Quantitative Spectrum Analysis Research Articles

Spectroscopic QSAR methods and self-organizing molecular field analysis for relating molecular structure and estrogenic activity.

The performance of three "spectroscopic" quantitative structure-activity relationship (QSAR) methods (eigenvalue (EVA), electronic eigenvalue (EEVA), and comparative spectra analysis (CoSA)) for relating molecular structure and estrogenic activity are critically evaluated. The methods were tested with respect to the relative binding affinities (RBA) of a diverse set of 36 estrogens previously examined in detail by the comparative molecular field analysis method. The CoSA method with (13)C chemical shifts appears to provide a predictive QSAR model for this data set. EEVA (i.e., molecular orbital energy in this context) is a borderline case, whereas the performances of EVA (i.e., vibrational normal mode) and CoSA with (1)H shifts are substandard and only semiquantitative. The CoSA method with (13)C chemical shifts provides an alternative and supplement to conventional 3D QSAR methods for rationalizing and predicting the estrogenic activity of molecules. If CoSA is to be applied to large data sets, however, it is desirable that the chemical shifts are available from common databases or, alternatively, that they can be estimated with sufficient accuracy using fast prediction schemes. Calculations of NMR chemical shifts by quantum mechanical methods, as in this case study, seem to be too time-consuming at this moment, but the situation is changing rapidly. An inherent shortcoming common to all spectroscopic QSAR methods is that they cannot take the chirality of molecules into account, at least as formulated at present. Moreover, the symmetry of molecules may cause additional problems. There are three pairs of enantiomers and nine symmetric (C(2) or C(2)(v)) molecules present in the data set, so that the predictive ability of full 3D QSAR methods is expected to be better than that of spectroscopic methods. This is demonstrated with SOMFA (self-organizing molecular field analysis). In general, the use of external test sets with randomized data is encouraged as a validation tool in QSAR studies.

Quantitative XANES Analysis of Cuprous Dibromide Complex Formed in the Oxidative Carbonylation of Phenols

Quantitative analysis of Cu K-edge XANES spectra representing mixed states of two cuprous compounds was studied to determine the composition of copper species formed in the oxidative carbonylation of phenols. The quantification of two Cu(I) species, Cu2O and an unusual cuprous dibromide complex in the linear configuration stabilized with tetrabutylammonium cation, could be achieved through detailed edge analyses to choose proper reference XANES spectra, followed by fitting the experimental XANES spectrum with the linear combination of the two reference spectra. The amount of cuprous dibromide complex obtained by this method showed an excellent correlation with the rate of formation of the desired para-position carbonylation products, indicating that the phase was the active and selective catalytic phase of copper.

Binary Interactions of Poly(Ethylene Covinyl Alcohol) with Poly(4-Vinyl Pyridine) and Poly(n-Butyl Methacrylate)

The effect of hydrogen bonding on the phase behavior of binary polymer blends of poly(ethylene covinyl alcohol) (EVOH) with poly(n-butyl methacrylate) (PBMA) and poly(4-vinyl pyridine) (PVPy) was studied by Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR/ATR). The association model of Painter, Coleman, and co-workers was used to analyze the effect of hydrogen bonding on miscibility of polymer blends containing EVOH. The equilibrium constants of solvation of EVOH with PVPy are determined from the quantitative analysis of spectra at 60, 100, and 140 °C and compared with previous results available at room temperature. The equilibrium constants of solvation of EVOH with PBMA were similarly determined at 60, 100, and 140 °C. Results for these binary blends are of interest in understanding the roles of compatibilizers and predicting results for multicomponent blend. Because the pyridine nitrogen and the carbonyl oxygen absorb in different regions of the IR spectrum, this choice of com...

Factor selection strategies for orthogonal signal correction applied to calibration of near-infrared spectra

Orthogonal signal correction (OSC) is a preprocessing technique used for correction of instrumental drift, bias and scatter in near-infrared spectra. OSC separates the variation into orthogonal factors, where the factors contain the variation within the X matrix data that is not correlated with the y matrix vector data. The aim of this study is to investigate different orthogonal factor selection methods, which will enhance the performance of the OSC routine for quantitative analysis of near-infrared spectra. In order for factor selection methods to be applied to OSC, an implementation of an existing OSC algorithm is used; this method computes OSC factors in a principal component manner. A binarized weighting matrix is then applied to the OSC factors for the purpose of OSC factor subset selection/nonselection. The optimization strategies used for subset selection of OSC factors were a genetic algorithm and stepwise selection. Three data sets were formed: (1) no preprocessing, (2) preprocessing by removal of sequential OSC factors and (3) preprocessing by removal of an OSC factor subset. Combinations of spectral predictors were selected from these data sets by hill climbing, feature selection, genetic algorithm and full-spectrum modeling. Partial least squares regression was undertaken to form calibration models. It was found that selection of OSC factor subsets produced better standard errors of prediction relative to data preprocessed by sequential selection of OSC factors.

