Structure confirmation

The applications highlighted in this section focus mainly on medicinal chemistry support. A review by Burdick and Stults indicates that a similar methodology may be adapted for the analysis of peptide synthesis products, using ESI-MS techniques (Burdick and Stults, 1997). The application of LC/MS for peptide analysis is similar to the previously described schemes for chemical synthesis and purification and focuses on confirmation of the desired peptide and identification of synthetic by-products. 

Structure Confirmation In the open-access LC/MS procedure described by Pullen and co-workers, the samples are directly introduced from solution for ease of automation and sample preparation. Chemists prepare samples in solvent to a suggested concentration range, then log the samples into the system. The sample log-in is done at any time during the continuous automated queue. Autosampler vials are used to hold the samples, and autosamplers are used to 

The LC/MS analyses were performed with either thermospray ionization (TSI) or particle beam (PB) interfaces. These systems successfully analyzed the labile, polar, or higher mass compounds, whereas a complementary gas chromatography (GC)/MS system was used for volatile compounds. The LC/MS system proved to be widely applicable to a range of chemically diverse compounds. The TSI and PB systems were both successful for 80-90% of the compounds analyzed. Automated, open-access LC/MS analyses performed well because sample throughput was expected to reach 250,000 in 1995. This throughput corresponds to approximately 1000 samples per day. 

Development of the method involved the installation of a system in an existing mass spectrometry laboratory and working with chemists for 3 months to determine specific needs and to develop a consistent, reliable procedure. The instrument was moved to an open-access laboratory and chemists were trained in its use. A key to making this approach a success is the fact that instrument downtime was kept to a minimum. Understandably, maintenance is done at off-peak times, and support mechanisms are put in place so problems are immediately addressed. Training and education was highlighted as a key factor for the successful implementation of this LC/MS system to optimize performance and to reduce the possibility of instrument contamination. 

In 1995, Taylor and co-workers also described the use of an open-access LC/MS system for routine structure confirmation, featuring atmospheric pressure chemical ionization (APCI). This system featured dual personal computers (PCs) for automated instrument control and sample log-in. A system-PC is responsible for running the Windows NT for Workgroups operating system and interfaces with the network for instrument control. A separate log-in PC, isolated from the LC/MS system, is used by the synthetic chemist to enter details about the samples. The analyst prepares the sample in an autosampler vial in one of several solvent options. The system specifies where to place the sample vial in the autosampler, and following analysis with a standard method, spectra are automatically processed and printed without any chemist intervention. 

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Thus, in the area of combinatorial chemistry, many compounds are produced in short time ranges, and their structures have to be confirmed by analytical methods. A high degree of automation is required, which has fueled the development of software that can predict NMR spectra starting from the chemical structure, and that calculates measures of similarity between simulated and experimental spectra. These tools are obviously also of great importance to chemists working with just a few compounds at a time, using NMR spectroscopy for structure confirmation. 

Likewise there are no reports of systematic photochemical studies, but the pyrido[2,3-ii]pyrimidine ring system appears relatively photostable, as photolytic removal of D-ribityl and hydroxyethyl A -substituents was employed in structural confirmation studies (74JCS(P1)1225). Photo adducts of deazafiavins with cyclohexadienes have been studied, however (77ZN(B)434), as have several other aspects of deazafiavin photochemistry. 

First, we perform an optimization of the transition structure for the reaction, yielding the planar structure at the left. A frequency calculation on the optimized structure confirms that it is a first-order saddle point and hence a transition structure, having a zero-point corrected energy of -113.67941 hartrees. The frequency calculation also prepares for the IRC computation to follow. 

The K-R reaction has also been useful for structural confirmation of natural products such as tambulin (71), a flavonoid isolated from the seeds of Xanthoxylum acanthopodium In the critical reaction (O-ethoxyphloroacetophenone (72) was allowed to react with anisic anhydride (38b) in the presence of sodium anisate (73) at 170 C to deliver flavone 74 in 65% yield. Flavone 74 was then converted after multiple steps to diethyl ether 75 which corresponded to the diethyl ether of tambulin (71). 

