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At least 343 records · Page 19Linked to original sources
PubMed2005

Fourier-transform infrared spectrum of aspartate hydroxo-aqua nickel (II) complex and DFT-B3LYP/3-21G and 6-311G structural and vibrational calculations.

Aspartate hydroxo-aqua nickel (II) complex was synthesized and the structural analysis was carried out through the following methods: determination of the C, N, O and H contents, thermogravimetry and infrared spectrum. Several hypothetic structures were calculated by means of DFT: B3LYP/3-21G and B3LYP/6-311G quantum mechanical method. For [Ni(Asp)(OH)(H(2)O)] we have obtained the minimum of energy and no imaginary frequencies in the calculated infrared spectrum. Moreover, the experimental FT-infrared spectrum shows that the two N-H stretching follow the Bellamy-Williams relation proposed for primary amines. Coordination water bands were also observed in the infrared spectrum. For reasons of accomplishment, the Fourier transforms infrared and Raman spectra of acid aspartic were also discussed.

Hydrogen↗
PubMed2004

Vibrational spectra and potential energy distributions for 4,5-dichloro-3-hydroxypyridazine by density functional theory and normal coordinate calculations.

The solid phase FT-IR and FT-Raman spectra of 4,5-dichloro-3-hydroxypyridazine have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The IR and Raman spectra were predicted theoretically and compared with the experimental spectra.

Carbon↗
PubMed2002

Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT).

The temperature dependence of the Raman spectrum of poly(dA).poly(dT) (dA: deoxyadenosine; dT: thymidine), a model for DNA containing consecutive adenine.thymine (A.T) pairs, has been analyzed using a spectrometer of high spectral precision and sensitivity. Three temperature intervals are distinguished: (a) premelting (10 < t < 70 degrees C), in which the native double helix is structurally altered but not dissociated into single strands; (b) melting (70 < t < 80 degrees C), in which the duplex is dissociated into single strands; and (c) postmelting (80 < t degrees C), in which no significant structural change can be detected. The distinctive Raman difference signatures observed between 10 and 70 degrees C and between 70 and 80 degrees C are interpreted in terms of the structural changes specific to premelting and melting transitions, respectively. Premelting alters the low-temperature conformation of the deoxyribose-phosphate backbone and eliminates base hydrogen bonding that is distinct from canonical Watson-Crick hydrogen bonding; these premelting perturbations occur without disruption of base stacking. Conversely, melting eliminates canonical Watson-Crick pairing and base stacking. The results are compared with those reported previously on poly(dA-dT).poly(dA-dT), the DNA structure consisting of alternating A.T and T.A pairs (L. Movileanu, J. M. Benevides, and G. J. Thomas, Jr. Journal of Raman Spectroscopy, 1999, Vol. 30, pp. 637-649). Poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) exhibit strikingly dissimilar temperature-dependent Raman profiles prior to the onset of melting. However, the two duplexes exhibit very similar melting transitions, including the same Raman indicators of ruptured Watson-Crick pairing, base unstacking and collapse of backbone order. A detailed analysis of the data provides a comprehensive Raman assignment scheme for adenosine and thymidine residues of B-DNA, delineates Raman markers diagnostic of consecutive A.T and alternating A.T/T.A tracts of DNA, and identifies the distinct Raman difference signatures for premelting and melting transitions in the two types of sequences.

Base Composition↗
PubMedDate not supplied

Vibrational analysis of peptides, polypeptides, and proteins. 3. alpha-Poly(L-alanine).

Starting with a force field transferred from our earlier studies on beta-polypeptides, we have calculated the optically active normal vibration frequencies of alpha-helical poly(L-alanine) and poly(L-alanine-N-d). The 47/13 helical structure was used, and all atoms were included. Only small modifications to the force field were required, and most of these could be justified. The analysis indicates that amide II' is in Fermi resonance with one component of CH3 asymmetric bend, thus leading to a small modification of C-N and C=O stretching force constants. The agreement between calculated and observed Raman and infrared bands is quite good. This has encouraged ls to calculate the influence of small structural changes on the spectrum as a means of explaining the observed effects of temperature changes.

Alanine↗
PubMed1992

Evidence of dithionite contribution to the low-frequency resonance Raman spectrum of reduced and mixed-valence cytochrome c oxidase.

The resonance Raman spectra of deoxygenated solutions of mixed-valence cyanide-bound and fully reduced cytochrome oxidase derivatives that have been reduced in the presence of aqueous or solid sodium dithionite exhibit two new low-frequency lines centered at 474 and 590 cm-1. These lines were not observed when the reductant system was changed to a solution containing ascorbate and N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD). Under enzyme turnover conditions, the addition of dithionite to the reoxidized protein (the 428-nm or "oxygenated" form) increases the intensity of these lines, while reoxidation and rereduction of the enzyme in the presence of ascorbate/TMPD resulted in the absence of both lines. Our data suggest that both lines must have contributions from species formed from aqueous dithionite, presumably the SO2 species, since these two lines are also observed in the Raman spectrum of a solution of aqueous dithionite, but not in the spectrum of an ascorbate/TMPD solution. Since heme metal-ligand stretch vibrations are expected to appear in the low-frequency region from 215 to 670 cm-1, our results indicate that special care should be exercised during the interpretation of the cytochrome a3 resonance Raman spectrum.

