Unknown Structures

There is a need to register and test batches of material whose structure is not yet known or is partially known, e.g. natural products, polymers and resin bound fragments. 

If the structure is partially known, it is valuable to record that part of the structure which is known, together with some descriptive chemically significant text (CST). Where the structure is attached to a resin or biomolecule, then the point of attachment can be indicated. The CST is attached to the whole structure as a labelled SGroup. 

If the structure is completely unknown then there is no structure to register In these cases, it is common to register a placeholder structure consisting of a single star atom to which the CST can be attached. 

Because the structure is not fully specified, it will be uncertain whether two batches are the same is one batch of green slime the same as another Determining whether they are the same (and if not, changing the CST to avoid a match) will require manual intervention by a registrar. 

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Surface crystallography started in the late 1960s, with the simplest possible structures being solved by LEED [14]. Such structures were the clean Ni (111), Cu(l 11) and Al(l 11) surfaces, which are unreconstructed and essentially unrelaxed, i.e. very close to the ideal temrination of the bulk shown in figure B 1.211 a) typically, only one unknown structural parameter was fitted to experiment, namely the spacing between the two outennost atomic layers. 

There are several levels of pepfide sfrucfure The primary structure is the ammo acid sequence plus any disulfide links With the 20 ammo acids of Table 27 1 as building blocks 20 dipeptides 20 tripeptides 20" tetrapeptides and so on are possible Given a peptide of unknown structure how do we determine its ammo acid sequence" ... 

Samples can be single substances complex mixtures of well-known, relatively simple substances complex mixtures of substances of totally unknown structure or combinations of such analyses. It is impossible to generalize in such situations, but it is possible to offer guidelines on some of the important issues. 

Numerous dyes structurally related to the safranines, such as the eurodines, e.g. (141), the indulines, e.g. (142), the nigrosines (143) and aniline black, a pigment of unknown structure used in the printing industry, are well known and a detailed account of their chemistry and applications has been presented (57HC(ll)l). 

Phenyl-l,2-benzisoxazole has been reported to give a disulfonic acid of unknown structure on treatment with 40% oleum (67AHC(8)277). The chlorosulfonation of 1,2-benzisoxazole-3-acetic acid has been reported to give a mixture of the two products shown in Scheme 26. 

The need for simple names to describe complex structures has been met in several ways, the most straightforward of which is to use a trivial name giving little or no structural information e.g. morphine, opuntiol). Such names are.often based on the Latin name of the species from which the compound was isolated e.g. opuntiol from Opuntia eliator). While this is acceptable for a newly isolated compound of unknown structure, it is less satisfactory once the structure is established. What is needed is some means of establishing the relationship of the compound to others in the same class, without going into too much detail with regard to structure and stereochemistry. This can be achieved by defining, for a particular group of structures, a parent structure. 

The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. 

A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the native protein has a molecular weight of 240,000. Chromatography in the presence of 6 M guanidine hydrochloride yields only a peak for a protein of M, 60,000. Chromatography in the presence of 6 M guanidine hydrochloride and 10 mM /3-mercaptoethanol yields peaks for proteins of M, 34,000 and 26,000. Explain what can be determined about the structure of this protein from these data. 

W. C. Zeise prepaied K[Pl(C H4)Cl3) and related compounds though of unknown structure at the time they later proved to be the first organometallic compounds. 

SC2CI3 and its Br analogue are of unknown structure, as are reported La2X3 phases, though Y2CI3 and Y2Br3 have been shown to consist of parallel chains of Ye octahedra, the chains being linked by Cl atoms ... 

The reaction of dichlorocarbene with 2 f-thiachromen (42) was exceptional since it gave none of the expected adduct but rather the products of substitution at the 2- (43) and 4-position (44) together with a bis-adduct of unknown structure. The substitution products could arise by reaction of the ambident anion 45 with dichlorocarbene, but the absence of these products in the same reaction of 4jy-thiachromen argues against this mechanism. The... 

The amination of 2-bromo-l,5-naphthyridine also proceeds without rearrangement to yield 2-amino-1,5-naphthyridine (up to 80%) together with 1,5-naphthyridine (10%) and a substance (CgH8N4,10% yield) of unknown structure as by-products. Thus, here also it remains uncertain whether a 2,3-aryne is an intermediate. 

An examination of the mass spectra of these isomeric compounds and of their D20-exchanged analogs leads to the conclusions that the spectra can be interpreted in terms of the structures 4-6 and that structural differences lead to extensive differences in fragmentation. These mass spectra now can be used for identification purposes and as models to aid in the interpretation of the mass spectra of similar compounds, possibly of unknown structure. 

A hydrocarbon of unknown structure has the formula CgHjQ. On catalytic hydrogenation over the Lindlar catalyst, 1 equivalent of H2 is absorbed. On hydrogenation over a palladium catalyst, 3 equivalents of H2 are absorbed. 

As noted in Section 6.2, it usually helps with compounds of known formula but unknown structure to calculate the compound s degree of unsaturation. In the present instance, a formula of C4H10O corresponds to a saturated, open-chain molecule. 

A compound of unknown structure gave the following spectroscopic data Mass spectrum M4 = 88.1... 

The values given in Table 19.2 are remarkably constant from one aldehyde or ketone to another. As a result, IR spectroscopy is a powerful tool for identifying the kind of a carbonyl group in a molecule of unknown structure. An unknown that shows an IR absorption at 1730 cm 1 is almost certainly an aldehyde rather than a ketone an unknown that shows an IR absorption at 1750 cm-1 is almost certainly a cvclopentanone, and so on. 

Pyrido[2, l-6]quinazolinone (analogous to 204) and its 2,8-dinitro derivative were brominated by bromine in acetic acid, but the products are of unknown structure. Reaction with a mixture of phosphoryl chloride and... 

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