Zn speciation in a soil contaminated by the deposition of a dredged sediment by synchrotron X-ray techniques

The nature and proportion of Zn species present in an agricultural soil overlaid by a dredged contaminated sediment have been untangled by the novel combination of three non-invasive synchrotron-based x-ray techniques: x-ray microfluorescence ({mu}SXRF), microdiffraction ({mu}XRD), and absorption spectroscopy (EXAFS). One primary (franklinite) and two secondary (phyllomanganate and phyllosilicate) Zn-containing minerals were identified in the initial soil, and another primary (ZnS) and a new secondary (Fe-(oxyhydr)oxide) Zn species in the covered soil. The quantitative analysis of EXAFS spectra recorded on bulk samples indicated that ZnS and Zn-Fe (oxyhydr)oxides amounted to 71+-10 percent and 27+-10 percent, respectively, and the other Zn species to less than 10 percent. The two new Zn species found in the covered soil result from the gravitational migration of ZnS particles initially present in the sediment, and from their further oxidative dissolution and fixation of leached Zn on F e (oxyhydr) oxides.

Quantitative Analysis of Optical Spectra from Individual Single-Wall Carbon Nanotubes

We discuss how tight-binding band-structure calculations with a chirality- and diameter-dependent nearest-neighbor hopping integral may be used to relate well resolved features in the UV-VIS-NIR spectra of individual single-wall carbon nanotubes (SWNTs) to electronic excitations in specific tube types. The assignment of (n,m) indices to interband transitions in specific tube types can support a quantitative analysis of absorption spectra which may eventually be used for rapid screening and optimization of sample composition during SWNT synthesis.

Depth profiles of Argon incorporated into Boron Nitride films during preparation and their temperature dependent evolution

Cubic (c-) as well as hexagonal (h-) Boron Nitride (BN) films, prepared by different ion beam assisted deposition techniques on top of Si(0 0 1) substrates, were studied with respect to the depth profiles of incorporated Argon using Rutherford backscattering (RBS). Quantitative analysis of such RBS spectra clearly demonstrated a preferential trapping of Ar close to the substrate, where high resolution transmission electron microscopy revealed the presence of an amorphous intermixed and an h-BN layer on top of each other. Subsequent annealing steps at 730, 960 and 1100 °C combined with RBS allowed to determine the total amount of Ar diffusing out of a sample as well as the depth profiles of the residual Ar. For temperatures below 750 °C neither in c-BN nor in h-BN any Ar diffusion is observed. At 970 °C a clear outdiffusion of Ar is found in h-BN samples, while in c-BN a redistribution of the profiles occurs with a significant accumulation of Ar towards the surface. At 1100 °C, a loss of Ar becomes visible also for c-BN films and is attributed to grain boundary diffusion, while Ar trapped within c-BN grains appears still to be immobile.

Hydration of hyaluronan polysaccharide observed by IR spectrometry. II. Definition and quantitative analysis of elementary hydration spectra and water uptake.

We recorded a series of spectra of sodium hyaluronan (HA) films that were in equilibrium with their surrounding humid atmosphere. The hygrometry of this atmosphere extended from 0 to 0.97% relative humidity. We performed a quantitative analysis of the corresponding series of hydration spectra that are the difference spectra of the film at a defined hygrometry minus the spectrum of the dried film (hygrometry = 0). The principle of this analysis is to use this series of hydration spectra to define a limited number (four) of "elementary hydration spectra" over which we can decompose all hydration spectra with good accuracy. This decomposition, combined with the measurements of the numbers of H(2)O molecules at the origin in these elementary hydration spectra of the three characteristic vibrational bands of H(2)O, allowed us to calculate the hydration number under different relative humidity conditions. This number compares well with that determined by thermogravimetry. Furthermore, the decomposition defines for each hygrometry value which chemical mechanisms represented by elementary hydration spectra are active. This analysis is pursued by determining for the elementary hydration spectra the number of hydrogen bonds established by each of the four alcohol groups found in each disaccharide repeat unit before performing the same analysis for amide and carboxylate groups. These results are later utilized to discuss the structure of HA at various stages of hydration.

