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At least 325 records · Page 18Linked to original sources
PubMed2003

FTIR-ATR analysis of brewed coffee: effect of roasting conditions.

FTIR-ATR was used to study the effect of roasting conditions on the flavor of brewed coffee using Guatemala Antigua coffee beans. The 1800-1680 cm(-1) carbonyl region for vinyl esters/lactones, esters, aldehydes, ketones, and acids was found to provide a flavor-print of the brewed coffee. A study of light, medium, and dark roasts indicated that when the rate of heating to the onset of the first and second cracks was kept constant, the types of carbonyl compounds formed were similar, varying only in their concentration. This difference in concentration is apparently due to the additional heating of the coffee bean beyond the second crack. When the heating rate to the onset of the first and second crack was varied, both the types and concentration of the carbonyl compounds formed during roasting were affected. Thus, heating rates of green coffee beans to the onset of the first and second cracks are important determinants of the basic taste and aroma of brewed coffee.

Coffea↗
PubMed2006

Characterization of surface treatments of cork stoppers by FTIR-ATR.

A general method is described for the identification of paraffin- and silicone-based surface treatments applied to single-piece natural and 1 + 1 (cork agglomerate with two natural cork disks) cork stoppers used to seal wine bottles. The method is based on Fourier transformed infrared spectroscopy (FTIR) and attenuated total reflectance (ATR) analysis of ready-for-use stoppers. The absorbance in seven wavelength bands selected as the most characteristic (2916 and 2850 cm(-)(1), for paraffins, and 2963, 1258, 1079, 1010, and 787 cm(-)(1), for silicones) was measured for both kinds of stoppers. Univariate analysis of the results enabled identification of stoppers that had received surface treatment by measuring the absorbance in two of the selected bands, representing paraffins and silicones, respectively. The type of surface treatment used was identified by discriminant analysis. Using this technique, we constructed a mathematical model using the seven bands studied. The model correctly classified 100% of the stoppers used to construct it and 91.7% of the stoppers used for validation.

Discriminant Analysis↗
PubMed2005

Observation of the first hydration layer of isolated cations and anions through the FTIR-ATR difference spectra.

The attenuated total reflectance-Fourier transform infrared (ATR-FTIR) difference spectra of the dilute aqueous (NH4)2SO4, Na2SO4, MgSO4, ZnSO4, NaClO4, and Mg(ClO4)2 solutions by pure water were obtained at various concentrations. In the difference spectra of aqueous (NH4)2SO4 solutions, a peak at approximately 3039 cm(-1), two shoulders at approximately 3155 and approximately 2894 cm(-1), and a peak at approximately 1445 cm(-1) were ascribed to N-H stretching and bending vibrations, respectively. A small negative peak was resolved at approximately 3660 cm(-1) in the difference spectra of (NH4)2SO4, which is the sole contribution of SO4(2-) either in the O-H stretching or in the O-H bending region. The positive peaks of the difference spectra in the O-H stretching region for Na2SO4, MgSO4, and ZnSO4 systems, which constantly appeared at approximately 3423, approximately 3136, and approximately 3103 cm(-1) respectively, were suggested to be the contribution of the interactions between metal cations (Na+, Mg2+, and Zn2+) and water molecules, especially from the first hydrated layer of the cations. In the region of 800-1200 cm(-1), the normally infrared-prohibited nu1 (SO4(2-)) band was observed as a weak peak at approximately 981 cm(-1) even at very dilute concentrations (0.10 mol dm(-3)) due to the disturbance of the water molecules hydrated with SO4(2-), even though such a feature may increasingly result from associated ions with increasing concentration. The spectra of the water molecules directly influenced by ClO4-, i.e., mostly the first layer of hydrated water, in NaClO4 and Mg(ClO4)2 solutions were obtained by subtracting the corresponding spectra of the same metal sulfate solutions at the same concentrations from the perchlorate solutions. A positive peak at approximately 3583 +/- 6 cm(-1) and a negative peak at approximately 3184 +/- 25 cm(-1) were obtained as the result of the subtraction. The positive peak was attributed to the water molecules weakly hydrogen-bonded with ClO4-, while the negative one to the reduction of water molecules with fully hydrogen-bonded five-molecule tetrahedral nearest neighbor structure on the introduction of ClO4-.

Journal Article↗
PubMed2005

Probing enantiospecific interactions between proline and an l-glutathione self-assembled monolayer by modulation excitation ATR-IR spectroscopy.