The discovery of junipal focused the attention of Sorensen, who had been investigating the occurrence of polyacetylenes in Com-positae, on the possibility that these acetylenes were accompanied by thiophenes. From Coreopsis grandiflora Hogg ex sweet, 2-phenyl 5-(1-propynyl) thiophene (240) was isolated and its structure confirmed by synthesis of the tetrahydro compound, 2-phenyl-5-n-propyl-thiophene. From the root of tansy, the cis and trans isomers of methyl 5-(l-propynyl)-2-thienylacrylate (241) have been isolated. The total synthesis of trans (241) was achieved by reacting junipal with methylcarbethoxy triphenylphosphonium bromide (Wittig reaction) Several monosubstituted thiophenes, (242), (243), and... 

Fig. 21. Crystal structure of the Valinomycin-K+ complex. Reproduced with permission from Ref.100). This crystal structure confirmed within tenths of an Angstrom the structure derived previously in solution 97 98) and by means of conformational energy calculations...

Kishi, Y., Tanino, H., and Goto, T. (1972). The structure confirmation of the light-emitting moiety of bioluminescent jellyfish Aequorea. Tetrahedron Lett. 27 2747-2748. 

Xylans as true homopolymers occur in seaweeds of the Palmariales and Nemaliales, however, their backbone consists of Xylp residues linked by -(1 3) (Type X3, Fig. la) or mixed -(1 3, 1 -> 4)-glycosidic linkages (Type Xmy Fig. lb). They are assumed mainly to have a structural function in the cell-wall architecture, but a reserve function cannot be ruled out [4]. From the microfibrils of green algae (Siphonales) such as Caulerpa and Bryop-sis sp., X3 was isolated and the structure confirmed by methylation analysis, C-NMR spectroscopy [7], as well as by mass spectrometry of enzymically released linear oligosaccharides up to a degree of polymerization (DP) of... 

The intermediate A -cyanoammonium bromide has been trapped, and its structure confirmed by chemical, analytical, and spectral data. The BrCN in this reaction has been called a counterattack reagent, that is, a reagent that accomplishes, in one flask, two transformations designed to give the product. ... 

The feasibility of partial synthesis has been demonstrated in the course of structural confirmation of a great number of betaxanthins. Due to incomplete hydrolyses, residual betanin and isobetanin may also accompany the respective target betaxanthin. Most importantly, the purification of betalamic acid does not appear to be possible because it exhibits both amino and aldehyde functions (Stintzing, unpublished observations), resulting in self-condensation. Therefore, data by Barth and co-workers reporting NMR data on purified betalamic acid should be carefully interpreted. ... 

GP 1] [R 1] A comparison of four micro reactors with different Pt loadings (Pt impregnated on anodically oxidized alumina support) and different Pt structures confirmed that cluster size has an impact on the single Pt-atom activity (6 vol.-% NHj, 88 vol.-% O2, balance He 0.51 ms 260-380 °C) [28, 98]. At low Pt loadings, isolated atoms are formed. Calculated ammonia consumption rates amount to 20 s at 300 °C. At high Pt loadings, clusters are formed. Turn over frequencies (TOP) of about 40 s are determined. 

Alternatively, competitive ELISA can be used to estimate the hapten density if an antibody that specitically recognizes the hapten is available. At first observation this approach seems circular because the immunoassay developed is used to determine hapten density on proteins used for immunization. However, if a small molecule mimic of the protein conjugate is used as a standard, the method can be accurate. For example, a hapten containing a carboxylic acid can be coupled to phenethylamine or tyramine, its structure confirmed and the material used to generate a calibratron curve to estimate hapten density. 

Goff (54) synthesized an Fe(III) porphyrin with a 2-hydroxyphenyl group at one meso position (35, Fig. 12a). Under basic conditions, the system spontaneously dimerizes due to phenolate-Fe(III) coordination. The complex is very stable and was isolated and fully characterized. In the solid state, the X-ray crystal structure confirmed the structure of the assembly as a macrocyclic head-to-tail dimer with two intermolecu-... 

