSe quantum dots with inorganic anions and cations

Shang

Wang

et al. 2011

Luminescence

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A facile method was developed for the preparation of water soluble β-Cyclodextrin (β-CD)-modified CdSe quantum dots (QDs) (β-CD-QDs) by directly replacing the oleic acid ligands on the QDs surface with β-CD in an alkaline aqueous solution. The as-prepared QDs show good stability in aqueous solution for several months. Oxoanions, including phosphoric acid ion, sulphite acid ion and carbonic acid ion, affect the fluorescence of β-CD-QDs. Among them, H(2)PO(4)(-) exhibited the largest quenching effect. For the polyprotic acids (HO)(3)AO, the effect of acidic anions on the fluorescence of β-CD-QDs was in the order: monoanion (HO)(2)AO(2)(-) > dianion (HO)AO(3)(2-) >> trianion AO(4)(3-). After photoactivation for several days in the presence of anions at alkaline pH, the β-CD-QDs exhibited strong fluorescence emission. The effect of various heavy and transition metal ions on the fluorescence properties of the β-CD-QDs was investigated further. It was found that Ag(+), Hg(2+) and Co(2+) have significant quenching effect on the fluorescence of the β-CD-QDs. The Stern-Volmer quenching constants increased in the order: Hg(2+) < Co(2+)

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Initial Excited-State Structural Dynamics of Thymine Are Coincident with the Expected Photochemical Dynamics

Cited by 8 publications

References 2 publications

Initial Excited-State Structural Dynamics of 9-Methyladenine from UV Resonance Raman Spectroscopy

Initial Excited-State Structural Dynamics of 9-Methyladenine from UV Resonance Raman Spectroscopy

Simulation of the Resonance Raman Spectrum for Uracil

Interaction of β‐cyclodextrin‐capped CdSe quantum dots with inorganic anions and cations

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