Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.     

Chemical markup,XML, and the World Wide Web. 4. CML schema

A revision to Chemical Markup Language (CML) is presented as a XML Schema compliant form, modularized into nonchemical and chemical components. STMML contains generic concepts for numeric data and scientific units, while CMLCore retains most of the chemical functionality of the original CML 1.0 and extends it by adding handlers for chemical substances, extended bonding models and names. We propose extension via new namespaced components for chemical queries, reactions, spectra, and computational chemistry. The conformance with XML schemas allows much greater control over datatyping, document validation, and structure.     

Orthogonal signal correction, wavelet analysis, and multivariate calibration of complicated process fluorescence data

In this paper, multivariate calibration of complicated process fluorescence data is presented. Two data sets related to the production of white sugar are investigated. The first data set comprises 106 observations and 571 spectral variables, and the second data set 268 observations and 3997 spectral variables. In both applications, a single response, ash content, is modelled and predicted as a function of the spectral variables. Both data sets contain certain features making multivariate calibration efforts non-trivial. The objective is to show how principal component analysis (PCA) and partial least squares (PLS) regression can be used to overview the data sets and to establish predictively sound regression models. It is shown how a recently developed technique for signal filtering, orthogonal signal correction (OSC), can be applied in multivariate calibration to enhance predictive power. In addition, signal compression is tested on the larger data set using wavelet analysis. It is demonstrated that a compression down to 4% of the original matrix size — in the variable direction — is possible without loss of predictive power. It is concluded that the combination of OSC for pre-processing and wavelet analysis for compression of spectral data is promising for future use.     

Emission spectral characteristics of Cu,Ag, Zn,and Cd neutral atoms in a glow discharge

Detailed spectra highlighting the neutral atom emission characteristics (i.e. I lines) for Cu, Zn, Ag and Cd in a glow discharge device are presented in this study. A particular focus is the presentation of spectra that document the many high excitation energy neutral atom lines that are observed in these spectra. For Cu, several spectral lines originating from levels close to the ionization potential of copper are observed including lines from the so-called autoionizing levels which are actually just above the ionization potential for copper. Generally similar results are seen for Ag, Zn and Cd, including the observation of many high excitation energy neutral atom lines of Zn originating from the upper levels on the triplet side of the energy level diagram. The spectral data point to ion–electron recombination processes followed by stepwise de-excitation and radiative decay as a key mechanism in setting the spectral character of neutral atom emission in a glow discharge device. Unambiguous identification of spectral lines for specific transitions was facilitated by the acquisition of all spectral data utilizing a UV–visible Fourier transform spectrometer. This spectrometer provided complete and continuous coverage of the spectral region from 200 to 650 nm and allowed spectral lines to be identified with an accuracy of 1–2 pm.     

Study of Matrix Effects on Determination of Trace Elements in Aluminum,Using Inductively Coupled Plasma Atomic Emission Spectrometry, 1) Selection of Spectral Lines.

Abstract

The effect of an aluminum matrix on the determination of B, Ca, Cd, Co, Cr, Cu, Fe, Mg, Mn, Ni, Si and Zn was studied. These elements are expected to be present in high purity Al base materials. 45 spectral lines of these elements were scanned in a spectral window of 60 pm. Background equivalent concentrations were calculated and compared with existing data. Interference free spectral lines, one for each element, have been recommended to be used for analysis. Depression effects due to the Al matrix were calculated at the selected lines.     

Diode array detection and simultaneous quantitation of the coeluting atenolol-related synthetic route impurities, PPA-Diol.

The diode array multichannel detector is used to acquire spectral information at specified intervals in the elution profile of atenolol and its related impurities for post-chromatographic data analysis. The applicability of a number of peak homogeneity testing methods, including spectral normalization, absorbance ratio, chromatographic derivatives, and spectral suppression (SS), are assessed for suitability in simultaneous determinations of the coeluting atenolol-related synthetic impurities, PPA-Diol. Spectral suppression displays a superior performance in comparison to all the other techniques in that both qualitative and quantitative information are acquired on the system.     

Descriptive,interactive computer-assisted interpretation of infrared spectra

A knowledge-based system for interpreting infrared spectra which explains the rationale behind the interpretation process, in a step-by-step fashion, has been developed. The user, having been informed of the basis for decisions made during interpretation of the data, is better able to understand, and thereby to utilize, the results. Additional features allow the informed user to participate in the interpretation of the spectral data, thereby increasing the quality and quantity of data available to the system. In addition to assisting researchers, this system can be used for computer- assisted instruction of the infrared spectral interpretation process.     

