Analysis Of Resonance Raman Spectra Research Articles

Efficient simulation of resonance Raman spectra with tight-binding approximations to density functional theory.

Resonance Raman spectroscopy has long been established as one of the most sensitive techniques for detection, structure characterization, and probing the excited-state dynamics of biochemical systems. However, the analysis of resonance Raman spectra is much facilitated when measurements are accompanied by Density Functional Theory (DFT) calculations that are expensive for large biomolecules. In this work, resonance Raman spectra are therefore computed with the Density Functional Tight-Binding (DFTB) method in the time-dependent excited-state gradient approximation. To test the accuracy of the tight-binding approximations, this method is first applied to typical resonance Raman benchmark molecules, such as β-carotene, and compared to results obtained with pure and range-separated exchange-correlation functionals. We then demonstrate the efficiency of the approach by considering a computationally challenging heme variation. Overall, we find that the vibrational frequencies and excited-state properties (energies and gradients) that are needed to simulate the spectra are reasonably accurate and suitable for interpretation of experiments. We can therefore recommend DFTB as a fast computational method to interpret resonance Raman spectra.

Iodine staining as a useful probe for distinguishing insulin amyloid polymorphs

It is recently suggested that amyloid polymorphism, i.e., structural diversity of amyloid fibrils, has a deep relationship with pathology. However, its prompt recognition is almost halted due to insufficiency of analytical methods for detecting polymorphism of amyloid fibrils sensitively and quickly. Here, we propose that iodine staining, a historically known reaction that was firstly found by Virchow, can be used as a method for distinguishing amyloid polymorphs. When insulin fibrils were prepared and iodine-stained, they exhibited different colors depending on polymorphs. Each of the colors was inherited to daughter fibrils by seeding reactions. The colors were fundamentally represented as a sum of three absorption bands in visible region between 400 and 750 nm, and the bands showed different titration curves against iodine, suggesting that there are three specific iodine binding sites. The analysis of resonance Raman spectra and polarization microscope suggested that several polyiodide ions composed of I3− and/or I5− were formed on the grooves or the edges of β-sheets. It was concluded that the polyiodide species and conformations formed are sensitive to surface structure of amyloid fibrils, and the resultant differences in color will be useful for detecting polymorphism in a wide range of diagnostic samples.

Determination of the tautomeric composition of adenine in the gas phase by vibrational spectroscopy methods: II. Analysis of resonance Raman spectra

The resonance Raman spectra of adenine in the gas phase under excitation with laser radiation at wavelengths of 266, 218, and 200 nm have been investigated experimentally. The quantum-mechanical calculations of the intensity distribution in the resonance Raman spectra of three adenine tautomers are performed in the Herzberg-Teller approximation with the inclusion of the Duschinsky and frequency effects. Conclusions regarding the tautomeric composition of adenine in the gas phase are drawn from comparison of the results of quantum-mechanical calculations with experimental data.

Two Stereoisomers of Spheroidene in the Rhodobacter sphaeroides R26 Reaction Center: A DFT Analysis of Resonance Raman Spectra

From a theoretical analysis of the resonance Raman spectra of 19 isotopomers of spheroidene reconstituted into the reaction center (RC) of Rhodobacter sphaeroides R26, we conclude that the carotenoid in the RC occurs in two configurations. The normal mode underlying the resonance Raman transition at 1239 cm −1, characteristic for spheroidene in the RC, has been identified and found to uniquely refer to the cis nature of the 15,15′ carbon-carbon double bond. Detailed analysis of the isotope-induced shifts of transitions in the 1500–1550 cm −1 region proves that, besides the 15,15′- cis configuration, spheroidene in the RC adopts another cis-configuration, most likely the 13,14- cis configuration.

Quantum mechanical analysis of resonance Raman spectra of thymine

A direct quantum mechanical calculation of the relative intensities of lines in resonance Raman (RR) spectra of thymine was performed. The method of calculation is based on the adiabatic model in the Herzberg-Teller approximation. It is shown that the basic features of the intensity distribution in the spectra can be explained only by taking into account the vibronic mixing of electronic states and the contribution to the components of the scattering tensor from excited electronic states located close to the resonance state. The calculated results agree satisfactorily with experimental RR spectra of thymine excited by laser radiation at 266, 240, 218, and 200 nm. A comparative analysis of the intensity distribution in the RR spectra of thymine and uracil is carried out.

Theoretical analysis of Raman and resonance Raman spectra of simple bases of nucleic acids

A theoretical analysis of the intensity distribution in Raman and resonance Raman spectra of simple bases of nucleic acids was made. Calculations of wavenumbers and line intensities in the Raman spectra of uracil and its deuterated analogues were carried out using the classical scheme in the valence-force approximation. In contrast, the intensity distribution in the resonance Raman spectra of uracil excited by laser radiation of wavelength 266 and 240 nm was calculated using a quantum-mechanical method. In both types of spectra the theoretical data showed good agreement with experimental results. Two types of H-bonding in uracil were determined and the mechanism of H-bond formation is discussed. The electronic–vibrational interaction in uracil was shown to be significant. The quantum-mechanical method using the Herzberg–Teller approximation is suitable for the analysis of the resonance Raman spectra of simple bases of nucleic acids. Copyright © 2000 John Wiley & Sons, Ltd.

