Resonance Raman Analysis Research Articles

Resonance Raman analysis of nonlinear solvent dynamics: Betaine-30 in ethanol

Resonance Raman profiles for 14 vibrational modes of betaine-30 in ethanol at room temperature were measured at wavelengths within the first charge-transfer absorption band. The absorption spectrum and resonance Raman profiles were analyzed using time-dependent theory and a Brownian oscillator model modified to account for nonlinear solvent response; i.e., dependence of the solvent reorganization energy on the electronic state of the solute. As in our previous study of betaine-30 in acetonitrile, the solvent reorganization energy for the excited electronic state, determined from resonance Raman spectroscopy, was found to be smaller than that for the ground electronic state, determined from the absorption spectrum. The mode-dependent internal reorganization energies of betaine-30 in ethanol were found to be slightly larger than those of betaine-30 in acetonitrile. Temperature-dependent solvent reorganization energies for the ground electronic state were determined from analysis of the absorption line shape from 279 to 332 K and were found to decrease with increasing temperature. The influence of hydrogen bonding on the solvent and internal reorganization energy of betaine-30 is considered, and the physical basis for nonlinear solvent response is discussed.

Carotenoid Specificity of Light-harvesting Complex II Binding Sites: OCCURRENCE OF 9-CIS-VIOLAXANTHIN IN THE NEOXANTHIN-BINDING SITE IN THE PARASITIC ANGIOSPERM CUSCUTA REFLEXA

The parasitic angiosperm Cuscuta reflexa has a highly unusual carotenoid composition in that it does not contain neoxanthin, an otherwise ubiquitous component of the major light-harvesting complex protein (LHCIIb) in all other higher plant species studied to date. Combined HPLC and mass spectrometric analysis has enabled us to detect in tissues of C. reflexa two new types of xanthophylls: lutein-5,6-epoxide and 9-cis-violaxanthin. We have isolated the LHCIIb complex from thylakoids and analyzed chlorophyll and carotenoid composition. The data show that the 9-cis-violaxanthin is present in amounts similar to that of neoxanthin in most plants. On the other hand, lutein-5,6-epoxide was found to be in substoichiometric quantities, suggesting a peripheral location similar to the loosely-associated all-trans-violaxanthin and also enabling suitable accessibility for the de-epoxidase (VDE). Absorption spectroscopy revealed close similarities of the excited state energies of neoxanthin and 9-cis-violaxanthin in vitro and in intact LHCIIb complex. Resonance Raman analysis clearly indicates a cis conformation of violaxanthin in the complex, confirming the pigment analysis data and proving that not only does violaxanthin replace neoxanthin as an intrinsic component of LHCIIb in C. reflexa but it also adopts the same 9-cis conformation of neoxanthin. These results suggest that the N1 binding site of LHCIIb preferentially binds 9-cis-5,6-epoxy carotenoids, which has implications for the features of this binding site and its role in the photosystem II antenna assembly and stability.

Resonance Raman and Ligand-Binding Analysis of the Oxygen-Sensing Signal Transducer Protein HemAT from Bacillus subtilis

Resonance Raman and Ligand-Binding Analysis of the Oxygen-Sensing Signal Transducer Protein HemAT from Bacillus subtilis

Characterization of an Fe III-OOH species and its decomposition product in a bleomycin model system.

To model the mononuclear Fe(III)-OOH species identified in the catalytic cycle of the anticancer drug bleomycin, the iron chemistry of the pentadentate ligand N-[bis(2-pyridylmethyl)aminoethyl]pyridine-2-carboxamide (H-PaPy(3)) has been investigated. The complex [Fe(III)(PaPy(3))OCH(3)](ClO(4)) was reacted with H(2)O(2) to form a red species (lambda(max)=480 nm, epsilon=1800 M(-1) cm(-1)) with an S=1/2 EPR signal at g=2.25, 2.17, and 1.95. This species has been identified by electrospray ionization mass spectrometry as [Fe(III)(PaPy(3))OOH](ClO(4)) and further characterized by resonance Raman and EXAFS analysis. The decomposition of this intermediate leads to the modification of the ligand, as revealed by (1)H NMR. One hydrogen atom is substituted by a solvent-derived methoxy group. The substitution at this site is a result of the two-electron oxidation of the ligand following the heterolytic cleavage of the O-O bond of the Fe(III)-OOH species. This is a plausible mechanism to rationalize related ligand modifications that have been proposed in the decay of activated bleomycin.

