Implementation of an expert system for the qualitative interpretation of X-ray fluorescence spectra

The implementation of an expert system for the automated qualitative interpretation of energy-dispersive x-ray spectra is discussed. The first step in the interpretation process is the extraction of the relevant data from the spectrum, which is done by a preprocessor program, written in FORTRAN. The expert system itself consists of three parts. The knowledge base contains specific information on energy-dispersive x-ray fluorescence spectrometry presented in the form of IF/THEN rules. The data base contains the reduced spectral data and an array of certainty factors associated with each element; the certainty factor for an element represents the probability of its being present in the sample from which the spectrum was taken. Finally, the inference engine performs manipulation of the knowledge. For a particular state of the data base, the certainty factors for all the elements are iteratively modified until convergence is reached by using the rules from the knowledge base. During each cycle, the inference engine selects one rule from the knowledge base and executes it. Rules are selected on the basis of the chemical elements contained in their IF part and according to their previously assigned focus levels. Execution of the THEN part of the selected rule modifies the certainty factors of a number of elements. At the end of the interpretation session, the system lists the elements which have a high probability of being present in the sample. Optionally, the user can be provided with explanations of the reasoning steps taken during the interpretation. Application of the expert system to a particular spectrum shows that it is useful for the reliable interpretation of spectral data obtained from electron microprobe analysis of industrial aerosol particles.     

A data base of data banks for toxicological information

The procedures necessary to find the appropriate data banks in seeking particular information or data are much less systematic than the way in which the information is stored at some data banks. Based on the information taken from several hundred direct-mailed questionnaires, a conceptual design is proposed for a data base of toxicological data banks relating to other areas such as medicine, pharmacology, biology, chemistry and environmental science. The system (not yet implemented) contains nearly 150 data banks (both computerized and manual) all over the world with data on the type of information, the way to obtain it, its cost, etc.     

Determination of degree of crystallinity of drawn polymers by means of density measurements

The well known procedure of determining the degree of crystallinity by means of measuring the density presupposes the knowledge of both the densities ρ_c and ρ_a of the crystalline and of the noncrystalline regions. By combination of small-angle and wide-angle x-ray scattering and of density measurements it can be shown that this method is not justified in the case of drawn polyethylene if the values of ρ_c and ρ_a known from isotropic material are used. Both ρ_c and ρ_a depend considerably on annealing and drawing conditions. In addition the effective density ρ_c^* of the more densely packed phase in a two-phase structure is much lower than the value ρ_c calculated from the positions of the x-ray reflections due to a large number of lattice defects. This conclusion is based on the results of three independent sets of experiments: determination of the mean-square fluctuation of density 〈η²〉 by means of x-ray small-angle scattering; x-ray wide-angle measurements of the positions of the crystal reflections and of the halo arising from the noncrystalline regions; and comparison of densities and long periods of samples treated at various annealing temperatures.     

Improving Matrix Corrections

 Except in the idealized case where the unknown and the standard are essentially identical obtaining accurate matrix corrections requires a knowledge of the absolute value and functional behavior of a number of quantities such the mass absorption coefficient, the electron stopping power, ionization cross sections and fluorescent yields. This talk examines the accuracy of the data available in each category, and the range of elements and compounds for which values have been published. It is found that the quality and quantity of data available varies greatly and that, with only a few exceptions, much more work is required to produce the reliable and inclusive data base required for accurate matrix corrections.     

Structures for controlling synthesis design and reaction modelling via knowledge acquisition

The performance of programs for computer-assisted organic synthesis (CAOS) is directly related to the knowledge base and to the procedures for deciding how the knowledge base should be used. The architecture of a knowledge base (text base, data base, rule base, model base and commonsense base) is discussed. The problem of knowledge acquisition is described with regard to pruning the productivity of CAOS systems. The commercial program 1stCLASS (for symbolic processing) is used with the SAAO (devised here for numeric processing) to form a commonsense base. For this purpose, knowledge was acquired by induction from the solutions provided by human experts to given problems. The general procedure is applied to the recognition of reaction sites which are crucial in the simulation of organic reactions.     

Structure of the quenched form of polypropylene

X-ray diffraction has been used to further investigate the quenched form of polypropylene. The diffractometer traces were analyzed by a mathematical peak separation procedure which assumed a combined Cauchy and Gaussian shape for the peaks. The results confirmed that the quenched form contains about 60% of amorphous polypropylene. In the remainder, the x-ray diffraction peak positions indicate that the chain helices are arranged in a square array and a cubic or tetragonal symmetry is proposed for this phase. The shape of the x-ray diffractometer peaks indicates a degree of strain in the structure. Crystallite sizes, determined from peak breadths, have been estimated as approximately 30 Å.     

