Stereochemical representations

Normally, the stereochemical features of the reaction type and the starting materials determine the stereochemical features of the products. Accordingly one can derive the operator T from E and R, and thus the transformation C - C. Such a representation requires a correlation of the ligand indices of the stereochemical representation used and the indices of the atoms that enter the representation of the constitution. 

The various polymerization steps along the series of alcohols may be visualized in stereochemical representation as follows ... 

If we consider a dimer, in a stereochemical representation, the bulk reaction of equation 9.72 is... 

Note how we have resorted to another form of representation of the ethane, ethylene, and acetylene molecules here, representations that are probably familiar to you (see Section 1.1). These line drawings are simpler, much easier to draw, and clearly show how the atoms are bonded - we use a line to indicate the bonding molecular orbital. They do not show the difference between a and rr bonds, however. We also introduce here the way in which we can represent the tetrahedral array of bonds around carbon in a two-dimensional drawing. This is to use wedges and dots for bonds instead of lines. By convention, the wedge means the bond is coming towards you, out of the plane of the paper. The dotted bond means it is going away from you, behind the plane of the paper. We shall discuss stereochemical representations in more detail later (see Section 3.1). 

The use of rotated Fischer projections has been retained in the present edition in order to provide a link with, and an explanation of, the bulk of existing published polymer literature, although the present common practice [4] is to depict main-chain bonds in planar, extended zigzag (all-trans) conformations, together with a stereochemical representation of side-groups at tetrahedrally-bonded atoms. 

MDL s Enhanced Stereochemical representation http //www.mdli.com/solutions/white papers/ stereochemistry-white-paper.jsp. 

Figure 2-12 Sterols. (A) Structure of the Steroid Nucleus, (B) Stereochemical Representation, and (C) Cholesterol...

Fig. 5. Photoreaction cycles of bacteriorhodopsin. Photointermediates, the absorption wavelength, lifetime, protonation state, and stereochemical representation of a Schiff base.

MDL s Enhanced Stereochemistry Representation, http jjwww.symyx. comjproducts pdfs j Enhanced Stereochemical Representation.pdf. 

The projected, numerical factual database BEILSTEIN-ONLINE represents a natural extension of the Beilstein Handbook of Organic Chemistry which has been published for more than 100 years in more than 300 volumes. The Handbook together with the structure file cards of the literature period 1960-1980 (E-V Period) contain factual and structural information on more than 4 million compounds. The computer representation of organic chemical structures therefore constitutes the centre part of the database design. The chemical structure is described in a post-topological format. Not only constitutional information is included but also a complete stereochemical representation. Bond orders are replaced by electronic information. This allows a much more global and unique representation of tautomers. This paper gives an overview not only of the data structure of chemical compounds but also of its associated physical numerical data and keywords. 

Newman projections and other stereochemical representations will be discussed in Chapter 2. 

Figure 2.19 shows three stereochemical representations for (2S,3S)-2-chloro-3-pentanol (40). One can interconvert these representations by imagining the view to be had from various perspectives. For example, viewing 40a from the perspective indicated by the eye would produce the bold/ dashed wedge figure 40b, which is properly oriented (substituents on a horizontal line project toward the viewer) to simply draw the Fischer projection, 40c. Note that a Fischer projection shows an eclipsed conformation of the structure, so ordinarily it does not represent the most stable conformation. 

Fig. 9.2. All structures generated for the formula C4H2CI4 with MOLGEN-MS. Run 1 all structures run 2 structures within dotted lines run 3 structures within the solid lines. Stereochemical representations are indicative only. Reproduced from [285] copyright (2008), with permission from Elsevier.

Dimerization resulting from bimolecular reaction among free radicals resulting from electronation of the protonated forms of the ketone (acetophenone) can occur according to the following stereochemical representations of the formation of pinacols ... 

Fischer projection (Section 22.2) A schematic stereochemical representation. In sugars, the aldehyde group is placed at the top and the primary alcohol at the bottom. Horizontal bonds are taken as coming toward the viewer and vertical bonds as retreating. 

The superficial similarity of J, to pentacovalent phosphorus systems is apparent in their common TBP geometries and is emphasized by structure 2. Structure 2 is useful for stereochemical representations and also because it is easily written, though we acknowledge its inability to represent accurately electronic structure. 

Although tropones give [4+2] adducts with maleic anhydride, the sulfur analog, cycloheptatrienethione, gives [8+2] cycloaddition [47]. Draw the structure of that product including stereochemical representation. 

Stereochemical representation has been an integral part of the CAS Chemical Registry System since its inception in 1965 (see Stereochemistry Representation and Manipulation). Stereoisomers are considered to be different, individual substances, and each is assigned its own CAS Registry Number. The unique identification of stereoisomers permits the storage and retrieval of information collected from scientific literature about a specific isomer. About one-fourth of the over 17 million substances in the Registry File contain stereo information. 

More research is required for other aspects of stereochemical representations. Partially known stereochemistry, of which missing absolute assignment and racemic mixtures are special cases, poses problems for the selection of a symmetry consistent, unique, and short representation that is amenable to canonicalization. There is also no standard interpretation of the corresponding structure diagrams, even for simple cases. 

Duhem criticised the indefiniteness of the atomic hypotheses, favouring the integration of mechanics and thermodynamics into a broader theory.For example he did not accept that van t Hoff s stereochemical representations should be understood as a fully fledged geometric picture of something real. Molecular structures do not have to be understood in terms of atoms, but can equally well be understood in terms of the chemical properties of the compounds. The importance of Duhem for the philosophy of chemistry is now well documented (see the chapter on Duhem). 

Either by hand or by computer, it s reasonably easy to draw and manipulate real stereochemical representations of molecules with two chiral centers, sometimes even with three. However, many biological molecules have many more chiral centers than this, and Fischer devised a way of representing these in a flat form, in which it is easy to see stereochemical relationships and, particularly, to identify meso-compounds. Fischer projections consist of a cross motif, 7.89, and in this, groups b and d are pointing toward us, out of the paper, while groups a and c point away from us, behind the paper. 

Even the coordinate systems which we employ are vulnerable to intellectual prejudice. It may be clear that we need to make provision for storing atomic coordinates in three dimensions. Yet the standard esthetically pleasing diagrams which we see in journals often have (X,Y) coordinates on the printed page which cannot be related to their (X,Y,Z) coordinates in real space. This is very true of stereochemical representations, where the so-called real shape of the molecule is translated into an unreal flat appearance. 

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