Excited Singlet (S1) State Resonance Raman Analysis of N,N,N‘,N‘-Tetramethylbenzidine and N,N,N‘,N‘-Tetramethyl-p-phenylenediamine

Vibrational data on the first excited singlet state (S 1 ) of N,N,N',N'-tetramethylbenzidine (TMB) and N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) have been obtained by using picosecond time-resolved Raman spectroscopyfor different isotopic derivatives and for the N,N,N',N'-tetraethyl analogues, TEB and TEPD. Reliable vibrational assignments are proposed. On this basis, the S 1 state structure and electronic configuration of these diamines are discussed and compared with the results previously reported for the ground state, the lowest excited triplet state, and the radical cation species.

Differences in changes of the alpha1-beta2 subunit contacts between ligand binding to the alpha and beta subunits of hemoglobin A: UV resonance raman analysis using Ni-Fe hybrid hemoglobin.

The alpha1-beta2 subunit contacts in the half-ligated hemoglobin A (Hb A) have been explored with ultraviolet resonance Raman (UVRR) spectroscopy using the Ni-Fe hybrid Hb under various solution conditions. Our previous studies demonstrated that Trpbeta37, Tyralpha42, and Tyralpha140 are mainly responsible for UVRR spectral differences between the complete T (deoxyHb A) and R (COHb A) structures [Nagai, M., Wajcman, H., Lahary, A., Nakatsukasa, T., Nagatomo, S., and Kitagawa, T. (1999) Biochemistry, 38, 1243-1251]. On the basis of it, the UVRR spectra observed for the half-ligated alpha(Ni)beta(CO) and alpha(CO)beta(Ni) at pH 6.7 in the presence of IHP indicated the adoption of the complete T structure similar to alpha(Ni)beta(deoxy) and alpha(deoxy)beta(Ni). The extent of the quaternary structural changes upon ligand binding depends on pH and IHP, but their characters are qualitatively the same. For alpha(Ni)beta(Fe), it is not until pH 8.7 in the absence of IHP that the Tyr bands are changed by ligand binding. The change of Tyr residues is induced by binding of CO, but not of NO, to the alpha heme, while it was similarly induced by binding of CO and NO to the beta heme. The Trp bands are changed toward R-like similarly for alpha(Ni)beta(CO) and alpha(CO)beta(Ni), indicating that the structural changes of Trp residues are scarcely different between CO binding to either the alpha or beta heme. The ligand induced quaternary structural changes of Tyr and Trp residues did not take place in a concerted way and were different between alpha(Ni)beta(CO) and alpha(CO)beta(Ni). These observations directly indicate that the phenomenon occurring at the alpha1-beta2 interface is different between the ligand binding to the alpha and beta hemes and is greatly influenced by IHP. A plausible mechanism of the intersubunit communication upon binding of a ligand to the alpha or beta subunit to the other subunit and its difference between NO and CO as a ligand are discussed.

A Comparative Resonance Raman Analysis of Heme-Binding PAS Domains: Heme Iron Coordination Structures of the BjFixL, AxPDEA1, EcDos, and MtDos Proteins,

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionA Comparative Resonance Raman Analysis of Heme-Binding PAS Domains: Heme Iron Coordination Structures of the BjFixL, AxPDEA1, EcDos, and MtDos Proteins,Takeshi Tomita, Gonzalo Gonzalez, Alan L. Chang, Masao Ikeda-Saito, and Marie-Alda Gilles-GonzalezCite this: Biochemistry 2002, 41, 20, 6572Publication Date (Web):April 23, 2002Publication History Published online23 April 2002Published inissue 1 May 2002https://doi.org/10.1021/bi025159yCopyright © 2002 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views229Altmetric-Citations-LEARN 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 (7 KB) Get e-Alerts Get e-Alerts

Time-resolved resonance Raman analysis of chromophore structural changes in the formation and decay of rhodopsin's BSI intermediate.

