Excited-state structural dynamics of cytosine from resonance Raman spectroscopy

Cytosine, a nucleobase found in both DNA and RNA, is known to form photoproducts upon UV irradiation, damaging the nucleic acids and leading to cancer and other diseases. To determine the molecular mechanism by which these photoproducts occur, we have measured the resonance Raman spectra of cytosine at wavelengths throughout its 267 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yields both the excited-state structural changes and electronic parameters. From this analysis, we have been able to determine that, at most, 31% of the reorganization energy upon excitation is directed along photochemically relevant modes.     

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.     

Genetic engineering combined with deep UV resonance Raman spectroscopy for structural characterization of amyloid-like fibrils

Elucidating the structure of the cross-beta core in large amyloid fibrils is a challenging problem in modern structural biology. For the first time, a set of de novo polypeptides was genetically engineered to form amyloid-like fibrils with similar morphology and yet different strand length. Differential ultraviolet Raman spectroscopy allowed for separation of the spectroscopic signatures of the highly ordered beta-sheet strands and turns of the fibril core. The relationship between Raman frequencies and Ramachandran dihedral angles of the polypeptide backbone indicates the nature of the beta-sheet and turn structural elements.     

Direct detection of 8-oxo-deoxyguanosine using UV resonance Raman spectroscopy

8-oxo-deoxyguanosine (8-oxo-dG) is a major oxidative lesion in DNA and is responsible for mutation and cancer. Current techniques for detecting 8-oxo-dG are indirect methods. Thus, development of new methodologies is needed to directly detect such oxidative lesions. In this article, we have used ultraviolet resonance Raman (UVRR) spectroscopy as a novel analytical technique for the detection of 8-oxo-dG. Here, the UVRR spectrum of 8-oxo-dG was acquired and compared to that of deoxyguanosine (dG) and deoxyadenosine (dA). Data analysis shows a distinct UVRR spectrum of 8-oxo-dG with characteristic peaks. Detection of 8-oxo-dG was easily achieved from a mixture with dG. These results reveal that UVRR spectroscopy shows promise as a direct method for detecting 8-oxo-dG.     

Direct observation of excited-state dynamics by hot UV absorption spectroscopy after IR multiphoton excitation

Fluoroethylcycloheptatriene has been irradiated by pulses from a TEA CO₂ laser. During and after the pulses, the hot UV absorption of the excited molecules was monitored. At very low gas pressures, time-resolved observation of the rate of unimolecular isomerization of the excited molecules was possible. By adding collision partners, stepwise collisional deactivation of excited molecules was also observed. By analysis of the transient spectra, the intra- and inter-molecular dynamics of the excited molecules was found to be quantitatively consistent with data from single-photon excitation experiments. The dependence of the observed dynamics on the laser fluence is demonstrated.     

Understanding excited-state structure in metal polypyridyl complexes using resonance Raman excitation profiles,time-resolved resonance Raman spectroscopy and density functional theory

This article discusses the use of Raman spectroscopy, in concert with density functional theory, as a strategy for understanding excited-state structure in metal polypyridyl complexes. The first sections of the article discuss how one can use resonance Raman spectra of the ground-state molecule to understand the resonant Franck-Condon excited state. The theories behind these analyses are based on the sum-over-states and time-dependent approaches; a brief introduction to each of these methods is given. The use of density functional theory and its use in the determination of normal modes of vibration and infrared and Raman band intensities are discussed, with reference to a number of recent papers. The application of these methods is illustrated through the analysis of a number of selected examples which exemplify the strategies used to extract data from probing the Franck-Condon region. These data include the displacements of the resonant excited state with respect to the electronic ground state, the reorganisation energies associated with photoexcitation, bond length changes with excitation and other electronic parameters. The use, and limitations, of these methods are discussed. The direct calculation of resonance Raman band intensities is introduced. The direct measurement of excited-state vibrational spectra through time-resolved methods is discussed in the latter section of the article; with particular regard to the use of transient resonance Raman and time-resolved resonance Raman techniques to probe structural changes in metal polypyridyl complexes.     