The interaction of proline with self-assembled monolayers (SAMs) of l-glutathione (gamma-glu-cys-gly) on gold was investigated by a combination of attenuated total reflection (ATR-IR) infrared and modulation excitation spectroscopy (MES). The latter technique makes use of phase-sensitive detection of periodically varying signals and allows discrimination between species with different kinetics such as dissolved proline and adsorbed molecules. By applying a convection-diffusion model coupled to adsorption and desorption, it was possible to extract relative adsorption and desorption rates from the experimental data for the two enantiomers of proline, fully accounting for mass transport within the flow-through cell. The results show that, in particular, the desorption kinetics is different for the two enantiomers. Therefore, the l-glutathione SAM can discriminate between enantiomers, d-proline being stronger bound. The IR spectra reveal that upon interaction with proline the adsorbed l-glutathione is protonated at the gly part of the molecule, which, in the absence of proline, is bound to the gold surface as carboxylate. The observed protonation of adsorbed l-glutathione upon interaction with proline goes along with a structural change of the former, which seems to play an important role for enantiodiscrimination.

Glutathione↗
PubMed2006

Combination of polarized TIRF and ATR spectroscopies for determination of the second and fourth order parameters of molecular orientation in thin films and construction of an orientation distribution based on the maximum entropy method.

This article describes two mathematical formalisms for the determination of the second and fourth order parameters of molecular films using optical spectroscopy. Method A uses polarized total internal reflection fluorescence (TIRF) to calculate the second and fourth order parameters, {P2(cos theta)} and {P4(cos theta)}, using an independently determined value for the angle between the absorption and emission dipoles, gamma. Method B uses {P2(cos theta)} obtained from attenuated total reflectance (ATR) data, along with polarized TIRF measurements to calculate {P4(cos theta)} and {cos2 gamma}. The choice of a specific method should rely on experimental considerations. We also present a method to separate the contributions of substrate surface roughness and dipole orientation with respect to the molecular axis from the spectroscopically determined second and fourth order parameters. Finally, a maximum entropy approach for construction of an orientation distribution from order parameters is compared with the commonly used delta and Gaussian distributions.

Entropy↗
PubMed2004

Structure and reactivity of mixed omega-carboxyalkyl/alkyl monolayers on silicon: ATR-FTIR spectroscopy and contact angle titration.

The structure, reactivity, and acid-base properties of mixed monolayers prepared by photochemical reaction of hydrogen-terminated silicon with mixtures of ethyl undecylenate and n-alkenes were studied by ATR-FTIR spectroscopy and contact-angle measurements. The surface composition of the mixed monolayers and its correlation with the hydrolysis reactivity of terminal ethoxycarbonyl (ester) groups were investigated by systematically varying the mole fraction of ethyl undecylenate and the chain length of the unsubstituted alkenes in the binary deposition solution. It has been shown that the mole fraction of ester groups on the surface deviates only slightly from the mole fraction of ethyl undecylenate in the solution. The efficiency of ester hydrolysis under acidic conditions is significantly influenced by the monolayer structure, i.e., the surface density of ester groups and length of the unsubstituted alkyl chains. In addition, we find that mixed omega-alkanoic acid/alkyl monolayers on silicon (prepared via hydrolysis) exhibit well-defined contact angle titration curves from which the surface acid dissociation constants were determined. The results were compared with the acid-base properties reported in the literature for carboxylic acid-terminated alkylsiloxane monolayers on hydroxylated silicon and for omega-mercaptoalkanoic acid/alkanethiolate monolayers on gold. The weak pKa dependence (deltapKa approximately 1) on the surface density of carboxylic acid groups and on the length of unsubstituted alkyl chains is attributed to variations of the microenvironment of the acid moieties. These experimental findings provide fundamental knowledge at the molecular level for the preparation of bioreactive surfaces of controlled reactivity on crystalline semiconductor substrates.

Journal Article↗
PubMed2004

An in situ FTIR-ATR study of polyacrylate adsorbed onto hematite at high pH and high ionic strength.

