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At least 19 recordsLinked to original sources
PubMed1996

Carbonate in struvite stone detected in Raman spectra compared with infrared spectra and X-ray diffraction.

BACKGROUND: In regard to identify the compositions of urinary stones, the infrared spectra is a contemporary routine method. However, it is difficult to detect the absorption of carbonate in struvite stone by infrared spectra, because NH4 absorption of magnesium ammonium phosphate overlaps CO3 absorption of carbonate at 1420-1435 cm-1. With the purpose of demonstrating the existence of carbonate in struvite stones, the analysis of these stones by means of Raman spectra has been tried. METHODS: Forty urinary stones, the chemical compositions of which were previously determined by infrared spectroscopy, were submitted to Raman spectrum analysis, and subsequently to analysis by x-ray diffraction. RESULTS: Thirty of 40 urinary stones were found to be composed of struvite and of mixed struvite-calcium oxalate by infrared analysis. Twelve of these stones were shown to have Raman spectra of magnesium ammonium phosphate, and the other stones to have spectra of apatite. By x-ray diffraction magnesium ammonium phosphate crystals were detected in 25 of these struvite stones and hydroxyl-apatite in another 3, and 2 cases were undeterminable. For other components, such as calcium oxalate, uric acid and cystine, the analytical results of infrared spectra coincided with those of Raman spectra and x-ray diffraction. Carbonate was detected in only a part of one struvite stone by Raman spectra. CONCLUSIONS: Above-mentioned results may indicate that carbonate is only a minor component of urinary stones. Therefore, most of 1420-1435 cm-1 bands on the infrared spectra of struvite stones do not indicate CO3 absorption of carbonate, but NH(4) absorption of magnesium ammonium phosphate.

Calcium Oxalate↗
PubMed2004

Copper selectively triggers beta-sheet assembly of an N-terminally truncated amyloid beta-peptide beginning with Glu3.

Metal ions have been suggested to induce aggregation of amyloid beta-peptide (Abeta), which is a key event in Alzheimer's disease. However, direct evidence that specific metal-peptide interactions are responsible for the amyloid formation has not previously been provided. Here we present the first example of the metal-induced amyloid formation by an Abeta fragment, which exhibits a clear-cut dependence on the amino acid sequence. A heptapeptide, EFRHDSG, corresponding to the amino acid residues 3-9 of Abeta (Abeta(3-9)) undergoes a conformational transition from irregular to beta-sheet and self-associates into insoluble aggregates upon Cu(II) binding. A Raman spectrum analysis of the Cu(II)-Abeta(3-9) complex and aggregation assays of mutated Abeta(3-9) peptides demonstrated that a concerted Cu(II) coordination of the imidazole side chain of His6, the carboxyl groups of Glu3 and Asp7, and the amino group at the N-terminus is essential for the amyloid formation. Although Abeta(1-9) and Abeta(2-9) also contain the metal binding sites, neither of these peptides forms amyloid depositions in the presence of Cu(II). The results of this study may not only provide new insight into the mechanism of amyloid formation, but also be important as a step toward the construction of proteinaceous materials with a specific function under the control of Cu(II).

Amino Acid Sequence↗
PubMed1964

INFRARED STUDY OF THE OH GROUPS IN EXPANDED KAOLINITE.

Expansion of kaolinite with potassium acetate and with hydrazine followed by deuteration, shifts the absorption frequency at 3695 cm(-1) to lower values, but does not aflect the intensity of the 3620-cm(-1) absorption band. The band at 3695 cm(-1) is correlated predominantly to inner-surface hydroxyls with the dipole at right angles to the basal plane and the band at 3620 cm(-1) is related to inner hydroxyls with the dipole inclined toward empty octahedral sites.

Hydroxyl Radical↗
PubMed1982

Normal coordinate analysis of the copper center of azurin and the assignment of its resonance Raman spectrum.

Normal coordinate analysis that utilizes a general valence force field and the Wilson FG matrix method has been applied to several structural models representing the active site of the blue copper protein, azurin. The models included tetrahedral and square planar CuN2SS', trigonal CuN2S, and trigonal bipyramidal CuN2SS'O structures in which the Ns are imidazole nitrogens of histidines, S is the thiolate sulfur of cysteine, S' is the thioether sulfur of methionine, and O is a peptide carbonyl oxygen. For constant Cu--ligand bond lengths and initial force constants, the force field was refined against the most intense of the observed frequencies (424, 404, 369, and 261 cm-1) in the resonance Raman spectrum of Pseudomonas aeruginosa azurin. The most satisfactory fit between observed and calculated frequencies occurs for tetrahedral and trigonal structures. The calculations provide detailed assignments for the resonance Raman spectrum of azurin and reveal considerable mixing of Cu--S(Cys) and Cu--N(His) vibrational modes. The trigonal model is favored because it is shown that the approximately equal to 260-cm-1 vibration is an invariant feature in the resonance Raman spectra of blue copper proteins, even those lacking a methionine in the vicinity of the copper atom. The present analysis ascribes the high frequencies of the Cu--ligand stretching modes and the resonance enhancement to the coupled nature of their vibrations and the Franck-Condon overlaps with predominant (Cys)S leads to Cu(II) charge transfer bands in the visible region.