Amino-2(l/7)-quinoxalmethione (19) gave 3-chlorothioquinoxaline-2-ylimi-nosulfur dichloride (20, Q = R = H) (substrate, MeCN, <5°C, Cl(, S2C12, 15 min 48%), 6-chloro-3-chlorothioquinoxaline-2-yliminosulfur dichloride (20, Q = Cl, R = H) (substrate, excess SC12, MeCN, 20°C, 1 h 66%), or 6,8-dichloro-3-chlorothioquinoxaline-2-yliminosulfur dichloride (20, Q = R = Cl) (excess S2C12, C1J, MeCN, reflux, 30 min 66% structure confirmed by X-ray analysis).1034... 

Chloro-3-(5-chloropyrazol-3-yl)quinoxaline (137, R = H) gave mainly 2-(2-acetyl-5-chloropyrazol-3-yl)-3-chloroquinoxaline (137, R = Ac) [neat Ac20, reflux, 7 min, then 20°C, 30 min 86% (after separation from a little of the 1-acetyl isomer) structure confirmed by X-ray analysis] or mainly 2-(l-acetyl-5-chloropyrazol-3-yl)-3-chloroquinoxaline [neat Ac20, 80°C, 2 min ( ), then 20°C, 12 h 70% (after separation from the 2-acetyl isomer)] an extraordinary pair of regioselective reactions.495... 

The zinc acetate complex of tris(3-/-butyl-5-methylpyrazol-l-yl)borate was prepared as a structural model for carbonic anhydrase and comparison with the enzyme active site structures confirmed that the complexes are excellent structural models.239 A mononuclear zinc hydroxide complex can also be formed with the tris(pyrazolyl) borate ligand system as a structural model for carbonic anhydrase.240... 

Since the corresponding endoperoxide precursors are all too unstable for isolation, the diimide reduction constitutes an important chemical structure confirmation of these elusive intermediates that are obtained in the singlet oxygenation of the respective 1,3-dienes. However, the aza-derivative 14 and the keto-derivative 15 could not be prepared,17> because the respective endoperoxides of the pyrroles 18) and cyclopentadienones suffered complex transformations even at —50 °C, so that the trapping by the diimide reagent was ineffective. 

Intermediates of the general form of (86) have been detected in super acid solution (cf. p. 102), and their structure confirmed by n.m.r. spectroscopy. 

Although the g tensor provides evidence for the identification of a particular spectrum, one should never really be certain until hyperfine structure confirms the identification. The spectrum of the superoxide ion affords a beautiful example of the application of hyperfine structure to establish... 

Axisonitrile-1 (1) and axisothiocyanate-1 (2) were the first pair of NC/NCS compounds isolated from Axinella cannabina, see Introduction [1]. That both compounds possessed a new skeleton was evident, when 1 was reduced (Li/EtNH2) to axane (6). Other transformations involving the exocyclic methylene which survived selective reduction (Na/NH3) of 1, coupled with evaluation of the lHNMR data, supported its gross structure. Confirmation of 2 was secured when 1 was heated with sulfur and the resultant purified product found to be identical to the natural product. 

FeSa—m type structure confirm that Hyp. 6 is approximately satisfied, the ratio (a2 +c2)/62 varying between 0.995 (CrSba) and 1.035 (FeSba) in class A, and between 1.023 (CuSea) and 1.093 (CoTea) in class B. The situation concerning Hyp. 7 is similar to that for Hyp. 5 but, since FeSa is the only compound for which accurate positional parameters are available for both modifications xv —0.3840(5) and y=0.37820(5), cf. (5, 6)], further experimental tests of the degree of validity of this postulate are called for. Note that the less accurate parameters for NaC>2 satisfy (8) the relation exactly (xp =y=0.43). 

The [16]annulene is nonplanar, with almost complete bond alternation. The single bonds (1.454 A) are alternately trans and gauche, and the double bonds (1.337 A) cis and trans. The average torsion angle at a gauche C—C bond is 41°. The molecule is therefore relatively flat with S4 noncrystallographic symmetry, and the structure confirms the lack of aromaticity in this [4n] annulene. 

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