Contribution of Fe and Protonic Sites in Calcined and Steamed ZSM-5 Zeolites to Oxidation of Benzene with N2O to Phenol and Selective Catalytic Reduction of NO with Propane to Nitrogen

NH4-(Fe)ZSM-5 zeolites with concentrations of Fe ranging from 30 to 2000 ppm, introduced into zeolites during their synthesis, either calcined in dry oxygen at 720 K or steamed at 870 K in oxygen stream with 30% water vapor, were investigated in benzene oxidation with N2O to phenol and selective catalytic reduction of NOx to nitrogen. The concentration of Brönsted and Lewis sites was determined by quantitative analysis of IR spectra of adsorbed d3-acetonitrile. The changes in Fe ion coordination were monitored by ESR spectra of Fe(III) ions. The Fe ions have been shown to control the activity of zeolites in the above reactions, while the Al-related acid sites play only a minor role. The steamed zeolites compared to calcined ones exhibited substantially higher activity in oxidation of benzene with N2O to phenol, while the reduction of NOx to nitrogen was considerably suppressed. The steaming resulted in a dramatic decrease in concentration of Brönsted sites, low concentration of Lewis sites and relocalization of Fe ions into cationic sites exhibiting distorted tetrahedral coordination (ESR signals at g = 6.0 and 5.6). It has been concluded that specific Fe sites are required for benzene oxidation to phenol without participation of Brönsted sites, while with the complex SCR-NOx reaction both Fe cationic sites and protonic sites are involved in the catalytic process. Fe sites contribute to oxidation of NO to NO2 and protonic sites control reduction of NO2 to molecular nitrogen.

Hydration of polysaccharide hyaluronan observed by IR spectrometry. I. Preliminary experiments and band assignments

This article is the first one in a series dedicated to the study of hyaluronan as observed by IR spectrometry. The goal is to determine its hydration mechanism and the structural changes this mechanism implies. Hyaluronan is a natural polysaccharide that is widely used in biomedical applications and cosmetics. Its macroscopic properties are significantly dependent on its degree of hydration. In this article we record the IR spectrum of a several micron thick dried film and deduce that four or five residual H(2)O molecules remain around each disaccharide repeat unit in the dried film. We then compare the spectra of sodium hyaluronan and its acid form to assign vibrational bands linked to the carboxylate group. We proceed with a qualitative analysis of the spectral changes induced by changes of temperature and hygroscopicity, two independent parameters that act by modifying the hydrogen bond network of the sample. This enables us to assign most of the vibrational bands of the hydrophilic groups and to distinguish the bands that are due to these hydrophilic groups when they are or are not hydrogen bonded. It constitutes a prerequisite for the quantitative analysis of hydration spectra that will be described in the following articles of this series.

Investigations of the Potential-Dependent Structure of Phenylalanine on the Glassy Carbon Electrode by Infrared−Visible Sum Frequency Generation

We investigated the structure of adsorbed l-phenylalanine (Phe) on the glassy carbon electrode (GCE) as a function of electrode potential using infrared-visible sum frequency generation (SFG) vibrational spectroscopy. Experiments using partially deuterated Phe confirmed that SFG signal originates from the CH stretch modes of the methylene group (CH2) in Phe. Quantitative analysis of SFG spectra revealed that Phe molecules adopt a conformation in which the dipole contribution of the asymmetric mode of the methylene group becomes greater than the symmetric mode with respect to the surface normal at highly positive electrode potential.

Arsenic adsorption and exchange with phosphorus on indium phosphide (001)