Azurin↗
PubMed1989

A temperature-dependent Z to B to single-strand transition in d(CGCG).

A thermally induced left- to right-handed helical interconversion for the self-complementary tetradeoxynucleotide d(CGCG) has been observed in the presence of NaCl at concentrations from 1.5 to 2.25M. Analysis of the Raman spectrum of d(CGCG) in aqueous solution as a function of temperature indicates that at low temperature a left-handed Z-helical form is the predominant species. An increase in temperature results in a decrease in the population of the left-handed form and an increase in the population of the right-handed form. Further elevation in temperature results in extensive disruption of base stacking and a loss of secondary structure. This unstacking presumably represents dissociation to a single-stranded structure. The data suggest that a temperature-dependent Z to B to single-strand transition occurs under the conditions employed. A direct Z to single-strand conversion was not identified. In contrast to previous examples, the thermally induced left- to right-handed helical conversion for d(CGCG) can occur in the absence of chemically modified nucleic acid bases, alcohol solutions, or divalent ions.

DNA, Single-Stranded↗
PubMed2002

From 2D framework to quasi-1D nanomaterial: preparation, characterization, and formation mechanism of Cu(3)SnS(4) nanorods.

An ion-ion reaction route under solvothermal condition at relatively low temperatures was first put forward to the preparation of tetragonal Cu(3)SnS(4) nanorods, on the basis of the strategy that 2D framework structure of Cu(3)SnS(4) containing layers could provide orientation for the growth of quasi-1D nanomaterials. X-ray diffraction (XRD) pattern, transmission electronic microscope (TEM) images, electronic diffraction (ED) pattern, X-ray photoelectron spectra (XPS), energy-dispersive X-ray analysis (EDXA), Mössbauer spectrum, Raman spectrum, thermal analysis (DTA and TGA), ultraviolet and visible light (UV-vis) spectrum, and photoluminescence (PL) spectrum were used to characterize the products. On the basis of a series of supplementary experiments and the result of infrared absorption spectrum (IR), a reaction mechanism was proposed: ethanol as solvent and reductant and trace water/CH(3)CSNH(2) as sulfur source and acid-making components could form 2D network through hydrogen bonds, which provided the orientation for the formation of a 2D framework structure; appropriate concentration of CH(3)CSNH(2), warming speed, reaction constant temperatures (T(rc)), and reaction time also played important roles.

Journal Article↗
PubMed2003

Concentration of small ring structures in vitreous silica from a first-principles analysis of the Raman spectrum.

Using a first-principles approach, we calculate Raman spectra for a model structure of vitreous silica. We develop a perturbational method for calculating the dielectric tensor in an ultrasoft pseudopotential scheme and obtain Raman coupling tensors by finite differences with respect to atomic displacements. For frequencies below 1000 cm(-1), the parallel-polarized Raman spectrum of vitreous silica is dominated by oxygen bending motions, showing a strong sensitivity to the intermediate range structure. By modeling the Raman coupling, we derive estimates for the concentrations of three- and four-membered rings from the experimental intensities of the Raman defect lines.

Journal Article↗
PubMed2000

[Synthesis and characterization of the oxidation product of the 1, 2, 3-trihydroxybenzene and its metallic complexes].

The oxidation reaction mechanism of the 1,2,3-trihydroxybenzene was studied by the Ab initio calculation of the quantum chemistry. The derivative of the hydrazine and THBO(the reaction product of the 1,2,3-trihydroxybenzene and H2O2) and its metal complexes were synthesized and characterized by the IR, Raman spectrum and thermogravimetric analysis. The composition of these complexes and the possible structure of THBO were confirmed.

Chelating Agents↗
PubMed1985

Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy.

The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an efficient light-energy convertor. Important unresolved questions involve the mechanism by which the protein catalyzes deprotonation of the L550 intermediate and the mechanism of the thermal conversion of M412 back to BR568. Also, it has been shown that under conditions of high ionic strength and/or low light intensity two protons are pumped per photocycle (Kuschmitz & Hess, 1981). How might this be accomplished?(ABSTRACT TRUNCATED AT 400 WORDS)

Bacteriorhodopsins↗
PubMed1988

Excited-state structure and isomerization dynamics of the retinal chromophore in rhodopsin from resonance Raman intensities.