FTIR-ATR was used to examine in situ the interaction of polyacrylate and hematite at pH 13. Static light scattering and mobility measurements were used to assess solution polyacrylate dimensions and hematite surface charge, respectively. Polyacrylate adsorption occurred only with the addition of electrolyte (e.g., NaCl), and it was found that excess cations, up to approximately 1 M, facilitated adsorption, above which the effect was found to plateau. At pH 13 and at low ionic strength, adsorption of polyacrylate onto hematite is facilitated by cations in solution shielding both the negative acrylate functionality of the polymer and the negative hematite surface. The shielding of the hematite surface continues to increase with increasing salt concentration up to a measured 3 M. Similarly, the shielding of the polymer increased with electrolyte concentration up to approximately 1 M salt, beyond which no further increase in shielding was observed. At this concentration the polymer assumes a finite minimum size in solution that ultimately limits the amount adsorbed. The dimension of the polymer in solution was found to be independent of monovalent cation type. Thus, at high pH and high ionic strength adsorption is determined by the degree of hematite surface charge reduction. The cation-hematite surface interaction was found to be specific, with lithium leading to greater polyacrylate adsorption than sodium, which was followed by cesium. The stronger affinity of lithium for the hematite surface over sodium and cesium is indicative of the inverse lyotropic adsorption series and has been rationalized in the past by the "structure-making-structure-breaking" model. These results provide a useful insight into the likely adsorption mechanism for polyacrylate flocculants at high pH and ionic strength onto residues in the Bayer processing of bauxite.

Journal Article↗
PubMed2006

Monitoring metal ion binding in single-layer Pseudomonas aeruginosa biofilms using ATR-IR spectroscopy.

The binding of metal ions to Pseudomonas aeruginosa PAO1 cells attached to a ZnSe surface has been observed in this research through cation exchange experiments using ATR-IR spectroscopy. A biofilm consisting of a single layer of Pseudomonas aeruginosa PAO1 cells was formed on a ZnSe prism by flowing a bacterial suspension in a 0.03 mol L(-)(1) NaNO(3) solution at pH 5.0 across its surface. Exposure of the biofilm to chromium(III) nitrate solution resulted in increases in all band absorbances. This absorbance increase has been attributed to the binding of chromium(III) to the bacterial exopolymers associated with the prism surface. The chromium(III) binding causes the exopolymers to contract and move the bacterial cell closer to the ZnSe surface. Further study of chromium(III) ion exchange using a mutant P. aeruginosa with a truncated lipopolysaccharide (LPS) chain resulted in much smaller absorbance changes. This observation supports the view that the extension of bacterial exopolymers and hence the distance of the bacterial cell from the surface is strongly influenced by environmental factors such as the presence of metal cations. Following chromium(III) cation exchange, the bacterial band absorbances remained constant even when the bacteria were washed with a 0.03 mol L(-)(1) NaNO(3) solution, indicating that the chromium(III) was irreversibly bound. Ion exchange with nickel(II) and cobalt(II) nitrate solutions within identical biofilms showed that these cations caused relatively small increases in absorbances that were reversible, indicating that nickel(II) and cobalt(II) are less strongly bound than chromium(III) within P. aeruginosa biofilms. The absence of discernible IR spectral changes with metal binding appears to indicate a predominantly electrostatic mechanism for binding of Cr(III), Ni(II), and Co(II) ions by bacteria in the early stages of biofilm formation.

Bacterial Adhesion↗
PubMed2006

ATR-IR spectroscopy of pendant NH2 groups on silica involved in the Knoevenagel condensation.

The liquid-phase Knoevenagel condensation between benzaldehyde and ethyl cyanoacetate catalyzed by aminopropyl-modified silica has been investigated using in situ attenuated total reflection infrared (ATR-IR) spectroscopy. The aim of the work was to demonstrate the different levels of information on the reaction mechanism that can be achieved by operating the spectroscopic cell in the absence and in the presence of a solvent, in flow-through and stop-flow modes and in combination with concentration modulation spectroscopy. The reaction mechanism involves the formation of an imine intermediate whose existence has been verified in situ by combining in one experiment continuous and stop-flow operations. Identical information has been gained more elegantly using concentration modulation spectroscopy, which additionally provided information on the possible origin of the solvent effect observed in the Knoevenagel reaction. Faster production and consumption of the imine intermediate was observed in cyclohexane solvent than in toluene. Identification of other species evolving on the catalyst surface and monitoring of the effluents of the spectroscopic cell provided some insight in possible catalyst deactivation.

Acetates↗
PubMed2006

In-situ infrared study of the adsorption and oxidation of oxalic acid at single-crystal and thin-film gold electrodes: a combined external reflection infrared and ATR-SEIRAS approach.