Fast gradient elution reversed-phase liquid chromatography with diode-array detection as a high-throughput screening method for drugs of abuse. II. Data analysis

In Part I of this work, we developed a method for the detection of drugs of abuse in biological samples based on fast gradient elution liquid-chromatography coupled with diode array spectroscopic detection (LC-DAD). In this part of the work, we apply the chemometric method of target factor analysis (TFA) to the chromatograms. This algorithm identifies the target compounds present in chromatograms based on a spectral library, resolves nearly co-eluting components, and differentiates between drugs with similar spectra. The ability to resolve highly overlapped peaks using the spectral data afforded by the DAD is what distinguishes the present method from conventional library searching methods. Our library has a mean list length (MLL) of 1.255 and a discriminating power of 0.997 when both retention index and spectral factors are considered. The algorithm compares a library of 47 different compounds of toxicological relevance to unknown samples and identifies which compounds are present based on spectral and retention index matching. The application of a corrected retention index for identification rather than raw retention times compensates for long-term and column-to-column retention time shifts and allows for the use of a single library of spectral and retention data. Training data sets were used to establish the search and identification parameters of the method. A validation data set of 70 chromatograms was used to calculate the sensitivity (correct identification of positives) and specificity (correct identification of negatives) of the method, which were found to be 92% and 94%, respectively.     

A spectral study of charge transfer and Penning processes for Cu,Zn, Ag,and Cd in a glow discharge

The occurrence of charge transfer and Penning process in glow discharge atomic emission sources can have a profound effect on the specific and overall spectral emission line characteristics of analyte species in these sources. A detailed spectral illustration of several of these effects is presented in this study for Cu, Zn, Ag and Cd with a particular focus on the ionic emission characteristics (i.e. II lines) of these elements. Charge transfer and Penning processes in glow discharge devices are driven by ionic and metastable species generated from the filler gas. Comparison of spectra obtained utilizing different filler gases is particularly effective for revealing the unique and specific excitation pathways for the analyte ions. Detailed high resolution spectra are presented and compared for Cu and Zn (brass) with Ar, Ne or He filler gases and for Ag and Cd with Ar or He as the filler gas illustrating several charge transfer and Penning processes. Unambiguous identification of spectral lines for specific transitions was facilitated by the acquisition of all spectral data utilizing a UV–visible Fourier transform spectrometer. This spectrometer provided complete and continuous coverage of the spectral region from 200 to 650 nm and allowed spectral lines to be identified with an accuracy of 1–2 pm.     

A general Monte Carlo simulation of ED-XRF spectrometers. II: Polarized monochromatic radiation,homogeneous samples

A general Monte Carlo code for the simulation of X-ray fluorescence spectrometers, described in a previous paper is extended to predict the spectral response of instruments employing polarized exciting radiation. Details of the calculation method specific for the correct simulation of photon-matter scatter interactions in case of polarized X-ray beams are presented. Comparisons are made with experimentally collected spectral data obtained from a monochromatic X-ray fluorescence setup installed at a synchrotron radiation source. The use of the simulation code for quantitative analysis of intermediate and massive samples is also demonstrated.     

Deuterium spin probes of side-chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time-scale side-chain motions

In the previous paper in this issue we have demonstrated that it is possible to measure the five different relaxation rates of a deuteron in (13)CH(2)D methyl groups of (13)C-labeled, fractionally deuterated proteins. The extensive set of data acquired in these experiments provides an opportunity to investigate side-chain dynamics in proteins at a level of detail that heretofore was not possible. The data, acquired on the B1 domain of peptostreptococcal protein L, include 16 (9) relaxation measurements at 4 (2) different magnetic field strengths, 25 degrees C (5 degrees C). These data are shown to be self-consistent and are analyzed using a spectral density mapping procedure which allows extraction of values of the spectral density function at a number of frequencies with no assumptions about the underlying dynamics. Dynamics data from 31 of 35 methyls in the protein for which data could be obtained were well-fitted using the two-parameter Lipari-Szabo model (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546). The data from the remaining 4 methyls can be fitted using a three-parameter version of the Lipari-Szabo model that takes into account, in a simple manner, additional nanosecond time-scale local dynamics. This interpretation is supported by analysis of a molecular dynamics trajectory where spectral density profiles calculated for side-chain methyl sites reflect the influence of slower (nanosecond) time-scale motions involving jumps between rotameric wells. A discussion of the minimum number of relaxation measurements that are necessary to extract the full complement of dynamics information is presented along with an interpretation of the extracted dynamics parameters.     

Time-resolved spectroscopy of the human forearm.

For spectroscopic purposes, the forearm is a conveniently large object to be investigated because consistent oxygenation and blood volume changes can be obtained. Human forearm spectral properties were investigated using picosecond near-IR laser spectroscopy. The behaviour of the temporal point spread function in resting conditions and during ischaemia, venous occlusion and exercise is reported. The effect of path length inaccuracy on muscle oxygen consumption, obtained by combining spectral data with the path length, is discussed.     

Pattern recognition. An application to the identification of some stereoisomeric N-acetylhexosamines by mass spectrometry

A method is reported for the identification of trimethylsilylated stereoisomeric N-acetyl-hexosamines by application of a pattern recognition procedure to mass spectral data. The selection of characteristic mass spectral data and the pattern recognition procedure are discussed.     

Structures of deacetyl glykenins-a,b, and c,glycosidic antibiotics from basidiomycetes sp.

The structures of deacetyl Glykenins (DG)-A, B, and C, basic structures of Glykenins, were elucidated by chemical degradation and interpretation of spectral data.     

Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM

We describe the development of a structured method of representing chemistry on the World-Wide Web using an object-oriented approach to information objects. We show how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML). Application of the CMLDOM to the development of chemical tools is described.     

Comprehensive software suite for the operation, maintenance, and evaluation of an ion mobility spectrometer

Scientific applications of Ion Mobility Spectrometry require the ability to easily compare data between different laboratories. Reduced mobility values attempt to provide this functionality, but no standard exists for the collection and manipulation of the raw data obtained during an IMS experiment. We have created a comprehensive software suite based on the LabVIEW programming language that can be used to collect and interpret IMS data. The software may be used to collect data from a stand-alone IMS cell, a voltage sweep IMS cell, or a coupled chromatography-IMS system, and this framework may be adapted to incorporate mass spectral data analysis as well. This software is provided under an open source license for the benefit of the IMS community.     

A new democratic phase coherent data-scatter technique for calibration, measurement, fingerprinting and rapid archival identification of ultraviolet-visible multi-component food spectra

The new theory of democratic phase coherent data-scatter (DPCD-S) is introduced. Basics of UV-visible spectrometry theory and error propagation have been presented. The qualitative spectral analysis provided is point-by-point over the complete data set and not just limited to Lambda-maxima. Equal weightings of the ‘voting’ data scattering algorithm are employed in the analysis of both the calibration and food colour data and this is consequently the democratic algorithm. The paper shows how the technique can be used with UV-visible standards to analyse the wavelength and photometric calibration of a spectrophotometer. The main results relate to the analysis of a series of spectra taken on complex mixtures of three important food dyes and their quantitative analysis using the phase coherent data-scatter technique. This method is shown to offer new possibilities for identifying and archiving UV-visible spectra from a single point in a transform space. Complex spectra can therefore be represented by a single point in this transform space, which is weighted by the ‘votes’ of all the data points in the complex data set. The software allows the user to interrogate the scatter results and locate the scatter point to the specific spectral positions. A new mathematical operator has been introduced to resolve any possible coincidence of two spectral projection points. Analysis of two close spectra from very-different admixtures of food colours shows powerfully the utility of this operator. Error propagation severely limits the accuracy of the usual UV-method of simultaneous equation secondary mixtures analysis.     

Studies on the constituents of Syringa species. XII. New glycosides from the leaves of Syringa reticulata (BLUME) HARA

Three new glycosides, 6'-O-alpha-D-galactopyranosylsyringopicroside (1), secologanoside 7-methyl ester (2) and (+)-lariciresinol 4'-O-beta-D-glucopyranosyl-(1-->3)-beta-D-glucopyranoside (3), were isolated from the leaves of Syringa reticulata. Their structures were established on the basis of chemical and spectral data. Compound 1 is the first naturally occurring iridoid di-glycoside having melibiose. Comparison of the spectral data of 2 and that previously recognized as secologanoside 7-methyl ester led to the conclusion that the recognized structure should be revised to the sodium salt of secoxyloganin (2').     

Analytical chemistry of synthetic routes to psychoactive tryptamines. Part II. Characterisation of the Speeter and Anthony synthetic route to N,N-dialkylated tryptamines using GC-EI-ITMS, ESI-TQ-MS-MS and NMR

The degree of alkylation of the side chain nitrogen in tryptamines is one important factor that affects psychoactivity. The method of Speeter and Anthony is considered to be one of the most important synthetic preparative methods. The final step in this reaction is based on the reduction of a (substituted) indole-3-yl-glyoxalylamide to the desired tryptamine with metal hydride. Twelve symmetrically and 13 asymmetrically N,N-disubstituted glyoxalylamides and their corresponding tryptamine derivatives have been synthesised and characterised by gas chromatography EI-ion trap mass spectrometry, electrospray-triple quadrupole-tandem mass spectrometry and NMR spectroscopy. Mass spectral and NMR similarities and differences between the investigated compounds are discussed. A solvent dependency is observed that has to be taken into consideration for the unambiguous assignment of (1)H- and (13)C-NMR chemical shifts. The (1)H-NMR study demonstrated that one can evaluate the rotamer populations of the asymmetrical glyoxalylamides. In a forensic or clinical scenario where single or multiple reaction monitoring approaches are contemplated, the appropriate ion transitions of choice may then focus on the two main fragmentations, namely beta-cleavage ([M+H](+)-->CH(2)N(+)R(2)R(3)) and/or alpha-cleavage ([M+H](+)-->[3-vinylindole](+)), respectively. The synthesis, NMR and MS analytical data presented provide the forensic analyst and clinical biochemist with a detailed and self-consistent body of information and mechanisms for the spectral identification of the more likely psychoactive tryptamines that may be met.     

Exciton dynamics in molecular crystals from line shape analysis. The use of spectral moments and correlation functions

A method for elucidating exciton dynamics from the profile of ω?_i(ω) is developed and illustrated by using anthracene crystal reflectance data. From the Green's function for the exciton-phonon system, terms contributing to each spectral moment are rendered explicit. The Green's function is related to certain correlation functions which together with the spectral moments are evaluated from the spectral data.