Initial Excited-state Structural Dynamics Research Articles

Initial Excited State Dynamics of Lumichrome upon Ultraviolet Excitation.

Lumichrome (LC) is the major photodegradation product of biologically important flavin cofactors. Since LC serves as a structural comparison with the flavins; understanding excited states of LC is fundamentally important to establish a connection with photophysics of different flavins, such as lumiflavin (LF), riboflavin (RF), flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Herein, we deduce the initial excited state structural dynamics of LC using UV resonance Raman (UVRR) intensity analysis. The UVRR spectra at wavelengths across the 260 nm absorption band of LC were measured and resulting Raman excitation profiles and absorption spectrum were self-consistently simulated using a time-dependent wave packet formalism to extract the initial excited state structural and solvent broadening parameters. These results are compared with those obtained for other flavins following UV excitations. We find that LC undergoes a very distinct instantaneous charge redistribution than flavins, which is attributed to the extended π-conjugation present in flavins but missing in LC. The homogeneous broadening linewidth of LC appears to be lower than that of LF, while the inhomogeneous broadening values are comparable, indicating greater solvent interaction with excited flavin on ultrafast timescale compared with LC, whereas on longer timescale these interactions are almost similar.

Initial excited-state structural dynamics of 2′-deoxyadenosine

Purine nucleobases (adenosine and guanosine) are prone to spontaneous breaking of the nucleosidic bond to form abasic sites in both DNA and RNA. However, the purines also undergo photochemical reactions, including oxidation and cycloaddition, to form damage sites, albeit at lower photochemical quantum yields than the pyrimidines. In this study, we use ultraviolet resonance Raman spectroscopy to measure the initial excited-state structural dynamics in the nucleoside, 2′-deoxyadenosine. The resonance Raman-derived initial excited-state structural dynamics throughout the 260 nm La excited electronic state of adenine are found to be smaller in the nucleoside than in the previously reported 9-methyladenine nucleobase derivative, consistent with what is found for the pyrimidines thymine and uracil. Interestingly, resonance-enhanced vibrational modes in this electronic state also contain internal coordinates localized on the sugar, which may represent a different energy dissipation mechanism than in the pyrimidine nucleosides. The results will be discussed in terms of the initial excited-state photophysics and photochemistry of DNA and RNA.

Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy.

Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers. Initial excited-state slopes, homogeneous and inhomogeneous broadening, and other excited-state parameters were extracted by self-consistent simulation of the resonance Raman excitation profiles and absorption spectra with a time-dependent formalism and are also similar to the initial excited-state slopes and broadening in the nucleotide monomers. The lack of differences between the initial excited-state structural dynamics of the nucleotides within the pentamer and the isolated nucleobases is consistent with a model in which the formation of photochemical products in oligonucleotides and DNA is dependent on the formation of the transition-state structure within these polymers, dictated by their large-scale dynamics. These results are discussed in light of the known photochemistry of DNA and the nucleobases.

Initial excited state structural dynamics of lumiflavin upon ultraviolet excitation

Excited state photophysics of flavin compounds has attracted great attention due to their involvement in several photobiological processes as a cofactor in photoreceptor enzymes. In this work, we have determined the initial excited state structural dynamics of flavin related compound, lumiflavin (LF), upon ultraviolet (UV) excitation through resonance Raman intensity analysis. A quantitative measurement of resonance Raman cross-sections across the 265 nm absorption band (257–275 nm) of LF have been performed, and Raman excitation profiles (REPs) are constructed for all the Raman active modes. The REPs and absorption cross sections have been simulated using time-dependent wave packet propagation (TDWP) formalism to extract the ultrafast dynamics of LF within 50 fs after photoexcitation. The total internal reorganization energy is estimated to be 470 cm−1, which is clear evidence for the significant structural distortion in the excited state from that of the ground state. By comparing the excited state structural changes between S1 state and 265 nm excited state, we found that different molecular distortions occur following photoexcitation to those two different states. The total reorganization energy is obtained to be 1542 cm−1, in which the maximum contribution comes from the inertial response of water (1070 cm−1). Additionally, our simulation also yields an instantaneous response of the first solvation shell within an ultrafast timescale, τ ∼ 30 fs, following photoexcitation. The current study provides the basis for future investigations to determine the excited state properties of flavin compounds upon UV excitations.

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited-State Structural Dynamics of Uracil More than C6 Substituents.