Time-resolved resonance Raman microchip flow experiments are performed to obtain the vibrational spectrum of the chromophore in rhodopsin's BSI intermediate and to probe structural changes in the bathorhodopsin-to-BSI and BSI-to-lumirhodopsin transitions. Kinetic Raman spectra from 250 ns to 3 micros identify the key vibrational features of BSI. BSI exhibits relatively intense HOOP modes at 886 and 945 cm(-1) that are assigned to C(14)H and C(11)H=C(12)H A(u) wags, respectively. This result suggests that in the bathorhodopsin-to-BSI transition the highly strained all-trans chromophore has relaxed in the C(10)-C(11)=C(12)-C(13) region, but is still distorted near C(14). The low frequency of the 11,12 A(u) HOOP mode in BSI compared with that of lumirhodopsin and metarhodopsin I indicates weaker coupling between the 11H and 12H wags due to residual distortion of the BSI chromophore near C(11)=C(12). The C=NH(+) stretching mode in BSI at 1653 cm(-1) exhibits a normal deuteriation induced downshift of 23 cm(-1), implying that there is no significant structural rearrangement of the Schiff base counterion region in the transition of bathorhodopsin to BSI. However, a dramatic Schiff base environment change occurs in the BSI-to-lumirhodopsin transition, because the 1638 cm(-1) C=NH(+) stretching mode in lumirhodopsin is unusually low and shifts only 7 cm(-1) in D(2)O, suggesting that it has essentially no H-bonding acceptor. With these data we can for the first time compare and discuss the room temperature resonance Raman vibrational structure of all the key intermediates in visual excitation.

Solvent effects on ground and excited electronic state structures of p-nitroaniline

Resonance Raman intensities of p-nitroaniline, a prototypical “push–pull” chromophore with a large first hyperpolarizability (β), have been measured in dilute solution in five solvents having a wide range of polarities (cyclohexane, 1,4-dioxane, dichloromethane, acetonitrile, and methanol) at excitation wavelengths spanning the strong near-ultraviolet charge-transfer absorption band. The absolute Raman excitation profiles and absorption spectra are simulated using time-dependent wave packet propagation techniques to determine the excited-state geometry changes along the five or six principal Raman-active vibrations as well as estimates of the solvent reorganization energies. The total vibrational reorganization energy decreases and the solvent reorganization energy increases with increasing solvent polarity in all solvents except methanol, where specific hydrogen-bonding interactions may be important. The dimensionless normal coordinate geometry changes obtained from the resonance Raman analysis are converted to actual bond length and bond angle changes with the aid of normal mode coefficients from a ground-state density functional theory calculation. The geometry changes upon electronic excitation involve predominantly the Cphenyl–Nnitro, N–O, and phenyl C2–C3 bond lengths, with little involvement of the amino group. Nonresonant Raman spectra in 1,4-dioxane, dichloromethane, ethyl acetate, acetone, acetonitrile, and methanol show only a very small solvent dependence of the vibrational frequencies. This suggests that changing the solvent affects the excited state more than the ground state, calling into question two-state models that treat the ground and charge-transfer excited states as linear combinations of neutral and zwitterionic basis states with solvent dependent coefficients.

UV resonance Raman detection and quantitation of domoic acid in phytoplankton.