Animals↗
PubMed1994

Analysis of surface layers on bioactive glasses.

FT-Raman spectroscopy proves to be a powerful technique to study surface reactions on bioactive glasses and it eliminates the fluorescence of the organic phase of whole bone, thereby making it possible to compare the reaction layers formed on bioactive glasses with the mineral phase of bone. The spectrum of hydroxycarbonate apatite (HCA) developed on the bioactive glasses is closer to that of bone than synthetic hydroxyapatite (HA) and closely matches that of bone mineral obtained by deproteination of whole human femoral cortical bone.

Apatites↗
PubMed1997

The use of reference materials in quantitative analyses based on FT-Raman spectroscopy.

The reliability with which an external reference sample can be used to standardise the intensities of Raman scattering spectra is assessed. By comparing the ratios of single band intensities of Raman scatter in a two component liquid mixture with those between the mixture and an external standard it is shown that the latter is more than adequate for most quantitative Raman analysis. Coefficients of variance in repeated experiments on the same sample are approximately 1%, when comparing single band heights on spectra recorded with modest laser powers over 2 min. When using the whole spectrum, these coefficients are significantly lower.

Fourier Analysis↗
PubMed2005

[Applications of moissanite anvil cell for Raman spectroscopy under high-temperature and high-pressure].

This paper introduces the structure and the feature of moissanite anvil cell, which is composed of moissanite anvil, supporting and creating pressure system, heater system and metal gasket. Because of its high hardness, high heat conductance, low thermal expansion, good thermal stability and low price, moissanite is a good material of anvil for high-temperature and high-pressure experimental studies. With this cell, the Raman spectrum of sodium carbonate solution, sodium sulfate solution and distilled water has been in situ measured under high-temperature and high-pressure. With increasing pressure, it can be observed that the 1066 cm(-1) Raman modes of sodium carbonate solution and the 982 cm(-1) Raman modes of sodium sulfate solution shift to high wave numbers obviously. With increasing temperature, the frequency at maximum intensity shifts to high wave numbers, the full width at half-maximum intensity decreases in the Raman spectrum of water.

Carbon Compounds, Inorganic↗
PubMed1984

Identity of acyl group conformations in the active sites of papain and cathepsin B by resonance Raman spectroscopy.

Resonance Raman spectroscopic data provide conclusive evidence for the existence of an acyl-enzyme intermediate during the reaction of a thionoester substrate, N-methyloxycarbonylphenylalanylglycine methyl thionoester (CH3OC(=O)-Phe-NHCH2C(=S) OCH3), with cathepsin B from porcine spleen. The resonance Raman spectrum of CH3OC(=O)-Phe-NHCH2C(=S)S-cathepsin B, where the thiol S is from the active-site cysteine residue, is compared to that of the corresponding papain acyl-enzyme. Within the limits of experimental error (+/-2 cm-1 for peak positions), there are no detectable spectral differences. Since the resonance Raman spectrum is sensitive to the torsional angles in the glycinic bonds and the cysteine linkages, the conformations are identical in those parts of the acyl-enzymes where chemical transformation occurs. A conformational analysis of the model compound CH3OC(=O)-Phe-NHCH2C(=S)SC2H5 demonstrates that the dithioacyl group in both dithioacyl-enzymes is present as a single population of a form known as conformer B. Conformer B is characterized by a small torsional angle about the glycinic NHCH2-CS(thiol) bond such that the nitrogen and S (thiol) atoms are in close contact. This conformer is widespread among the dithioacyl intermediates of plant cysteine proteinases, and it is apparent that the same chemistry is retained in a mammalian cysteine proteinase. Steady-state kinetic parameters are also reported for CH3OC(=O)-Phe-NHCH2C(=S)OCH3 reacting with papain and cathepsin B. The similarity of the Kcat values, 0.53 and 1.15 s-1, for papain and cathepsin B, respectively, provides further evidence for a conserved deacylation process.

Animals↗
PubMed1996

Structural analysis of heparin by raman spectroscopy.

The Raman spectra of commercially available heparin disaccharide standards exhibit bands associated with the N-sulfate and the 6-O-sulfate groups of the glucosamine and the 2-O-sulfate of the iduronic acid. The N-sulfate has a strong band at 1039 cm-1. The 6-O-sulfate and the 2-O-sulfate exhibit bands at 1055 and 1065 cm-1, respectively. The pattern of these modes, which are assigned to the symmetric SO3 vibrations, was supported by semiempirical quantum mechanical calculations. The above bands were identified in the Raman spectrum of a commercial preparation of porcine mucosal heparin and were used to determine the relative proportion of the N-sulfate, 6-O-sulfate, and 2-O-sulfate groups in the heparin molecule. This information, which is complementary to that obtained by NMR spectroscopy, is of particular importance in relation to biological activity. This study also extends the usefulness of Raman spectroscopy to include structural details required for the quality assurance of pharmaceutical preparations of heparin.

Animals↗