Amides, structure identification

However, if side-chain carbon assignments are wanted, C(CC)(CO)NH experiments [33] that start directly with carbon magnetization and transfer it further to the amide proton for detection are available. If protonated substituents, for example methyl groups, have been introduced into the otherwise perdeuterated protein, the usual HC(C)(CO)NH-TOCSY pulse sequence can be used to obtain the proton chemical shifts. These protons can provide a small number of NOEs that, together with residual dipolar couplings and the secondary structure identification from chemical shifts, make the determination of the global fold of large proteins possible. 

The similarity of the crustacean blanching substance (Factor A) found in crustacean sinus glands and insect corpora cardiaca has been confirmed by the structural identification of a family of neuropeptides common to arthropods. The first identified member of this family is RPCH (red pigment concentrating hormone), an octapeptide (pGlu-Leu-Asn-Phe-Ser-Pro-Gly-Trp-amide) isolated from eyestalks of the shrimp Pandalus borealis (28). Shortly thereafter, a related peptide--designated as adipokinetic hormone (AKH)--was purified from locust... 

A second method uses permethylation of the dephosphated (48% aqueous HF, 48 h, 4°C) and 2H-reduced fipid A. This approach allowed the assignment of amide-bound fatty acids linked to GlcN(I) and GlcN(II), as well as the identification of the backbone structure as a HexpN disaccharide (85). Mass-spectrometric analysis of the products was performed by using either a short g.l.c. column (0.3 X 5 cm) or by direct insertion-probe analysis (87). In the case of C. violaceum (85), the mass spectra obtained from the permethyl-ated HexpN disaccharide bearing attached TV-methylacyl residues revealed unequivocally that both amino groups carried 12 0(3-OH). 

IR spectroscopy is useful for the identification of some of the functional groups in an organic molecule. The technique also provides a fingerprint of the molecule and its comparison with authentic specimen often confirms the structure of that molecule. The IR spectra of AHLs show characteristic absorption peaks at 1780,1710,1650 cm-1 arising from the lactone ring, 3-oxo (when present), and amide carbonyl, respectively [15,16]. 

Dynamic combinatorial libraries (DCLs) are continuously interconverting libraries that evenmally evolve to an equilibrium distribution [61-65]. This approach has been used successfully in the discovery of stable supramolecular assemblies from mixtures. Due to the nearly endless possible peptide sequences that can potentially be synthesised, the DCL approach is attractive for the identification of supramolecular peptide interactions. Indeed, disulfide exchange between cysteine residues has been explored for this purpose [66, 67] as has peptide-metal binding [68]. We have recently demonstrated protease-catalysed amide exchange in this context, which allows for the evolution of the self-assembled peptide structures, and will therefore allow exploration of peptide sequence space for biomaterials design. 

The 1,4-conjugate addition of ester enolates to a, 3-enones was first reported by Kohler in 1910,138a c as an anomalous Reformatsky reaction, but chemoselectivity was dependent on the structure of the a,(3-enone and restricted to bromozinc enolates obtained from either a-bromoisobutyrate or bromomalonate esters (Scheme 66).138d,e Further evaluation, with lithio ester enolates and lithio amide enolate additions, has resulted in identification of four factors that affect the chemoselectivity and diastereoselectivity of additions to a, 3-enones.139 These factors are (a) enolate geometry, (b) acceptor geometry, (c) steric bulk of the -substituent on the acceptor enone and (d) reaction conditions. In general, under kinetic reaction conditions (-78 °C), ( )-ester enolates afford preferential 1,2-addition products while (Z)-ester enolates afford substantial amounts of 1,4-addition products however, 1,2 to 1,4 equilibration occurs at 25 C in the presence of HMPA. The stereostructure of the 1,4-adducts is dependent on the initial enolate structure for example, with ( )-enones, (Z)-ester enolates afford anti adducts, while (E)-ester enolates afford syn adducts (Scheme 54). In contrast, amide enolates show a modest preference for anti diastereomer formation. 

Wendt, M. D., et al., Identification of novel binding interactions in the development of potent, selective 2-naphthamidine inhibitors of urokinase. Synthesis, structural analysis and SAR of jV-phenyl amide 6-substitution. J Med Chem, 2004, 47, 303-324. 

Highly sensitive targeted lipidomic approaches are rapidly leading to the identification of new analogs of anandamide (Tan et al., 2006). The two major families of lipids that share common chemical structure with anandamide are FAEs and fatty acid amides. Although many of these lipids show no activity at CB receptors, they are known to bind and activate other receptors, such as transient receptor potential vanilloid type-1 (TRPV-1) and the nuclear receptor peroxisome proliferator-activated (PPAR-a). 

High-throughput screening of the company sample collection in an AChE inhibition assay resulted in identification of a novel structural class exemplified by lead compound 5. Subsequent SAR studies were performed by a series of modification to the (a) phenyl group, (b) amide moiety, (c) linker unit, (d) piperidine ring, and (e) benzyl group. Para-... 

The manufacture of the large variety of polyamides (commonly referred to as nylons) occurs through polycondensation of amino carboxylic acids (or functional derivatives of them, e.g. lactams) and from diamines and dicarboxylic acids. Labeling the amino groups with A and the carboxyl groups with B allows differentiation of the different chemical structures between the two types AB (from amino carboxylic acids) and AA-BB (from diamines and dicarboxylic acids). The number of C atoms in the monomers acts as a code number for the identification of the polyamides. The polycaprolactam manufactured from caprolactam (type AB) is then called polyamide 6 (PA 6). The number of carbon atoms in the diamine is given first for type AA-BB followed by the number of atoms in the dicarboxylic acid, e.g. PA 66 for polyhexamethylenedia-dipic amide from hexamethylenediamine and adipic acid. For copolymers the components are separated by a slash, e.g. PA 66/6 (90 10) is a copolymer composed of 90 parts PA 66 and 10 parts PA 6. 

Identification and structural characterization of an unknown class of substrates for FAAH. (A) By high-resolution mass spectrometry, the high-accuracy mass measurements of a compound of this class gives an exact mass of 446.3310 that corresponds to a molecular formula of C24H48N04S. (B) By MS/MS analysis, the structure of this compound is assigned as the C24 0 fatty acyl amide of taurine (NAT). Reproduced from Saghatelian A., Trauger S.A., Want E.J., Hawkins E.G., Siuzdak G. and Cravatt B.F., Biochemistry, 43,14332-14339, 2004, with permission. 

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