Arsenic adsorption and exchange with phosphorus on indium phosphide (001) have been studied by scanning tunneling microscopy, low-energy electron diffraction, and x-ray photoelectron spectroscopy. The surface phase diagram as a function of temperature has been obtained. At 285 \ifmmode^\circ\else\textdegree\fi{}C, arsenic adsorbs on the InP $\ensuremath{\sigma}(2\ifmmode\times\else\texttimes\fi{}4)$ surface $(\mathrm{P}\mathrm{}\mathrm{coverage}=0.25\mathrm{ML}),$ forming a disordered $(1\ifmmode\times\else\texttimes\fi{}4)$ with double layers of arsenic $(\mathrm{As}+\mathrm{P}\mathrm{}\mathrm{coverage}\ensuremath{\sim}1.5\mathrm{ML}).$ At 330 \ifmmode^\circ\else\textdegree\fi{}C, arsenic adsorbs on the $\ensuremath{\sigma}(2\ifmmode\times\else\texttimes\fi{}4),$ producing a $(2\ifmmode\times\else\texttimes\fi{}1)$ structure with a complete monolayer of group-V dimers. By contrast, some phosphorus desorption occurs above 350 \ifmmode^\circ\else\textdegree\fi{}C, allowing arsenic to displace the phosphorus in the top few layers and converting the $\ensuremath{\sigma}(2\ifmmode\times\else\texttimes\fi{}4)$ to the \ensuremath{\beta}2 and \ensuremath{\alpha}2(2\ifmmode\times\else\texttimes\fi{}4) reconstructions (As coverage 0.75 and 0.50 ML, respectively). Above 430 \ifmmode^\circ\else\textdegree\fi{}C, arsenic exchange with InP yields an InAs $(4\ifmmode\times\else\texttimes\fi{}2)$ reconstruction. Quantitative analysis of the x-ray photoemission spectra has revealed that substitution of arsenic for phosphorus is limited to the top two to three surface bilayers.

Quantitative trace element analysis of individual fly ash particles by means of X-ray microfluorescence.

A new quantification procedure was developed for the evaluation of X-ray microfluorescence (XRF) data sets obtained from individual particles, based on iterative Monte Carlo (MC) simulation. Combined with the high sensitivity of synchrotron radiation-induced XRF spectroscopy, the method was used to obtain quantitative information down to trace-level concentrations from micrometer-sized particulate matter. The detailed XRF simulation model was validated by comparison of calculated and experimental XRF spectra obtained for glass microsphere standards, resulting in uncertainties in the range of 3-10% for the calculated elemental sensitivities. The simulation model was applied for the quantitative analysis of X-ray tube and synchrotron radiation-induced scanning micro-XRF spectra of individual coal and wood fly ash particles originating from different Hungarian power plants. By measuring the same particles by both methods the major, minor, and trace element compositions of the particles were determined. The uncertainty of the MC based quantitative analysis scheme is estimated to be in the range of 5-30%.

A Quantitative Analysis of Two-Colour Pump and Probe Spectra from Bound Excitons in Compensated II–VI Semiconductors

Excitonic energy transfer processes were investigated with time-resolved two-colour pump and probe spectroscopy in the ps-region. In highly compensated ZnSe epilayers, characteristic induced absorption and transmission resonances related to donor bound excitons (I2) and acceptor bound excitons (I1) could be observed. To explain the experimental results quantitatively a set of coupled rate equations was developed.

Growth and Physical Characterization of La-Doped Bi 4 Ti 3 O 12 Crystals

The crystals of La-doped Bi 4 Ti 3 O 12 were grown by a conventional flux growth method using Bi 2 O 3 , TiO 2 and La 2 O 3 . The quantitative analysis of x-ray photoelectron spectra and change of band gap make an estimate of La sites in the La doped Bi 4 Ti 3 O 12 crystals. All of the La ions doped in the Bi 4 Ti 3 O 12 crystals are well substituted with Bi ions. The remanent polarization, P r and the coercive field, E c were 3.2, 5.2 and 0.3 w C/cm 2 , and 5.6, 7.6 and 0.6 kV/cm for Bi 4.3 Ti 3 O 12.4 , Bi 3.65 La 0.47 Ti 3 O 12.17 and Bi 2.76 La 1.67 Ti 3 O 12.65 crystals, respectively. However, Bi 2.76 La 1.67 Ti 3 O 12.65 crystal seems to be not saturated.

A Quantitative Analysis of Two-Colour Pump and Probe Spectra from Bound Excitons in Compensated II-VI Semiconductors

Excitonic energy transfer processes were investigated with time-resolved two-colour pump and probe spectroscopy in the ps-region. In highly compensated ZnSe epilayers, characteristic induced absorption and transmission resonances related to donor bound excitons (I 2 ) and acceptor bound excitons (I 1 ) could be observed. To explain the experimental results quantitatively a set of coupled rate equations was developed.