Resonance Raman excitation profiles have been measured for the bovine visual pigment rhodopsin using excitation wavelengths ranging from 457.9 to 647.1 nm. A complete Franck-Condon analysis of the absorption spectrum and resonance Raman excitation profiles has been performed using an excited-state, time-dependent wavepacket propagation technique. This has enabled us to determine the change in geometry upon electronic excitation of rhodopsin's 11-cis-retinal protonated Schiff base chromophore along 25 normal coordinates. Intense low-frequency Raman lines are observed at 98, 135, 249, 336, and 461 cm-1 whose intensities provide quantitative, mode-specific information about the excited-state torsional deformations that lead to isomerization. The dominant contribution to the width of the absorption band in rhodopsin results from Franck-Condon progressions in the 1,549 cm-1 ethylenic normal mode. The lack of vibronic structure in the absorption spectrum is shown to be caused by extensive progressions in low-frequency torsional modes and a large homogeneous linewidth (170 cm-1 half-width) together with thermal population of low-frequency modes and inhomogeneous site distribution effects. The resonance Raman cross-sections of rhodopsin are unusually weak because the excited-state wavepacket moves rapidly (approximately 35 fs) and permanently away from the Franck-Condon geometry along skeletal stretching and torsional coordinates.

Animals↗
PubMed2004

New background correction method for liquid chromatography with diode array detection, infrared spectroscopic detection and Raman spectroscopic detection.

A new method to eliminate the background spectrum (EBS) during analyte elution in column liquid chromatography (LC) coupled to spectroscopic techniques is proposed. This method takes into account the shape and also intensity differences of the background eluent spectrum. This allows the EBS method to make a better estimation of the background eluent spectrum during analyte elution. This is an advantage for quantification as well as for identification of analytes. The EBS method uses a two-step procedure. First, the baseline spectra are modeled using a limited number of principal components (PCs). Subsequently, an asymmetric least squares (asLS) regression method is applied using these principal components to correct the measured spectra during elution for the background contribution. The asymmetric least squares regression needs one parameter, the asymmetry factor p. This asymmetry factor determines relative weight of positive and negative residuals. Simulations are performed to test the EBS method in well-defined situations. The effect of spectral noise on the performance and the sensitivity of the EBS method for the value of the asymmetry factorp is tested. Two applications of the EBS method are discussed. In the first application, the goal is to extract the analyte spectrum from an LC-Raman analysis. In this case, the EBS method facilitates easy identification of unknown analytes using spectral libraries. In a second application, the EBS method is used for baseline correction in LC-diode array detection (DAD) analysis of polymeric standards during a gradient elution separation. It is shown that the EBS method yields a good baseline correction, without the need to perform a blank chromatographic run.

Spectrophotometry, Infrared↗
PubMed2003

Theoretical and pH dependent surface enhanced Raman spectroscopy study on caffeine.

The surface enhanced Raman spectroscopy (SERS) spectrum of caffeine is recorded on a silver colloid at different pH values. It is discussed on the basis of the SERS "surface selection rules" in order to characterize its vibrational behavior on such a biological artificial model. To improve the previous assignments in the Raman spectrum and for a reliable, detailed analysis of SERS spectra, density functional theory calculations (structural parameters, harmonic vibrational wavenumbers, total electron density, and natural population analysis of the molecule) are performed for the anhydrous form of caffeine and the results are discussed. The predicted geometry and vibrational Raman spectra are in good agreement with the experimental data. The flat orientation of the mainly chemisorbed caffeine attached through the pi electrons and the lone pair of nonmethylated N atoms of the imidazole ring are proposed to occur at neutral and basic pH values. At acid pH values caffeine is probably adsorbed on the Ag surface through one or both oxygen atoms, more probably through the O atom of the conjugated carbonyl group with an end-on orientation. However, the changes in the overall SERS spectral pattern seem to indicate the electromagnetic mechanism as being the dominant one.

Caffeine↗
PubMed2005

Spectroscopic and kinetic studies of Arabidopsis thaliana sulfite oxidase: nature of the redox-active orbital and electronic structure contributions to catalysis.