The adsorption and oxidation of oxalic acid at gold electrodes were studied by in-situ infrared spectroscopy. External reflection experiments carried out with gold single-crystal electrodes were combined with internal reflection (ATR-SEIRAS) experiments with gold thin-film electrodes. These gold thin films, with a typical thickness of ca. 35 nm, were deposited on silicon substrates by argon sputtering. As previously reported for evaporated gold films, the voltammetric curves obtained in sulfuric acid solutions after electrochemical annealing show typical features related to the presence of wide bidimensional (111) domains with long-range order. The in-situ infrared data collected for solutions of pH 1 confirmed the potential-dependent adsorption of either oxalate (Au(100)) or a mixture of bioxalate and oxalate (Au(111), Au(110), and gold thin films) anions in a bidentate configuration. The better signal-to-noise ratio associated with the SEIRA effect in the case of the gold thin-film electrodes allows the observation of the carbonyl band for adsorbed bioxalate that was not detected in the external reflection experiments. Besides, additional bands are observed between 2000 and 3000 cm(-)(1) that can be tentatively related to the formation of hydrogen bonds between neighboring bioxalate anions. The intensities of these bands decrease with increasing solution pH values, disappearing for pH 3 solutions in which adsorbed oxalate anions are the predominant species. The analysis of the intensities of the nu(s)(O-C-O) and nu(C-OH) + delta(C-O-H) bands for adsorbed oxalate and bioxalate, respectively, suggests that the pK(a) for the surface equilibrium between these species is significantly lower than that for the solution equilibrium.

Journal Article↗
PubMed2006

ATR-FTIR spectroscopy reveals bond formation during bacterial adhesion to iron oxide.

The contribution of various bacterial surface functional groups to adhesion at hematite and ZnSe surfaces was examined using attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. When live Shewanella oneidensis, Pseudomonas aeruginosa, and Bacillus subtilis cells were introduced to a horizontal hematite (alpha-Fe(2)O(3))-coated internal reflection element (IRE), FTIR peaks emerged corresponding to bacterial phosphate group binding. These IR peaks were not observed when bacteria were introduced to the uncoated ZnSe IRE. When cells were added to colloidal suspensions of alpha-Fe(2)O(3) at pH 7, spectra included peaks corresponding to P-OFe and nu(COOH), the latter being attributed to bridging of carboxylate at mineral surface OH groups. Selected model organic compounds with P-containing functionalities (phenylphosphonic acid [PPA], adenosine 5'-monophosphate [AMP], 2'-deoxyadenyl(3'-->5')-2'-deoxyadenosine [DADA], and deoxyribonucleic acid [DNA]) produce spectra with similar peaks corresponding to P-OFe when adsorbed to alpha-Fe(2)O(3). The data indicate that both terminal phosphate/phosphonate and phosphodiester groups, either exuded from the cell or present as surface biomolecules, are involved in bacterial adhesion to Fe-oxides through formation of innersphere Fe-phosphate/phosphonate complexes.

Adsorption↗
PubMed2005

Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1.

Eukaryotic cells coordinately regulate histone and DNA synthesis. In mammalian cells, most of the regulation of histone synthesis occurs post-transcriptionally by regulating the concentrations of histone mRNA. As cells enter S phase, histone mRNA levels increase, and at the end of S phase they are rapidly degraded. Moreover, inhibition of DNA synthesis causes rapid degradation of histone mRNAs. Replication-dependent histone mRNAs are the only metazoan mRNAs that are not polyadenylated. Instead, they end with a conserved stem-loop structure, which is the only cis-acting element required for coupling regulation of histone mRNA half-life with DNA synthesis. Here we show that regulated degradation of histone mRNAs requires Upf1, a key regulator of the nonsense-mediated decay pathway, and ATR, a key regulator of the DNA damage checkpoint pathway activated during replication stress.

Ataxia Telangiectasia Mutated Proteins↗
PubMed1999

Germline and gonosomal mosaicism in the ATR-X syndrome.

We have identified two females who are mosaic for an ATRX mutation. One case, in whom the mutation was undetectable in peripheral blood and buccal cells, has two affected sons and is therefore presumed to be a germline mosaic. In another case, the ATRX mutation is weakly detectable in the peripheral blood but only one of her three children who share the disease-associated haplotype carries the mutation and therefore it is concluded that she is a gonosomal mosaic. These cases provide the first molecular evidence for the occurrence of post-zygotic mutation in X-linked alpha thalassaemia mental retardation syndrome. The possibility of germline mosaicism must therefore be considered in the genetic counselling of ATR-X families.

DNA Methylation↗
PubMed2004

Esc4p, a new target of Mec1p (ATR), promotes resumption of DNA synthesis after DNA damage.