Small-angle x-ray scattering study of density fluctuation in pressure-densified polystyrene glasses

Densified polystyrene glasses, prepared by cooling from the liquid state under elevated pressure, were studied by small-angle x-ray scattering at ambient pressure. The density fluctuation, determined from the x-ray data, showed a decrease with increasing pressure up to about 1.5 kbar, and then leveled off to a fairly constant value. The reduction in the density fluctuation produced by the pressure is much greater than the associated decrease in the specific volume. The observed change in density fluctuation is consistent with the view that the density fluctuation in glassy polymers consists of dynamic and quasistatic components and that the first of these can be correlated with the compressibility of the glass. The present data on the density fluctuation, in conjunction with the available data on volume and enthalpy, can be interpreted to mean that in pressure-densified glasses unfavorable chain configurations are trapped in local energy minima, and the strain energy thus stored can promote segmental motion leading to volume expansion at temperatures far below T_g. Some preliminary evidence indicating the formation of microcavities in these pressure-densified glasses is also presented.     

Application of a text search system based on boolean strategy to mass spectral data identification

A general algorithm for text searching, operated on a tape-based minicomputer, has already been reported. This paper presents the application of the general text-searching algorithms to the Registry of Mass Spectral Data of 18,806 different entries. The text format allows multi-information input to be used to search the spectral library on the basis of data not necessarily extracted from mass spectra. Two library files have been generated; one is approximately half the size of the other, less important information having been deleted. The shorter library contains all 18,806 entries but enjoys much faster search times. Batch processing of searches is also possible. The text search is shown to be versatile in its operation, as the user can construct searches to be either broad or very selective, depending on the application. The search also has the capability to examine the data base internally and to check certain data for their validity.     

Alkaloids from Arundo donax. XVII. Structure of the Dimeric Indole Alkaloid Arundaphine

The newdimeric alkaloid arundaphine, a tryptamine-tryptamine base, was isolated from roots and rhizomes of Arundo donax (Poaceae). Spectral data and an x-ray structure analysis established its structure as 1-[3-(2-dimethylaminoethyl)-5-hydroxy-1H-4-indolyl]-3-hydroxy-3-(2-methylaminoethyl)-2-indolinone.     

Development of algorithms for automated elucidation of spectral feature/substructure relationships in tandem mass spectrometry

A pattern-recognition/artificial-intelligence program, referred to as MAPS (method for analyzing patterns in spectra), is described for the identification of relationships that exist between the presence of substructures in molecules and the characteristic features they produce in mass spectrometry (MS) and MS/MS data. The MAPS algorithm discovers these relationships by intelligent analysis of a data base of MS and MS/MS spectra. The relationships found are expressed as rules, which may then be used to identify characterized substructures in “unknowns”. No prior knowledge of fragmentation pathways or rearrangements is assumed in the rule-generation process. While MAPS currently uses MS and MS/MS data, the approach (and much of the software) is equally suited to multiple-stage mass spectrometric data.     

QCLDB—Quantum chemistry literature data base—a trial

A brief account of a quantum chemistry literature data base (QCLDB ) is described, which contains the key information of about 2000 papers of ab initio calculations of atoms and molecules published in 1977–1979. The QCLDB is stored in a computer and can be sorted and rearranged into author and substance indices. Selection of the items for each paper in a computer-readable data base is discussed.     

运用模糊神经网络表达和预测链烷烃pVT性质

采用一种基于遗传算法的新型模糊神经网络方法研究链烷烃类化合物的pVT性质。该方法综合神经网络、遗传算法与模糊系统三种柔性智能计算技术的优点,具有良好的学习能力,不易陷入局部最小区域,学习速度较快,网络知识以模糊语言变量的形式加以表达,易于理解。用分子连接性指数对24种链烷烃化合物结构和pVT数据进行学习,进而预测另外14种未知化合物的pVT性质,较好地揭示出化合物分子结构与pVT性质之间的关系,并给出了良好的关联与预测结果。     

ELDAR, a knowledge base system on microcomputer for electrolyte solutions. The factual knowledge of ELDAR

The knowledge base system ELDAR (ELectrolyte DAta Regensburg), consisting of data base, method base, rule base, and communication manager, classifies the knowledge of electrolyte solutions into factual, algorithmic, and rule knowledge. In this paper information is given on the factual knowledge of ELDAR and the mapping of facts in Codd's relational data model with an extension of its "1st Normal Form" to repeating attributes. ELDAR offers equal user interfaces for all factual knowledge services, such as literature, data, thesaurus, module, parameter, basic data, and rule retrieval.     

Toward a designed, functioning genetic system with expanded-size base pairs: solution structure of the eight-base xDNA double helix

We describe the NMR-derived solution structure of the double-helical form of a designed eight-base genetic pairing system, termed xDNA. The benzo-homologous xDNA design contains base pairs that are wider than natural DNA pairs by ca. 2.4 A (the width of a benzene ring). The eight component bases of this xDNA helix are A, C, G, T, xA, xT, xC, and xG. The structure was solved in aqueous buffer using 1D and 2D NMR methods combined with restrained molecular dynamics. The data show that the decamer duplex is right-handed and antiparallel, and hydrogen-bonded in a way analogous to that of Watson-Crick DNA. The sugar-phosphate backbone adopts a regular conformation similar to that of B-form DNA, with small dihedral adjustments due to the larger circumference of the helix. The grooves are much wider and more shallow than those of B-form DNA, and the helix turn is slower, with ca. 12 base pairs per 360 degrees turn. There is an extensive intra- and interstrand base stacking surface area, providing an explanation for the greater stability of xDNA relative to natural DNA. There is also evidence for greater motion in this structure compared to a previous two-base-expanded helix; possible chemical and structural reasons for this are discussed. The results confirm paired self-assembly of the designed xDNA system. This suggests the possibility that other genetic system structures besides the natural one might be functional in encoding information and transferring it to new complementary strands.     

