Initial Excited-State Structural Dynamics of Uracil from Resonance Raman Spectroscopy Are Different from Those of Thymine (5-Methyluracil)

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.

Section: ' Resultsmentioning

confidence: 99%

Section: ' Resultsmentioning

confidence: 99%

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

Oladepo

2011

J. Phys. Chem. B

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“…The general implementation of these equations for absorption and resonance Raman spectroscopy have been described in detail previously. [4][5][6][7][8][9][10][11][12][13][14]16,17 The vibrational mode assignments described in Tables 1 and 2 were obtained by DFT computation at the B3LYP/6-311G(d,p) level of theory, with the default gradients implemented in the Gaussian09 18 package performed on the initial planar C s structures of uracil and 6-MeU in the diketo tautomer form. The isotope effect was calculated for 6-d-U from the uracil frequencies, which are not scaled.…”

Section: ■ Theorymentioning

confidence: 99%

Initial Excited-State Structural Dynamics of 6-Substituted Uracil Derivatives: Femtosecond Angle and Bond Lengthening Dynamics in Pyrimidine Nucleobase Photochemistry

Teimoory

2014

J. Phys. Chem. A

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Substituents on the pyrimidine ring of nucleobases appear to play a major role in determining their initial excited-state structural dynamics and resulting photochemistry. To better understand the determinants of nucleobase initial excited-state structural dynamics, we have measured the absorption and resonance Raman excitation profiles of 6-deuterouracil (6-d-U) and 6-methyluracil (6-MeU). Simulation of the resonance Raman excitation profiles and absorption spectrum with a self-consistent, time-dependent formalism shows the effect of the deuterium and methyl group on the photochemically active internal coordinates, i.e. C5C6 stretch and C5X and C6X bends. The methyl group on either the C5 or C6 position of uracil equally increases the excited-state reorganization energies along the C5C6 stretch. However, a lower reorganization energy of the C5X + C6X bends in 6-MeU than uracil and 5-MeU shows that C6 methyl substituents reduce the bending reorganization energy. In addition, deuterium substitution at either C5 or C6 has a much smaller effect on the initial excited-state structural dynamics than methyl substitution, consistent with a mass effect. These results will be discussed in light of the resulting photochemistry of pyrimidine nucleobases.

“…The effect of N1 substitution on initial excited‐state structural dynamics in nucleobases has been studied previously. In thymine, the presence of the sugar does not change the relative magnitudes of the excited‐state potential energy slopes at the Franck–Condon region but does decrease the overall initial excited‐state structural dynamics . The observed decrease in the initial excited‐state dynamics has been attributed to the presence of less‐steep excited‐state potential energy surfaces and a shift in the potential energy surface at the Frank–Condon region in nucleosides .…”

Section: Introductionmentioning

confidence: 93%

“…For example, the intensities of the resonance Raman peaks are proportional to the slopes of the excited‐state potential energy surface along each vibrational coordinate. The power of resonance Raman spectroscopy to probe the initial excited‐state structural dynamics of the molecules has been exploited by Loppnow et al in studying thymine, uracil, and their derivatives . The initial excited‐state structural dynamics of uracil in the photochemically relevant excited state is mostly directed along C5H and C6H bending modes, whereas it is oriented along the CC stretching mode in thymine …”

Section: Introductionmentioning

confidence: 99%

Initial excited‐state structural dynamics of uridine from resonance Raman spectroscopy

Sasidharanpillai

Dempster

2018

J Raman Spectroscopy

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The effect of the N1 ribose sugar on the initial excited‐state structural dynamics of uridine is explored with ultraviolet resonance Raman spectroscopy. Excited‐state slopes and broadening parameters were obtained by simulating the resonance Raman excitation profiles and absorption spectrum using a self‐consistent, time‐dependent formalism. The initial excited‐state structural dynamics of uridine look similar to those of uracil, in terms of the distribution of percentage of reorganization energy along different modes, but there is an overall decrease in the excited‐state slopes along most of the modes in uridine compared with uracil. Only about 30% of the total initial reorganization energy in both uracil and uridine are oriented along the photochemically reactive coordinates. The results are also similar to those of thymine and thymidine, upon attachment of the sugar. These differences between thymine, thymidine, uracil and uridine are examined, and the possible effect on the resulting differences in photochemistry is discussed.