Resonance Raman derived initial excited-state structural dynamics provide insight into the photochemical mechanisms of pyrimidine nucleobases, in which the photochemistry appears to be dictated by the C5 and C6 substituents. The absorption and resonance Raman spectra and excitation profiles of 5,6-dideuterouracil were measured to further test this photochemical dependence on the C5 and C6 substituents. The resulting set of excited-state reorganization energies of the observed internal coordinates were calculated and compared to those of other 5- and 6-substituted uracils. The results show that the initial excited-state dynamics along the C5C6 stretch responds to changes in mass at C5 and C6 in the same manner but that the in-plane bends at C5 and C6 are more sensitive to substituents at the C5 position than at the C6 position. In addition, the presence of two deuterium substituents at C5 and C6 decreases the initial excited-state structural dynamics along these in-plane bends, in contrast to what is observed in the presence of two CH3 groups on C5 and C6. The results are discussed in the context of DNA nucleobase photochemistry.

Initial excited-state structural dynamics of 6-substituted uracil derivatives: femtosecond angle and bond lengthening dynamics in pyrimidine nucleobase photochemistry.

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.

Initial excited-state dynamics of an N-alkylated indanylidene-pyrroline (NAIP) rhodopsin analog.

N-Alkylated indanylidene-pyrroline-based molecular switches mimic different aspects of the light-induced retinal chromophore isomerization in rhodopsin: the vertebrate dim-light visual pigment. In particular, they display a similar ultrashort excited-state lifetime, subpicosecond photoproduct appearance time, and photoproduct vibrational coherence. To better understand the early light-induced dynamics of such systems, we measured and modeled the resonance Raman spectra of the Z-isomer of the N-methyl-4-(5'-methoxy-2',2'-dimethyl-indan-1'-ylidene)-5-methyl-2,3-dihydro-2H-pyrrolium (NAIP) switch in methanol solution. It is shown that the data, complemented with a <70 fs excited-state trajectory computation, demonstrate initial excited-state structural dynamics dominated by double-bond expansion and single-bond contraction stretches. This mode subsequently couples with the five-membered ring inversion and double-bond torsion. These results are discussed in the context of the mechanism of the excited-state photoisomerization of NAIP switches in solution and the 11-cis retinal in rhodopsin.

Initial excited-state structural dynamics of 5,6-dimethyluracil from resonance Raman spectroscopy.

In order to understand the effect of methyl substitution patterns on the initial excited-state structural dynamics of uracil derivatives, we measured the resonance Raman spectra of 5,6-dimethyluracil (5,6-DMU). The results show that the resonance Raman spectrum is a combination of that of 5-methyl- and 6-methyluracil. The resonance Raman excitation profiles (RREPs) and absorption spectrum are simulated with a self-consistent, time-dependent formalism to yield the excited-state slopes and broadening parameters. The initial excited-state structural dynamics occur primarily along the C5═C6 stretching mode, as expected, but with lesser excited-state slopes along each mode compared to 5-methyluracil and 6-methyluracil. This study along with previous experiments with different uracil derivatives show that the presence and positions of the methyl groups seems to determine the partitioning of initial excited-state structural dynamics.

Initial Excited-State Structural Dynamics of Thymine Derivatives

Thymine is one of the pyrimidine nucleobases found in DNA. Upon absorption of UV light, thymine forms a number of photoproducts, including the cyclobutyl photodimer, the pyrimidine pyrimidinone [6-4] photoproduct and the photohydrate. Here, we use UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of the N(1)-substituted thymine derivatives N(1)-methylthymine, thymidine, and thymidine 5'-monophosphate in an effort to understand the role of the N1 substituent in determining the excited-state structural dynamics and the subsequent photochemistry. The UV resonance Raman spectrum of thymidine and thymidine 5'-monophosphate are similar to that of thymine, suggesting that large masses at N(1) effectively isolate the vibrations of the nucleobase. However, the UV resonance Raman spectrum of N(1)-methylthymine is significantly different, suggesting that the methyl group couples into the thymine ring vibrations. The resulting resonance Raman intensities and absorption spectra are self-consistently simulated with a time-dependent expression to quantitatively extract the initial excited-state slopes, homogeneous and inhomogeneous linewidths, and electronic parameters. These results are discussed in the context of the known photochemistry of thymine and its derivatives.

