Template structure identification

The identification of unknown structures can often seem daunting, particularly when an authentic standard is not available. As a result, 

By observing sequential neutral losses, further information is obtained to determine the sequence of substructures or molecular connectivity within the analyte (Lee et al., 1996). This procedure is analogous to two-dimensional nuclear magnetic resonanse (NMR) techniques used to sequentially connect substructures. A familiar example of molecular connectivity is the determination of the amino acid sequence of a peptide. Specific neutral losses are diagnostic of specific amino acids, and the sequence of these losses identifies the peptide (Roepstorff and Fohlman, 1984). 

The MS/MS identification strategy is based on the premise that much of the parent drug structure will be retained in the metabolites, impurities, or degradants (Perchalski et al., 1982 Lee et al., 

1986 Straub et al., 1987 Lee and Yost, 1988). In addition, the product ions associated with a unique substructure(s) are also expected to be retained. Direct comparison of molecular weight and product ions reveal substructural differences and lead to an interpreted or proposed structure. 

This strategy is highly successful for impurity identification (Kerns et al., 1995) during preclinical development. When information is stored within a comparative database, this approach is also highly effective for protein identification (Arnott et al., 1995). In these applications, the characteristic fragmentation corresponding to amino acid residues provides the searchable template for identification. This approach is particularly useful when identification studies are required for vast numbers of compounds or for samples that contain many analytes of interest. 

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Nine strategies consistently appear in LC/MS-based methods for accelerated development (Table 5.1). The nine strategies are standard methods, template structure identification, databases, screening, integration, miniaturization, parallel processing, visualization, and... 

Standard methods Template structure identification Databases Method development (molecular structure) Qualitative and quantitative analysis... 

Figure 5.1 Template structure identification of a base-induced degradant of paclitaxel. (A) Product ion spectrum of the ion at m/z 829 (H+NH4)+ of a base-induced degradant of paclitaxel. (B) Product ion spectrum of the m/z 871 (H+NH4)+ ion of paclitaxel used as a template. The product ions and neutral losses that correspond to specific substructures are indicated. (Reprinted with permission from Volk et al., 1997. Copyright 1997 Elsevier.)...

Figure 6.27 Product ion spectrum of the [M+NFL ion of paclitaxel and correspondence of ions to specific substructures diagnostic of the compound, used as a template for structure identification of paclitaxel impurities. (Reprinted with permission from Kerns et al., 1994. Copyright 1994 American Chemical Society.)...

The first non-peptide oxytocin antagonists, based on a spiropiperidine template, were described by Merck in 1992 [68-70]. The binding affinity data for key compounds from this series are summarised in Table 7.2. The initial screening hit, L-342,643, (23), had modest (4/iM) affinity for rat uterine oxytocin receptors and very little vasopressin selectivity [71]. A structure activity relationship (SAR) study was carried out around this template, focussing on the toluenesulphonamide group. This work led to the identification of bulky lipophilic substitution as key to improved oxytocin potency, while the introduction of a carboxylic acid group led to improved... 

Fig. 14. Structural prediction and modeling of a fragment of FHA from B. pertussis containing Rl-repeats. (A) Successive stages in the modeling. From top to bottom identification of the consensus sequence repeat, generation of 2D template of the coil, and the modeled 3D structure. In the consensus sequence, letters indicate residues that are conserved at the level of >60% identity, x is any residue and filled circles represent bulky nonpolar residues. Apolar residues are in red glycine in green. In the 2D template, open circles denote any (but mainly polar) residues, while filled circles denote conserved, mainly nonpolar, residues. Circles inside the coil contour indicate side chains located inside the structure and circles outside the contour denote side chains facing the solvent. Arrows indicate /(-strands. (B) A fragment of the crystal structure of FHA (Clantin et al, 2004) (on the top, in green color) and the 3D model (bottom, in brown).

The use of block copolymers to form a variety of different nanosized periodic patterns continues to be an active area of research. Whether in bulk, thin film, or solution micelle states, block copolymers present seemingly unlimited opportunities for fabricating and patterning nanostructures. The wealth of microstructures and the tunability of structural dimensions make them a favorable choice for scientists in a variety of research fields. As reviewed here, they can function as nano devices themselves, or act as templates or scaffolds for the fabrication of functional nanopatterns composed of almost all types of materials. However, there are still two obvious areas which require more work control of the long-range 3D nanostructure via more user-friendly processes and the identification of new materials with different functional properties. 

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