Structural units, identification

To assure consistency and speed in multidisciplinary structure analysis of low-MW compounds involving various techniques (IR, NMR, MS, etc.) most industrial laboratories use a Standard Operating Procedure (SOP). In such schemes IR analysis is frequently used as a cheap filter for a quick starting control and as a means for verification. As IR detects only structural units identification of an unknown compound on the basis of IR is difficult. Mass spectrometry is used as the prime identification tool and is especially important in the determination of the exact mass and gross formulae. While structural prognostication on the basis of MS is difficult for the non-expert, a posteriori interpretation is quite feasible. H NMR is both easy and cheap, however requires greater sample quantities than either... 

Globular proteins were much more difficult to prepare in an ordered form. In 1934, Bernal and Crowfoot (Hodgkin) found, that crystals were better preserved if they were kept in contact with their mother liquor sealed in thin-walled glass capillaries. By the early 1940s crystal classes and unit cell dimensions had been determined for insulin, horse haemoglobin, RNAase, pepsin, and chymotrypsin. Complete resolution of the structures required identification of the crystal axes and some knowledge of the amino acid sequence of the protein—requirements which could not be met until the 1950s. 

The utilily of measuring lattice vibrations for obtaining information about zeolites has been widely demonstrated. Applications include determining the structure of zeobtes by the identification of the structural units present, measuring changes in the framework Si/Al within materials with the same zeolite structure and tracking the formation of zeolite during synthesis. 

Eggleston and Bailey (1967) published a study on dioctahedral chlorite and gave five examples of chlorites having a pyrophyllite-like layer and a brucite-like sheet (designated di/trioctahedral by the authors with the trioctahedral sheet including all species of chlorite with 5 to 6 octahedral cations per formula unit and dioctahedral 4 to 5 octahedral cations per formula unit). Identification of di/trioctahedral chlorites is indirectly accomplished. Eggleston and Bailey stated that identification depends on the intermediate value of c (060), on chemical analysis of impure material, and on the ideal compositions of the recrystallization products of static heating . The composition of one such chlorite for which they refined the structure is ... 

Identification of structural units. This involves the search for secondary structural units (more precisely, for units that are superposable on standard units to within a specified error), or for combinations of them. The operator will want to specify the range of the search — within a certain molecule, or over a class of proteins, or over the entire available set of coordinates. He or she will also need to be able to qualify the object of the search, specifying perhaps a range of lengths of... 

Following Adler s identification of comferaldehyde units as the structural type giving rise to color in the Wiesner reaction, many other color reactions were re-examined and found attributable to the same structural unit These include the reaction of ligmfied tissue with methanol-hydrochloric acid (Brauns... 

The conditio sine qua non for structure-based drug design is the identification and functional annotation of the relevant binding site(s) in a target protein. A number of methods, closely related to the characteristics of binding sites and the restraints imposed on the formation of functional structural units, are discussed in Section 4.2. The most commonly used methods can be classified into geometry-based methods for cavity detection, methods for identifying specific patterns, and evolutionary methods. 

Gene shuffling and recombination has been used as a tool to engineer heme proteins. This research endeavor is aided by identification of exons and their corresponding protein structural units called modules. For example, human... 

Of considerable importance in the determination of polymer composition and structure is nuclear magnetic resonance (NMR) spectroscopy. A large number of literature reports are available regarding the application of this technique in the study of polymers (see e g. [5]). This technique allows the identification of various structural units in polymers based on the chemical shift and spin-spin coupling either in proton NMR spectra or... 

Triketides are relatively rare. Triacetic acid lactone (4.2) has been detected in Penicillium patulum. It is also produced by fatty acid synthase in the absence of the reductant NADPH. Radicinin (4.3) is a major phytotoxin isolated from Ahernaria radicina (Stemphyllium radicinum) which causes a black rot of carrots. It is also formed by other Ahernaria species. Its pyrano[4,3- ]pyran structure, the identification of which had eluded purely chemical degradative studies, was established in one of the earlier applications of NMR spectroscopy to natural product structure elucidation. The biosynthesis of radicinin from acetate units was studied in 1970 by both radio-isotope methods using carbon-14 and by carbon-13 enrichment studies with NMR methods of detection. This was one of the first applications of this NMR technique to biosynthetic problems. These results established the labelling pattern for radicinin shown in 4.3. 

Kilpelainen, I., Sipila, J., Brunow, G., Lundquist, K., and Ede, R. M. (1994) Application of two-dimensional NMR spectroscopy to wood lignin determination Identification of some minor structural units of hard- and softwood lignins. J. Agr. Food Chem. 42(12), 2790-2794. 

Table 5.2 attempts to categorize NMR experiments from a chemist s point of view based upon the structural parameters that can be obtained using different experiments. Structural analysis usually depends upon the identification of small structural units and the combination of these units to generate the complete molecular skeleton. Further information might be required to determine the conformation or stereochemistry of the unknown compound. 

One of the major goals of vibrational spectroscopy is to associate measured frequencies with structural features of a molecule and, thereby, to facilitate its identification. These efforts have led to a number of rules that concern the similarity and transferability of force constants and frequencies from one molecule to another provided they contain similar structural units [1-9]. To provide a mathematical basis for the comparison of measured vibrational frequencies and force constants, the adiabatic internal vibrational modes were defined [18], which enable one to investigate molecular fragments in terms of their internal vibrations defined by the pair (qn, Vn). 

Despite the diflBculties of interpretation of these measurements and of identification of the various anomalies, the diflFusion coeflBcient is a valuable parameter which provides structural information at a level that no other technique can provide. Furthermore, because diflFusion proceeds inwards from a polymer surface, the surface is the prime structural unit studied by this technique. DiflFusion analysis is expected to be an important tool for investigating the eflFect of processing on polymer surface structure. 

The concept of a supramolecular synthon places the geometrical notion of a pattern in a chemical context More significantly, this concept lends itself to retrosynthetic analysis and to the identification of similar crystal structures that can be derived from dissimilar molecules. Supramolecular synthons are critical sub-structural units that contain the maximum of structural information encapsulated in patterns of the most economical size. A full three-dimensional structure contains all possible structural information for a given crystal but is too detailed to permit reahstic comparisons with other crystal structmes. Structural simplification is therefore necessary. 

Mid-IR radiation corresponds to fundamental transitions in which one vibrational mode is excited from its lowest energy state to its first excited state. For routine analysis a spectrum is normally taken from 400 to 4000 cm The mid-IR spectrum of a substance is effectively a unique fingerprint that can be used for the purpose of identification by comparison with a reference spectrum. When no reference spectrum is available, an IR spectrum can be used to identify the presence of certain structural units that, irrespective of their molecular environment, give rise to characteristic spectral features in a narrow frequency range. 

A description of the protein-structure hierarchy is incomplete without a discussion of structural motifs, which are critical to an understanding of protein structure [17]. Identification of recurring motifs in protein structures has refined our knowledge of the protein-structure hierarchy these motifs occur at all levels from primary to tertiary. The Phe-Asp-Thr-Gly-Ser sequence found in the active site of all aspartic acid proteinases, and the Gly-Gly-X-Leu sequence (where X represents any amino acid residue) that predicts a 3-strand for the last two residues [17], are examples of sequence motifs a-helices, P-strands, and turns are examples of secondary-structural motifs PaP and PxP units, P-hairpins, and Greek keys are examples of supersecondary-structural motifs and four-a-helix bundles and TIM barrels are examples of tertiary-structural motifs. The tertiary fold of a protein is characterized by its tertiary-structural motif. 

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