Ultrafast dynamics of myoglobin probed by time-resolved resonance Raman spectroscopy

Recent experimental work carried out in this laboratory on the ultrafast dynamics of myoglobin (Mb) is summarized with a stress on structural and vibrational energy relaxation. Studies on the structural relaxation of Mb following CO photolysis revealed that the structural change of heme itself, caused by CO photodissociation, is completed within the instrumental response time of the time-resolved resonance Raman apparatus used (approximately 2 ps). In contrast, changes in the intensity and frequency of the iron-histidine (Fe-His) stretching mode upon dissociation of the trans ligand were found to occur in the picosecond regime. The Fe-His band is absent for the CO-bound form, and its appearance upon photodissociation was not instantaneous, in contrast with that observed in the vibrational modes of heme, suggesting appreciable time evolution of the Fe displacement from the heme plane. The band position of the Fe-His stretching mode changed with a time constant of about 100 ps, indicating that tertiary structural changes of the protein occurred in a 100-ps range. Temporal changes of the anti-Stokes Raman intensity of the v4 and v7 bands demonstrated immediate generation of vibrationally excited heme upon the photodissociation and decay of the excited populations, whose time constants were 1.1 +/- 0.6 and 1.9 +/- 0.6 ps, respectively. In addition, the development of the time-resolved resonance Raman apparatus and prospects in this research field are described.     

Emission spectroscopy and excited-state dynamics of chromyl-chloride vapor

A tunable dye laser has been used to excite single vibronic features in the low-pressure vapor of CrO₂Cl₂. The fluorescence spectrum, fluorescence excitation spectrum and time-resolved fluorescence decay are discussed. It is shown that the active ν′₄ and ν″₄ modes are the same frequency in the gas phase, thus collapsing the sequence congestion normally observed in gas-phase spectra. This degeneracy makes impossible the excitation of single vibronic levels. It is shown that the fluorescence lifetime of the excited state in all except the vibrationally cold level is severely shortened by unimolecular radiationless decay. This radiationless rate is strongly dependent upon the partitioning of energy into various excited-state modes. The radiative lifetime of the vibrationally cold excited state is (1.34 ± 0.08) μs and the apparent bimolecular quenching rate is (5.9 ± 0.2) × 10^?10 cm³/molecules. No evidence of emission from the lowest-energy excited electronic state recently reported by Spoliti [J. Mol. Spectrosc. 52 (1973) 146] is observed.     

Photodecay dynamics of octaethylporphine in the condensed phase explored via resonance Raman spectroscopy and density functional theory calculation

Resonance Raman spectra of free-base octaethylporphine (OEP) were obtained with 368.9 nm, 397.9 nm and 416.0 nm excitation wavelengths, and density functional calculations were done to help the elucidation of Soret (B(x) and B(y)-band) electronic transitions and the corresponding photo relaxation dynamics of OEP. The RRs indicate that the Franck-Condon region photo relaxation dynamics upon S(0)→S(8) electronic transition is predominantly along the totally symmetric C(m)C(α) stretch, the C(β)C(β) stretch, and simultaneously along the asymmetric δ(pyr deformation),γ(CH(2)) vibrational relaxation processes. The excited state structural dynamics of OEP determined from resonance Raman spectra show that the internal conversion between B(y) and B(x) electronic states occurs in tens of femtoseconds and the electronic relaxation dynamics were firstly interpreted with account of the time-dependent wave packet theory and Herzberg-Teller (vibronic coupling) contributions.     

Molecular dynamics of liquid acetone determined by depolarized Rayleigh and low-frequency Raman scattering spectroscopy

Slow to ultrafast dynamics of liquid acetone at variable temperature was investigated by depolarized Rayleigh and low-frequency Raman scattering spectroscopy, in the region 0-200 cm(-1). A detailed analysis was performed on the spectra and corresponding time responses, and a consistent view of the molecular dynamics of this dipolar solvent was obtained. The effects of temperature on the spectra were interpreted, and distinct dynamical processes identified. At very low frequencies, or long time scales, acetone dynamics is characterized by a slow diffusive reorientation obeying the Stokes-Einstein-Debye hydrodynamic theory only in the limit of subslip boundary conditions. An alternative model based on the microviscosity concept proved to be able to reproduce this correlation time and its temperature dependence. A comparative analysis of collective and single-molecule reorientational times, these latter estimated from intramolecular Raman spectra, led to an orientational correlation parameter g(2) of unity, which denotes a statistical disorder of molecular polarizability tensors. A fast local restructuring process is putatively responsible for an additional contribution at subpicosecond time scales often referred to as intermediate response in other molecular liquids. The high frequency portion of the dynamical susceptibility showed the signature of librational intermolecular motions, giving rise to an ultrafast decay of the time correlation function of polarizability anisotropy. The overall approach, which provided valuable information on dynamics, structure and molecular interactions of neat acetone, will be applied to acetone electrolytic solutions.     