The DNA damage-responsive protein kinases ATM and ATR phosphorylate SQ/TQ motifs that lie in clusters in most of their in vivo targets. Budding yeast Esc4p contains a cluster of SQ/TQ motifs, suggesting that it might be a target of Mec1p/Tel1p (yeast ATR/ATM). Here it is reported that Esc4p is phosphorylated by Mec1p in response to DNA damage during DNA replication and that cells lacking Esc4p are hypersensitive to DNA damage specifically during S phase. Esc4p is not required for the intra-S-phase checkpoint but is essential for resumption of chromosome replication after DNA damage, and its role in promoting restart appears to be distinct from that of Rad53p. Mutation of Esc4p SQ/TQ motifs phosphorylated by Mec1p or mutation of the BRCT domains of Esc4p also renders cells unable to restart DNA replication after DNA damage and causes hypersensitivity to genotoxins. These results identify Esc4p as an important new S-phase-specific target of Mec1p.

Chromosomal Instability↗
PubMed2003

Chemometric resolution of ATR-IR spectra data for polycondensation reaction of bis(hydroxyethylterephthalate) with a combination of self-modeling curve resolution (SMCR) and local rank analysis.

Self-modeling curve resolution (SMCR) methods, simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) and alternating least squares (ALS) were used to calculate pure concentration profiles and pure spectra for the two-way spectral data collected during the on-line polycondensation reaction of bis(hydroxyethylterephthalate) with an ATR-FT-IR spectrometer. In order to improve the resolution results, SIMPLISMA was combined with local rank analysis method, fixed size moving window evolving factor analysis (FSMWEFA) to search for selective regions of various components and then look for the purest wavenumber variables in the selective regions. Such combination allows more accurate determination of the number of chemical components in the reaction system and the calculations of more accurate concentration profiles and spectra.

Journal Article↗
PubMed2005

ATR-FTIR membrane-based sensor for the simultaneous determination of surfactant and oil total indices in industrial degreasing baths.

Monitoring the exhaustion of alkaline degreasing baths is one of the main aspects in metal mechanizing industrial process control. The global level of surfactant, and mainly grease, can be used as ageing indicators. In this paper, an attenuated total reflection-Fourier transform infrared (ATR-FTIR) membrane-based sensor is presented for the determination of these parameters. The system is based on a micro-liquid-liquid extraction of the analytes through a polymeric membrane from the aqueous to the organic solvent layer which is in close contact with the internal reflection element and continuously monitored. Samples are automatically processed using a simple, robust sequential injection analysis (SIA) configuration, on-line coupled to the instrument. The global signal obtained for both families of compounds are processed via a multivariate calibration technique (partial least squares, PLS). Excellent correlation was obtained for the values given by the proposed method compared to those of the gravimetric reference one with very low error values for both calibration and validation.

Metallurgy↗
PubMed2001

Difference between the E1 and E2 conformations of gastric H+/K+-ATPase in a multilamellar lipid film system. Characterization by fluorescence and ATR-FTIR spectroscopy under a continuous buffer flow.

A liquid flow cell was used for an attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) study of conformational changes taking place in the gastric H+/K+-ATPase. Shifting from E1 to E2 form is induced by replacing Na+ by K+ ions. Introducing ions through a flow passing over a protein multilayer film induced the conformational change without cell manipulations. Measurement sensitivity was thereby improved by about one order of magnitude. The detection threshold allowed the possibility to detect a change affecting five amino acids out of the 1324 that compose the H+/K+-ATPase molecule. It appeared that fewer than five amino-acid residues undergo a conformational change upon replacing Na+ by K+ ions in the medium. Evidence that conformational changes occur in an identical system was brought by monitoring the fluorescence of fluorescein isothiocyanate-labeled H+/K+-ATPase in similar conditions. Our data suggest that essentially the tertiary structure of the protein is modified.

Adenosine Triphosphatases↗
PubMed2002

Rapid and non-destructive determination of the echinacoside content in Echinacea roots by ATR-IR and NIR spectroscopy.

NIR reflection and ATR-IR spectroscopy methods are developed to determine the echinacoside content in roots of Echinacea angustifolia and Echinacea pallida. Based on the recorded spectra and the HPLC reference data, chemometrical analyses are performed using a partial least squares (PLS) algorithm. Generally, good calibration statistics are obtained for the prediction of the echinacoside content presenting comparatively high coefficients of determination (R(2)) and low root mean standard errors of cross validation (RMSECV). It is demonstrated that optimal predictions are possible when using a dispersive spectrometer covering the spectral range from 1,100 to 2,500 nm. In contrast to the time-consuming HPLC method, the described non-destructive measurements allow us to predict the echinacoside content already after an analysis time of approx. one minute. Both spectroscopic techniques presented in this paper are shown to be useful in agricultural practice as well as in the phytopharmaceutical industry.

Chromatography, High Pressure Liquid↗