Cultures of the phytoplankton diatom, Pseudonitzschia multiseries, have been harvested under controlled growth conditions ranging from late logarithmic to late stationary phase (17-58 days). The amount of domoic acid (DA) present in the growth media and in the homogenized cells has been determined by HPLC. Defined samples of media, homogenized cells, whole cells, and whole cells in media have been laser excited at 251 nm for the purpose of selectively exciting intense UV resonance Raman spectra from DA in the samples. Neither media nor cell component spectra from algae seriously interfere with DA spectra. The spectral cross sections for the dominant 1652-cm-1 mode of DA have been determined for 242-, 251-, and 257-nm excitation. Maximum sensitivities are achieved with 251-nm excitation because cross sections for DA are a maximum, and interference from other algal components becomes very small. DA concentrations that have been determined with 251-nm excitation by resonance Raman methods correlate closely with values determined independently with HPLC, especially at higher DA concentrations. The UV resonance Raman analysis of DA in phytoplankton algae is shown to be very sensitive and quantitative as well as rapid and nonintrusive.

1F1715 近位軸配位子がFe-CO振動に及ぼす影響 : 共鳴ラマン法によるシトクロムb562多重変異体の解析

1F1715 近位軸配位子がFe-CO振動に及ぼす影響 : 共鳴ラマン法によるシトクロムb562多重変異体の解析

Suicide inactivation of cytochrome c oxidase: catalytic turnover in the absence of subunit III alters the active site.

The catalytic core of cytochrome c oxidase is composed of three subunits: I, II, and III. Subunit III is a highly hydrophobic membrane protein that contains no redox centers; its role in cytochrome oxidase function is not obvious. Here, subunit III has been removed from the three-subunit mitochondrial-like oxidase of Rhodobacter sphaeroides by detergent washing. The resulting two-subunit oxidase, subunit III (-), is highly active. Ligand-binding analyses and resonance Raman spectroscopy show that its heme a(3)-Cu(B) active site is normal. However, subunit III (-) spontaneously and irreversibly inactivates during O(2) reduction. At pH 7.5, its catalytic lifetime is only 2% that of the normal oxidase. This suicide inactivation event primarily alters the active site. Its ability to form specific O(2) reduction intermediates is lost, and CO binding experiments suggest that the access of O(2) to reduced heme a(3) is inhibited. Reduced heme a accumulates in response to a decrease in the redox potential of heme a(3); electron transfer between the hemes is inhibited. Ligand-binding experiments and resonance Raman analysis show that increased flexibility in the structure of the active site accompanies inactivation. Cu(B) is partially lost. It is proposed that suicide inactivation results from the dissociation of a ligand of Cu(B) and that subunit III functions to prevent suicide inactivation by maintaining the structural integrity of the Cu(B) center via long-range interactions.

Influence of the working electrode metal on the polythiophene structure. Raman and x-ray photoelectron spectroscopic investigations of the aluminium/polythiophene interface

Polythiophene films of different thicknesses were obtained by electrochemical polymerization of thiophene on to oxidizable (Zn, Fe and Al) and noble (Pt) metals. Resonance Raman and x-ray photoelectron analyses indicated, on the one hand, a better structural organization of the films synthesized on to Zn, Fe and Al in comparison with those deposited on to Pt and, on the other hand, an increase in disorder with the film thickness for each metal. In the case of Al electrodes, on the basis of experimental data, it was suggested that during the first stages of electropolymerization, interactions between Al and Cα atoms occur at the interface and lead to the formation of real covalent bonds between the metal and the organic coating. This, in part, could explain the strong adhesion of the polymer on the electrode surface, its significant thermal stability towards the laser local heating and the enhancement of the Raman intensity. © 1998 John Wiley & Sons, Ltd.