Structure and dynamics of the solvated electron in alcohols from resonance Raman spectroscopy

Resonance Raman (RR) spectroscopy is used to probe the structure and excited-state dynamics of the solvated electron in the primary liquid alcohols methanol (MeOH), ethanol (EtOH), n-propanol (n-PrOH), and n-butanol (n-BuOH). The strong resonance enhancements (>or=10(4) relative to pure solvent) of the libration, CO stretch, COH bend, CH3 bend, CH2 bend, and OH stretch reveal significant Franck-Condon coupling of the intermolecular and intramolecular vibrational modes of the solvent to the electronic excitation of the solvated electron. All enhanced bands are fully accounted for by a model of the solvated electron that is comprised of several nearby solvent molecules that are only perturbed by the presence of the electron; no new molecular species are required to explain our data. The 340 cm(-1) downshift observed for the OH stretch frequency of e-(MeOH), relative to pure solvent, strongly suggests that the methanol molecules in the first solvent shell have the hydroxyl group directed linearly toward the excess electron density. The smaller downshifts observed for e-(EtOH), e-(n-PrOH), and e-(n-BuOH) are explained in terms of a OH group that is bent 28-40 degrees from linear. The Raman cross sections and absorption spectra are modeled, lending quantitative support for the inhomogeneous origin of the broad absorption spectra, the necessity of OH local motion in all enhanced Raman modes of the alcohols, and the dominant librational response of the solvent upon photoexcitation of the electron.     

Probing the interaction between prostacyclin synthase and prostaglandin H2 analogues or inhibitors via a combination of resonance Raman spectroscopy and molecular dynamics simulation approaches

In an aim to probe the structure-function relationship of prostacyclin synthase (PGIS), resonance Raman (RR) spectroscopy and molecular dynamic (MD) simulation approaches have been exploited to characterize the heme conformation and heme-protein matrix interactions for human PGIS (hPGIS) and zebrafish PGIS (zPGIS) in the presence and absence of ligands. The high-frequency RR (1300-1700 cm(-1)) indicates that the heme group is in the ferric, six-coordinate, low-spin state for both resting and ligand-bound hPGIS/zPGIS. The low-frequency RR (300-500 cm(-1)) and MD simulation reveal a salient difference in propionate-protein matrix interactions between hPGIS and zPGIS, as evident by a predominant propionate bending vibration at 386 cm(-1) in resting hPGIS, but two vibrations near 370 and 387 cm(-1) in resting zPGIS. Upon binding of a substrate analogue (U46619, U51605, or U44069), both hPGIS and zPGIS induce a distinctive perturbation of the propionate-protein matrix interactions, resulting in similar Raman shifts to ~381 cm(-1). On the contrary, the bending vibration remains unchanged upon binding of inhibitor/ligand (minoxidil, clotrimazole, or miconazole), indicating that these inhibitors/ligands do not interfere with the propionate-protein matrix interactions. These results, together with subtle changes in vinyl bending modes, demonstrate drastically different RR shifts with heme conformational changes in both hPGIS and zPGIS upon different ligand bindings, suggesting that PGIS exhibits a ligand-specific heme conformational change to accommodate the substrate binding. This substrate-induced modulation of the heme conformation may confer high product fidelity upon PGIS catalysis.     

Analytical applications of ultraviolet resonance Raman spectroscopy

UV resonance Raman spectroscopy (UVRR) is a new analytical technique with a unique selectivity which is capable of speciating individual analytes in complex samples. The new instrumentation is discussed as are applications of this technique to studies of polycyclic aromatic hydrocarbons (PAHs) in coal liquids and in tissue. UVRR can also be used to speciate PAHs eluting from high-performance liquid chromatography columns. Other applications to studies of protein structure are also described.     

Evolution of quantitative methods in protein secondary structure determination via deep-ultraviolet resonance Raman spectroscopy

Deep-ultraviolet resonance Raman (DUVRR) spectra is sensitive to secondary structural motifs but, similar to circular dichroism (CD) and infrared spectroscopy, requires the application of multivariate and advanced statistical analysis methods to resolve the pure secondary structure Raman spectra (PSSRS) for determination of secondary structure composition. Secondary structure motifs are selectively enhanced by different excitation wavelengths, a characteristic that inspired the first methods for quantifying secondary structures by DUVRR. This review traces the evolution of multivariate methods and their application to secondary structure composition analyses of proteins by DUVRR spectroscopy from the first experiments using two-wavelengths, and culminating with recent studies utilizing time-resolved DUVRR measurements.     