A pictorial query language for use with any data base

The query language discussed can be used with any type of data base and requires neither familiarity with formal logic nor knowledge of the data-base organization. The system is illustrated by creating a data base for the Lactobacillus hierarchy from a reference manual.     

Oleogels—Their Applicability and Methods of Characterization

Oleogels or, more precisely, non-triglyceride structured lipid phases have been researched excessively in the last decade. Yet, no comprehensive knowledge base has emerged, allowing technology elevation from the laboratory bench into the industrial food application. That is partly due to insufficient characterization of the structuring systems studied. Examining a single composition decided upon by arbitrary methods does not stimulate progress in the research and technology area. A framework that gives much better guidance to product applications can easily be derived. For example, the incremental structure contribution concept is advocated as a parameter to compare the potency of structuring systems. These can straightforwardly be determined by combining solubility data and structural measurements in the recommended manner. The current method to determine the oil-binding capacity suffers from reproducibility and relevance. A newly developed method is suggested to overcome these shortcomings. The recommended new characterization of oleogels should contribute to a more comprehensive knowledge base necessary for product innovations.     

HEAVY-ATOM LABELLED RETINAL ANALOGUES LOCATED IN BACTERIORHODOPSIN BY X-RAY DIFFRACTION*

Abstract– The location of the heavy-atom label of three different retinal analogues in the plane of the purple membrane was determined by x-ray diffraction. The three analogues, i.e. 9-bromoretinal and 13-bromoretinal labelled in the polyene chain as well as the ring-labelled HgCI-retinal, were incorporated into bacteriorhodopsin (BR) either biosynthetically using a retinal-deficient mutant strain of Halobacterium halobium or with photochemically bleached bacterioopsin. All BR samples regenerated with retinal analogues were functionally active as proton pumps. The diffraction data show that the cyclohexene ring of retinal is situated in the corner formed by helices 4E and 5D. the 13-methyl group adjacent to helix 6C and therefore the Schiff's base nitrogen about midway between helices 6C and 2G. The 9-bromo label is found slightly off the line connecting the two other labels, directed towards helix 3F, suggesting torsion of the polyene chain or slight incline of the ring. The position and orientation of retinal obtained in our experiments are in agreement with data from neutron diffraction and high-resolution electron microscopy. This indicates that the heavy-atom labeled chromophores, 9-bromo- and 13-bromo- as well as HgCI-retinal, are isomorphously incorporated into BR. These samples will allow kinetic investigation of light-induced structural changes of retinal during BR's pumping cycle using x-ray diffraction as well as extended x-ray absorption fine structure experiments probing changes in the retinal neighbourhood between different intermediaies of the photocycle.     

Gerphytine,a new furanoquinoline alkaloid from <Emphasis Type="Italic">Haplophyllum griffithianum</Emphasis>

A series of known alkaloids and the new base gerphytine were isolated from total alkaloids from the aerial part of Haplophyllum griffithianum growing in Surkhandar′ya Oblast, Republic of Uzbekistan. Gerphytin was identified based on spectral data and an x-ray crystal structure analysis as a furanoquinoline derivative and had the structure 7-O-allyl-4,8-dimethoxyfuranoquinoline.     

Base-Dependent Cascade Synthesis of Novel Pyrano[3,2-c]coumarin Derivatives from Baylis–Hillman Bromide

5-Oxo-2,3,4,5-tetrahydropyrano[3,2-c]chromene-3-carboxylates derived from 4-hydroxycoumarin and Baylis–Hillman bromides are efficiently obtained in excellent yields within a short time. The transformation is depends on a base, which goes through SN₂-SN₂ nucleophilic substitution and intramolecular Michael addition. The product structures are confirmed by x-ray crystallography, and a tentative mechanism of the cascade process is presented.     

Representation of extended infrared spectrum-structure-correlations based on fuzzy theory

The theory of fuzzy sets was applied to specific infrared spectrum-structure-correlations. The scheme was translated into a rule base named CorTab (from Correlation Tables). The data are split into three main data files consisting of the structural information, the spectral properties and the cross references. The first two files contain the fragments and the ranges of the spectroscopic features, i.e. position, intensity and band width, and also the empirical knowledge about the plausibility or constraints of the correlations. The cross references assign the spectral to the structural properties and contain the connections between the fragments in the network of the fragments. The flexibility of the design allows the ongoing accumulation of spectrum-structure-correlations from different literature sources or the storage of computer derived rules. The rule base CorTab is a prerequisite for the structure elucidation performed by an ensemble of interpretation systems relying on fuzzy logic. A survey of the arrangement and contents of the rule base and the procedures that transform the verbally given knowledge into linguistic – fuzzified – variables are reported herein. Received: 17 June 1996 / Revised: 9 October 1996 / Accepted: 16 October 1996