On background subtraction for quantitative analysis of X-ray photoelectron spectra of rare earth fluorides

The applicability of Tougaard's method of a “universal” form of background correction in photoelectron spectra was investigated for thin films of the wide gap insulators YbF x , DyF x , SmF x , and YF x . These films were produced by ion assisted deposition with varying fluorine content x⩽3, caused by preferential sputtering. For YbF x , in particular, acceptable accuracy was obtained for x⩾2.4 by shifting the universal background function by the band gap energy, while for x<2.4, no reasonable fit of the experimental background could be obtained. More realistic profiles of the inelastic scattering background were calculated on the basis of published fast-electron energy-loss data of DyF 3, which yielded highly accurate quantification of spectra of YbF x in the whole range of x between 2 and 3. This was confirmed by measurements of the intensity ratios of the 4f peaks of Yb 2+ and Yb 3+, representing valence states 2 and 3, respectively, which are directly correlated with the fluorine content. Stoichiometry values from XPS data were compared with Rutherford backscattering analysis and yielded good agreement.

Exchange of Co(II) ions in H-BEA zeolites: identification of aluminum pairs in the zeolite framework

The Co(II) ion exchange in NH 4-, HNa- and H-BEA zeolites (Zeolite beta, BEA) was employed to monitor framework Al pairs in these zeolites balancing the charge of the divalent cations. The character and concentration of unperturbed bridging OH groups or those perturbed via hydrogen bonding, and Lewis sites (defective and tricoordinated framework Al) of NH 4-, HNa- and H-BEA zeolites, and their changes induced by Co(II) ion exchange were investigated by quantitative analysis of IR spectra in the region of OH groups and vibrations of CN groups of adsorbed d 3-acetonitrile. It is shown that the Co(II) ions in dehydrated BEA zeolites, requiring two AlO 2 − framework groups for their charge balance, are at cationic sites which were occupied in the parent zeolites by Na ions or by mutually interacting protons or by those exhibiting a high tendency to be dehydroxylated with the formation of Lewis sites. A part of the unperturbed bridging OH groups is not exchanged by divalent Co(II) ions, indicating the far distances of the respective framework aluminum atoms. This indicates that the framework local structures bearing close AlO 2 − groups in BEA represent an unstable environment with weakened framework Al–O bonds. Metal cations, both Na(I) and Co(II) ions greatly prefer occupation of cationic sites containing two close framework AlO 2 − groups. Thus metal ion exchange brings about a high stabilization of the BEA framework, and protects the local environment of the aluminum framework against substantial rearrangements leading to the formation of Lewis sites.

Outer-Valence Green's Function Study of Cycloalkane and Cycloalkyl−Alkane Compounds

In this contribution, we report a quantitative analysis of gas-phase ultraviolet photoelectron spectra (HeI) of model compounds such as cyclopentane, cyclohexane, and cycloalkyl−1-alkane derivatives, by means of outer-valence Green's function (OVGF) calculations. These spectra and their OVGF theoretical simulations are also compared with UPS measurements on α-cycloalkyl−ω-alkanethiol monolayers adsorbed on gold. This theoretical study analyses the dependence of valence ionization spectra of saturated hydrocarbons on structural characteristics (configuration, conformation, and torsional flexibility).

Catalytic Activity of Cu-Beta Zeolite in NO Decomposition: Effect of Copper and Aluminium Distribution

Catalytic activity in NO decomposition of Cu-Beta zeolites with different Cu/Al/Si composition, diffuse reflectance UV–vis–NIR spectra of Cu ions of hydrated Cu-Beta zeolites, and concentration of Brønsted and Lewis sites in parent Beta zeolites, determined by quantitative analysis of FTIR spectra of adsorbed d3-acetonitrile, were investigated. Cu-Beta zeolites exhibit high and stable activity in NO decomposition in the temperature range 580–750 K and Si/Al ratio 12.7–42. Strong dependence of activity in NO decomposition per Cu ion (TOF) on Cu/Al loading indicates the presence of three Cu species in Cu-Beta zeolites. Cu ions incorporated at low Cu loading are balanced by two framework Al atoms and are inactive in NO decomposition. Species responsible for NO decomposition are formed at medium Cu loading and represent Cu ions balanced by single-framework Al atoms. At high Cu loading, a new type of inactive, noncationic Cu species (small clusters of Cu2O) is formed. Brønsted and Lewis sites themselves do not contribute to the catalytic activity of Cu-Beta zeolites in NO decomposition. However, the presence of Lewis sites in the parent zeolites is connected with the occurrence of the framework sites containing two close Al atoms and bonding the Cu ions which are not active in NO decomposition. A comparison of Cu ion activity in Beta and ZSM-5 is discussed.