Inclusions of black-green serpentine jade determined by Raman spectroscopy

This work aims to determine the formation mechanism as well as the major mineral and inclusions of black-green serpentine jade by Raman spectroscopy. Scanning electron microscopy with energy-dispersive spectrometry was used to analyze the chemical composition of the inclusions and major mineral. The major mineral of black-green serpentine jade was antigorite, and the inclusions were actinolite, chlorite, calcite, quartz, magnetite, and goethite. Jade quality was preliminarily evaluated based on the area ratio of antigorite to the inclusions by optical microscopy. Formation mechanism of black-green serpentine jade was inferred based on the analysis of the inclusions, which demonstrated a new application of Raman spectroscopy in mineralogy.     

Vibrational and vibronic processes in coherent 2D resonance Raman spectroscopy

Coherent 2D resonance Raman spectroscopy is a multidimensional technique that is capable of separating and sorting peaks that appear heavily congested and disordered in conventional 1D spectra. It can sort rovibrational peaks according to rotational and vibrational quantum number, vibrational sequence, and rotational selection rule. New results suggest that pattern recognition methods can also be used to determine whether the highly detailed rovibrational information is coming from the ground electronic state or the excited electronic state. This capability is demonstrated using experimental results from I(2) and C(2).     

The dushinsky effect in resonance Raman spectroscopy

The effect of normal-coordinate rotation on resonance Raman excitation profiles and depolarization dispersion curves is investigated theoretically for two nontotally symmetric modes of the same symmetry.     

Fast Raman spectroscopy of cytochrome c using intracavity resonance Raman amplification

The resonance Raman spectrum of cytochrome c (5 × 10^?4 M) was obtained using the method of resonance Raman amplification (RRA) in a dye laser resonator in 30 ns. The second harmonic of a Q-switched Nd glass laser was used as an excitation source and the spectra were recorded using a photographic plate.     

Tuning of switching properties and excited-state dynamics of fulgides by structural modifications

The ultrafast photo-induced dynamics of the E-isomers of four selected photochromic fulgides with distinct structural motifs have been elucidated by femtosecond broadband transient absorption spectroscopy in n-hexane as solvent. E→C and E→Z isomerisations, respectively, with time constants of ～0.12 ± 0.02 ps and ～0.34 ± 0.03 ps taking place in parallel were found for derivatives with a methyl substituent at the central hexatriene (HT) unit. In contrast, fulgides with increased steric constraints by an iso-propyl substituent or by intramolecular bridging displayed virtually zero E→Z isomerisation, but instead a desired accelerated and more efficient ring closure in a reaction time of only ～50 ± 10 fs. Both photoisomerisations appear to follow excited-state pathways with distinctive conical intersections. For the ring closure, direct barrierless pathways with steep downhill gradients are likely. Furthermore, the results indicate conformer-specific reactions, with ring closure exclusively by the E(α) conformer and E→Z isomerisation predominantly by the E(β) conformer, because the E(α)→Z channel is unfavoured by the faster and kinetically more competitive E(α)→C reaction. DFT calculations of the equilibrium structures showed that the sterically demanding groups at the HT unit shift the conformer equilibria towards the E(α) conformers. At the same time, they appear to cause a favourable pre-orientation of the furyl unit that accelerates the conrotatory ring closure in the E(α)→C reaction. Benzo-annulation of the furyl unit has little effect on the observed dynamics. Overall, the results demonstrate how the excited-state dynamics and thereby the photoswitching properties of fulgides can be successfully tuned and improved by structural modifications at the chromophores.     

Structural analysis of lignin by resonance Raman spectroscopy

Resonance Raman (RR) spectroscopy, combined with Kerr gated fluorescence rejection in the time domain, has recently elucidated lignin structure with unique sensitivity and selectivity. This promises structural studies of fluorescent natural macromolecules, such as lignin, which were previously not possible. Such studies rely on an improved understanding of the RR spectral behavior of lignin, which is today scarcely understood. We explain for the first time this behavior by a semi-empirical theory, and observe its pertinent features for lignin in vascular plants. We have used well-defined oxidative treatments as means of probing lignin structural elements, and show that RR sensitivity and selectivity depend crucially on excitation wavelength. Through the theory we relate these results to basic structural aspects of lignin. Spectra obtained by blue light laser excitation (400 nm) are dominated by low redox potential syringyl lignin groups, whereas lower photon energy (500 nm) decreases the selectivity markedly. RR bands depend on molecular structure but also on molecular environment. Thus charge transfer donor-acceptor interactions within lignin reduce the intensity of bands associated with electron rich moieties. New possibilities for basic and selective structural information on fluorescent natural materials, such as lignin, have thus appeared.