Plant sulfite oxidase from Arabidopsis thaliana has been characterized both spectroscopically and kinetically. The enzyme is unusual in lacking the heme domain that is present in the otherwise highly homologous enzyme from vertebrate sources. In steady-state assays, the enzyme exhibits a pH maximum of 8.5 and is also found to function as a selenite oxidase. Sulfite at the lowest experimentally feasible concentrations reduces the enzyme within the dead-time of a stopped-flow instrument at 5 degrees C, indicating that the A. thaliana enzyme has a limiting rate constant for reduction, k(red), at least 10 times greater than that of the chicken enzyme (190 s(-1)). The EPR parameters for the high- and low-pH forms of the A. thaliana enzyme have been determined, and the g-values are found to resemble those previously reported for the vertebrate enzymes. Finally, the A. thaliana enzyme has been probed by resonance Raman spectroscopy. A detailed analysis of the vibrational spectrum in the region where Mo=O stretching modes are anticipated to occur has been performed with the help of density functional theory calculations, evaluated in the context of the Raman data. Calculated frequencies obtained for two model systems have been compared to experimental resonance Raman spectra of oxidized A. thaliana sulfite oxidase catalytically cycled in both H2(16)O and H2(18)O. The vibrational frequency shifts observed upon (18)O-labeling of the enzyme are consistent with theoretical models in which either the equatorial oxygen or both equatorial and axial atoms of the dioxomolybdenum center are labeled. Importantly, the vibrational mode description is consistent with the active site possessing geometrically inequivalent oxo ligands and a Mo d(xy) redox-active molecular orbital oriented in the equatorial plane forming a pi-bonding interaction solely with the equatorial oxo, O(eq). Electron occupancy of this Mo=O(eq) pi* redox orbital upon interaction with substrates would effectively labilize the Mo=O(eq) bond, providing the dominant contribution to lowering the activation energy for oxygen atom transfer.

Arabidopsis↗
PubMed2006

New lanthanum (III) complex--synthesis, characterization, and cytotoxic activity.

The complex of lanthanum (III) was synthesized reacting the respective inorganic salt with 5-aminoorotic acid in amounts equal to the metal:ligand molar ratio of 1:3. The complex was prepared by adding an aqueous solution of lanthanum (III) nitrate to an aqueous solution of the ligand, subsequently raising the pH of the mixture gradually to approx. 5.0 through addition of a dilute solution of sodium hydroxide. The structure of the final complex was determined by means of spectral data (IR, Raman,( 1)H-NMR) and elemental analysis. Significant differences in the IR spectrum of the complex were observed as compared to the spectrum of the ligand. A comparative analysis of the Raman spectrum of the complex with that of the free 5-aminoorotic acid allowed a straightforward assignment of the vibrations of the ligand groups involved in coordination. The ligand and the complex were tested for the cytotoxic activities on the chronic myeloid leukemia derived K-562, overexpressing the BCR-ABL fusion protein and the non-Hodgkin lymphoma derived DOHH-2, characterized by a re-expression of the anti-apoptotic protein bcl-2 cell lines. The results obtained indicate that the tested compounds exerted a considerable cytotoxic activity upon the evaluated cell lines in a concentration-dependent matter, which enabled the construction of dose-response curves and the calculation of the corresponding IC(50 )values. The inorganic salt exerted a very weak cytotoxic effect on these cells, which is in contrast to the lanthanum (III) complex.

Antineoplastic Agents↗
PubMed1998

Raman linear intensity difference of membrane-bound peptides: indole ring orientations of tryptophans 11 and 13 in the gramicidin A transmembrane channel.

A Raman linear intensity difference (RLID) method has been developed to determine orientations of chromophores in membrane-bound peptides and proteins. The method involves orientation of the peptide or protein in lipid bilayer membranes and measurement of intensity differences between Raman spectra excited with two orthogonal laser polarizations. Analysis of the RLID spectrum is simplified when the chromophore exhibits a vibrational mode for which the Raman band is enhanced through resonance with a single molecular electronic transition. To examine the indole ring orientations of Trp residues in the gramicidin A transmembrane channel, we have prepared analogues of gramicidin A, in which one of four Trp residues is replaced by deuterated Trp (Trp-2,4,5,6,7-d5). Two vibrational Raman bands omega(d)3 and omega(d)2 of deuterated Trp have been shown to gain intensity predominantly through resonance with the Bb and La electronic transitions, respectively, when excited at 244 and 257 nm. By examining the RLID spectra of the omega(d)3 and omega(d)2 bands of gramicidin A channels oriented in phospholipid bilayer membranes, we have determined the inclination angles of the Bb and La transition moments with respect to the channel axis in the absence and presence of Na+. The orientations of the Trp-11 and Trp-13 indole rings in the gramicidin channel structure have been derived from the inclination angles of the transition moments. The indole rings of Trp-11 and Trp-13, which are known to shift along the channel axis upon binding of Na+, do not reorient during their positional shifts.

Binding Sites↗