Mass-Tuned Initial Excited-State Structural Dynamics of DNA Nucleobases from UV Resonance Raman Spectroscopy: 5-Deuterouracil

5-Deuterouracil (5-d-U) is an analogue of uracil (RNA) and thymine (DNA), which differ only in the mass of their 5-substituent. Previous work has shown that the initial excited-state structural dynamics primarily lie along C5═C6 bond lengthening in thymine, while these dynamics primarily lie along C5 and C6 pyramidalization in uracil. To test whether the 5-substituent mass determines these dynamics, the resonance Raman spectra of 5-d-U, with a 5-substituent mass intermediate between uracil and thymine, is measured at wavelengths throughout its 262 nm absorption band. The resulting spectrum of 5-d-U is intermediate between that of thymine and uracil, indicating both bond-lengthening and pyramidalization motions in the excited state. Self-consistent analysis of the resonance Raman excitation profiles and absorption spectra show that the initial excited-state structural dynamics of 5-d-U are indeed intermediate between those of thymine and uracil, supporting the mass-tuning model of initial excited-state structural dynamics in DNA and RNA pyrimidine nucleobases.

Initial Excited-State Structural Dynamics of 2′-Deoxyguanosine Determined via UV Resonance Raman Spectroscopy

The resonance Raman spectra of 2'-deoxyguanosine, a DNA nucleoside, were measured in aqueous solution at wavelengths throughout its 260 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism with two electronic states yielded the initial excited-state structural dynamics in both states. The vibrational modes containing the N(7)═C(8) stretching and C(8)-H bending internal coordinates were found to exhibit significant initial structural dynamics upon photoexcitation to either state and are coincident with the photochemical reaction coordinate involving the formation of the 2'-deoxyguanosine cation radical.

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

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.

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

To explore the origin of the differences in UV photochemistry of uracil (RNA) and thymine (DNA) nucleobases, we have measured the UV resonance Raman spectra of uracil in aqueous solution at wavelengths throughout the lowest-energy absorption band and analyzed the resulting resonance Raman excitation profiles and absorption spectra using a time-dependent wave-packet formalism to obtain the initial excited-state structural changes. In contrast to thymine, which differs from uracil only by the presence of a methyl group at C(5), most of the resonance Raman intensity and resulting initial excited-state structural dynamics for uracil occur along in-plane hydrogen-bond angle deformation, ring stretching, and carbonyl vibrational modes. Weaker intensities and less significant structural dynamics are observed along the C=C stretching mode. These results suggest that the initial excited-state structural dynamics of uracil occur along a carbon pyramidalization coordinate. These dynamics are different from those of thymine, which distorts primarily along a C(5)=C(6) bond lengthening coordinate. These differences in initial excited-state structural dynamics can explain the different primary photoproducts observed for these two pyrimidine nucleobases.

Role of Ribose in the Initial Excited State Structural Dynamics of Thymidine in Water Solution: A Resonance Raman and Density Functional Theory Investigation

Resonance Raman spectra were obtained for thymidine and thymine with excitation wavelengths in resonance with the approximately 260 nm band absorption spectrum. The spectra indicate that the Franck-Condon (FC) region photodissociation dynamics of thymidine have multidimensional character with motion predominantly along the nominal C5=C6 stretch + C6-H bend nu17 (delta = 0.75, lambda = 468 cm(-1)), the nominal thymine ring stretch + C6-H bend + N1-C1, stretch nu29 (delta = 0.73, lambda = 363 cm(-1)), the nominal thymine ring stretch + C5-CH3/ N1-C1, stretch nu37 (delta = 0.69, lambda = 292 cm(-1)), and accompanied by the moderate and minor changes in the nu40, nu20 and nu23, nu55, nu60, nu61, nu63 modes. A preliminary resonance Raman intensity analysis was done, and these results for thymidine and thymine were compared to each other. The roles of ribose in the FC structure dynamics of thymidine were explored and the results were used to correlate to its lifetime constants tau1 and tau2 for two nonradiative decay channels. Spi/Sn conical intersection versus a distorted structure of Spi,min in the FC region was briefly discussed.

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

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

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

To explore the excited-state structural dynamics of thymine, a DNA nucleobase, we measured the resonance Raman spectra of thymine in aqueous solution at wavelengths throughout the lowest-energy absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yielded the excited-state structural dynamics. The photochemically relevant C=C stretching and C-H deformation vibrational modes were found to exhibit maximum resonance Raman intensity and structural change upon photoexcitation for thymine, suggesting that the initial dynamics of thymine lie along the photochemical reaction coordinate.