Raman spectral mapping of photo-oxidised polypropylene

Raman spectral mapping at a microscopic scale has been used to probe the heterogeneous photo-oxidation of unstabilised single particles and films of polypropylene (PP). Analysis of resonance Raman spectra in conjunction with SEM/EDX data allowed determination of the distribution of polymerisation catalyst residues throughout the polymer. However, the distribution of oxidation products was found not to correlate with the distribution of catalyst. Consequently, a conclusion was drawn that the catalyst residues, for the type of PP studied, tend to stabilise the polymer in the immediate vicinity, but also form reactive species that diffuse away from the catalyst to initiate oxidation

Excited-state geometries derived from the analysis of resonance Raman spectra. Example: state of 3,5-di-tert-butyl-o-benzoquinone

Resonance Raman spectra of 3,5-di-tert-butyl- o -benzoquinone were obtained by exciting its lowest 1 (π-π ∗ ) state. The resonance enhancement of two stretching modes (CC, CO) and of one CH bending mode was analyzed applying the Kramers-Heisenberg-Dirac relation. The mathematical fitting of the experimentally derived spectra yielded the magnitude of the Dushinsky mode mixing and the displacements of the potential curves along the considered normal modes. These displacements were transformed to bond-length changes with the use of the eigenvector matrix L of the ground-state vibrations. The excited-state geometry is characterized by the unsymmetric lengthening of the CC bonds within the acrolein subunits and a shortening of the CC bond inside the butadiene subsystem.

Theoretical analysis of resonance Raman spectra from the blue copper protein azurin

Using a time domain methodology, we have simulated low-temperature resonance Raman data from the blue copper protein azurin in an effort to determine an effective harmonic potential surface (relative to the ground-state geometry and normal coordinates) for the 600-nm transition of the blue copper active site. We find that utilization of overtone and combination intensities greatly facilitates the extraction of reliable parameter values. We are able in this manner to obtain accurate results for the linear displacements of the excited-state surface.

Quantitative analysis of resonance Raman spectra of purple membrane from Halobacterium halobium: L550 intermediate

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative analysis of resonance Raman spectra of purple membrane from Halobacterium halobium: L550 intermediatePramod V. Argade and Kenneth J. RothschildCite this: Biochemistry 1983, 22, 14, 3460–3466Publication Date (Print):July 5, 1983Publication History Published online1 May 2002Published inissue 5 July 1983https://doi.org/10.1021/bi00283a024RIGHTS & PERMISSIONSArticle Views52Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (869 KB) Get e-Alerts Get e-Alerts

Relative intensity of near resonance Raman lines evaluated by the A-term

A simple formulation is obtained for the relative intensities of near resonance Raman lines of different modes. The Raman intensity is evaluated by the A-term. Franck-Condon factors are calculated using the shift of the equilibrium molecular configuration during electronic excitation. This formulation is useful for the analysis of resonance Raman spectra.

Theoretical Analysis of Resonance Raman Spectra of Rhodopsin and Isorhodopsin

Resonance Raman (RR) Spectra of rhodopsin and isorhodopsin are theoretically analyzed and compared with those of free protonated retinylidene Schiff bases (PRSB). We used the multibond twisted chromophore conformations of rhodopsin and isorhodopsin which were previously obtained through the optical spectral analysis. The calculated frequencies and relative intensities of RR spectra of rhodopsin and isorhodopsin are almost similar to those for the corresponding free PRSB's. Furthermore the correlation between the frequencies ν's of normal modes and the maximum wavelength of the absorption λ is analyzed for the following three cases; a) torsion around a double bond, b) a counter-anion near N atom and c) an anion near C5 atom. As a result, the experimental fact that ν's of C=C stretchings decrease considerably as λ increases and those of C–C stretchings increase is best reproduced in case a). The frequency of C=N + H stretching shows drastic decrease in case b), but moderate decrease in cases a) and c) with increase of λ.

Resonance Raman spectroscopy in biochemistry and biology

Resonance Raman (RR) spectroscopy provides detailed information on the vibrational and electronic properties of biochemical and biological chromophores. The analysis of RR spectra, using for example model compounds or a group frequency approach, enables us to form an accurate structural picture of the chromophore in its natural biological site. Moreover, the insight gained into the electronic states of a biological chromophore can be crucial to our understanding of its function. Thus the RR technique represents a powerful means of eliciting precise structural and electronic data from a coloured species and of focusing upon key aspects of its function. It has even been possible to obtain RR spectra from some natural chromophores invivo, giving spectra detailed and informative enough to please a spectroscopist from a system complex enough to satisfy a biologist.