Resonance Raman analysis of a fluorescently labeled oligonucleotide forming a very stable hairpin

An oligodeoxynucleotide has been synthesized, which mimics an ``antigene'' oligonucleotide with a polypyrimidic stretch on its 5′ side and is protected on its 3′ side against nucelases by a naturally forming and very stable hairpin, 5′GCGAAGC3′. The in vitro degradation of the resulting oligonucleotide d(5′TTCTCGCGAAGC3′) has already been studied by fluorescence resonance energy transfer (FRET) (Refregiers et al. 1996, J Biomol Struct Dyn 14: 365 – 371). The technique required the grafting of fluorophores at both ends of the oligonucleotide. In the present work we have compared the hairpin formed in the presence and in the absence of such fluorophores. This was achieved by the study of the Raman spectra (excitation at 257 nm) of the oligodeoxynucleotides H, which forms the hairpin (5′TTCTCGCGAAGC3′), and a con-trol C (5′TTCTCCGGAAGC3′) which is unable to form the hairpin. Resonance Raman spectroscopy with 257 nm excitation greatly favors the resonance of purines and therefore the study of the 3′ part of the oligonucleotides. The difference spectrum obtained from resonance Raman spectra of C and H showed marker peaks specific for hairpin formation. The search for these marker peaks in difference spectra involving the Raman spectrum of H labeled by fluorophores and either C or H proved that the fluorophores do not modify the structure of the hairpin but only the vibrations of the two terminal bases on which the fluorophores are grafted. The use of such labeling is then justified in order to allow oligonucleotides protected by a hairpin on their 3′ side to be studied by fluorescence spectroscopy.

Resonance Raman, Infrared, and Normal Coordinate Analysis of Free-Base Tetraphenylbacteriochlorin: A Model for Bacteriopheophytins

Resonance Raman (RR) and FT-IR spectra are reported for free-base tetraphenylbacteriochlorin and its pyrrole-15N4, β-D8, meso-13C4, and phenyl-D20 isotopomers. A normal mode analysis is carried out in order to assign observed RR and IR modes, using a NiTPP-based force field, with bond-distance scaling of force constants and the introduction of long-range interaction constants. The modes correlate well with those of NiTPP, once due allowance is made for direct effects of pyrrole ring reduction: inequivalent Cβ−Cβ and Cα−Cβ bonds and extra Cβ−H bending modes. Although the Cα−Cm and Cα−N bonds of the 16-membered inner ring are not strictly equivalent, there is little tendency for mode localization with respect to these bonds. The absence of a central metal lowers the frequencies of Cα−Cm stretching and pyrrole translational modes. The RR enhancement pattern is quite different than for porphyrins. Totally symmetric modes dominate spectra in resonance with the Qx band, due to a larger transition moment than in porphyrins, while non-totally symmetric modes are strongly enhanced in the region of the close-lying Bx and By transitions, reflecting vibronic coupling between them.

Resonance Raman analysis of charge-transfer reorganization energies in a covalent dicyanoethylene-aza-adamantane

Resonance Raman cross sections have been measured for a covalent electron donor-acceptor substituted aza-adamantane. Excitation near the maximum of the strong charge-transfer absorption results in resonance enhancement of a number of Raman fundamentals, overtones, and combination bands. The reorganization energy in each molecular mode and the solvent contribution to the electronic linewidth are determined through quantitative modeling of the absorption, Raman, and fluorescence spectra, which are sensitive to solvent dynamics on different time scales. The results suggest that the solvent-induced broadening in methanol has components that fluctuate on a wide range of timescales.

Resonance raman analysis of chromophore structure in the lumi-R photoproduct of phytochrome.

Resonance Raman vibrational spectra of the Pr, lumi-R, and Pfr forms of phytochrome have been obtained using low-temperature trapping and room temperature flow techniques in conjunction with shifted-excitation Raman difference spectroscopy (SERDS). The Pr to lumi-R photoconversion exhibits a thermal barrier and is completely blocked at 30 K, indicating that thermally assisted protein relaxation is necessary for the primary photochemistry. When Pr is converted to lumi-R, new bands appear in the C = C and C = N stretching regions at 1651, 1636, 1590, and 1569 cm-1, indicating that a significant structural change of the chromophore has occurred. The photoconversion also results in an 18 cm-1 decrease in the N-H rocking band in lumi-R. Normal mode calculations correlate this frequency drop with a change in the geometry of the C15 methine bridge of the phytochromobilin chromophore. Additionally, a C = N stretching mode marker band shifts from 1576 cm-1 in Pr to 1569 cm-1 in lumi-R and to 1552 cm-1 in Pfr. Normal mode calculations show that the frequency drop of this band in the lumi-R-->Pfr interconversion is an indication of a C14-C15 syn-->anti conformational change. Moderately intense hydrogen out-of-plane modes that occur at 805 cm-1 in Pr shift to 829 and 847 cm-1 upon photoconversion to lumi-R and are replaced by a very intense mode at 814 cm-1 in Pfr. These observations indicate that the C and D rings of the chromophore in Pr and lumi-R are moderately planar but that they become highly distorted in Pfr. This information suggests that the primary photochemistry in phytochrome is a Z-->E isomerization of the C15 = C16 bond of Pr giving lumi-R. This is followed by a thermal syn-->anti C14-C15 conformational relaxation to form Pfr. A four-state model is presented to explain the chromophore structural changes in Pr, lumi-R, and Pfr that uses hydrogen bonding to the surrounding protein to stabilize the high-energy Pfr C15 = C16, C14-C15, E,anti chromophore structure. This implicates an anchor and release mechanism between the chromophore and protein that might lead to altered biological signaling in the plant.

Cytochrome aa3 of Rhodobacter sphaeroides as a model for mitochondrial cytochrome c oxidase. Purification, kinetics, proton pumping, and spectral analysis.

Aerobically grown Rhodobacter sphaeroides synthesizes a respiratory chain similar to that of eukaryotes. We describe the purification of the aa3-type cytochrome c oxidase of Rb. sphaeroides as a highly active (Vmax > or = 1800 s-1), three-subunit enzyme from isolated, washed cytoplasmic membranes by hydroxylapatite chromatography and anion exchange fast protein liquid chromatography. The purified oxidase exhibits biphasic kinetics of oxidation of mammalian cytochrome c, similar to mitochondrial oxidases, and pumps protons efficiently (H+/e- = 0.7) following reconstitution into phospholipid vesicles. A membrane-bound cytochrome c is associated with the aa3-type oxidase in situ, but is removed during purification. The EPR spectra of the Rb. sphaeroides enzyme suggest the presence of a strong hydrogen bond to one or both of the histidine ligands of heme a. In other respects, optical, EPR, and resonance Raman analyses of the metal centers and their protein environments demonstrate a close correspondence between the bacterial enzyme and the structurally more complex bovine cytochrome c oxidase. The results establish this bacterial oxidase as an excellent model system for the mammalian enzyme and provide the basis for site-directed mutational analysis of its energy transducing function.

Time-resolved resonance Raman analysis of the lowest triplet (T1) state of benzil

The transient resonance Raman spectra of the photoreduced lowest triplet state (T 1 ) of benzil and of its 18 O 2 and d 10 isotopomers are discussed by analogy with the ground-state (S 0 ) IR and Raman spectra. The detailed comparative analysis of these spectra leads to the following conclusions: (i) The electronic excitation in T 1 is mainly localized on the dicarbonyl fragment and affects weakly the phenyl rings

Structure and Morphology of Metallic-Conductive Polyacetylene

ABSTRACTWe have carried out structural analyses of highly conductive polyacetylene in order to elucidate the relationship between stucture and electrical properties. Sharp X-ray diffraction lines were observed for the heavily iodine-doped polyacetylene showing high conductivity, in contrast with the diffused diffractions of the conventional one. SEM observation reveals that granular structure of the new polyacetylene is composed of densely packed micro-fibrils. The result from the resonance Raman analysis indicates that the new cis-polyacetylene contains more longer conjugated segments than conventional polyacetylene. The relationship between the structure and conductivity is discussed, basing on the crystal structure and morphology observed.