Structure representation rings

In the following, we will discuss two-dimensional (2D)-to-3D conversion in this context. However, it should be emphasized that we do so only for the sake of brevity. In reality, none of the conversion programs uhlizes informahon of a 2D image of a chemical structure. Only the information on the atoms of a molecule and how they are cormected is used (i.e. the starhng informahon is the conshtution of the molecule). One could even refer to linear structure representations such as SMILES as one-dimensional. However this is not true since SMILES allows for branches and ring closure which makes its informahon content essentially 2D. Thus, all structure representahons which lack 3D atomic coordinates will in the following simply be referred to as 2D. 

For the depiction of structural formulas of hexofuranoses, a combination of a three-dimensional, Haworth-perspective tetrahydrofuran ring with a Fischer projection of the C-5-C-6 side-chain is commonly used, as exemplified by formulas 3 and 6. With the formal closure of the second ring and formation of a 2,6-dioxabicyclo[3.3.0]octane system, however, the depiction of the C-6-C-3 ring, as in formula 7, also assumes three-dimensional geometry, and this does not correspond to the Fischer projection rule.11 Consequently, structural representations of such bicyclic molecules should be as close as possible to the actual steric situation, as shown by structures 4 and 8. 

Cycloalkanes are alkanes that are cyclic with the general formula C H2 . The simplest members of this class consist of a single, unsuhstituted carhon ring, and these form a homologous series similar to the unbranched alkanes. The C3 to Ce cycloalkanes with their structural representations are shown below. 

Another approach is to label the selected chemical fragments of easily recognizable features (for example -OH or -C( = 0)- group, aromatic ring, structural skeletons, etc.) with consecutive numbers, letters, or special characters. The full structure representation is than either a list of all present or a list of all different structural features. If different fragments are labeled as fi, then structure S can be written as a set of m fragments ... 

Fig. 10.12. Structural representation of ZSM-5. a)Schematic of the intersecting tunnel systems b) framework structure c) 10-ring tunnel size, (a and b reproduced, with permission, from Ref. 64.)...

Figure 3. Two structural representations of the calculated geometry of anti-J-methyl-2-pyridiniumcarbaldoxime cation (V) in its most stable form. The second structure is a perpendicular view to the first one to depict the oxime geometry better. The oxime group is 80° out of the plane of the ring. The oxime hydrogen is trans and essentially planar with respect to the oxime. The methyl group hydrogens are rotated 20, 140, 260° respectively relative to the pyridine ring, thus occupying the least hindered position from the oxime.

Figure 9. Two structural representations of the calculated geometry of the most stable form of C-protonated a.nti-1-methyl-3,6-dihydropyridine-2-carbaldoxime ion (XVIII). The second structure is a perpendicular view.The oxime group is rotated 90° from the plane of the ring with the oxime hydrogen trans and in the plane of the oxime group. The methyl hydrogens are rotated 33, 153, 273° with respect to the ring, the ring is essentially planar.

Strained four- and five-membered rings are found to span axial-equatorial sites according to the following general structural representation. 

Extension of the principle of axial-equatorial ring placement to spirobicyclic systems leads to the following general structural representation for a trigonal bipyramidal geometry ... 

Figure 5-8. Structural representations of morphine. The C ring has the boat conformation the D ring is in the chair conformation. Carbons 5, 6, 9, 13, and 14 are chiral.

There have been several structural representations of benzyne. The one most generally used represents benzyne as similar to benzene, but with a weak 7r-bond in the plane of the ring formed using two sp -orbitals. Molecular-orbital calculations... 

Structural representations of humic and fulvic acids are purely hypothetical and should just be considered as an attempt to rationalize chemical behavior. Several structural models have been proposed based on data gathered from degradative and nondegradative models. The different proposed models should be considered as complementary since each emphasizes certain particular properties. Briefly, humic acids are macromolecular and complex, and composed of substituted aromatic and aliphatic hydrocarbon core materials. It is probable that some aliphatic and aromatic ring compounds are heterocyclic with N, O, or S as the heteroatom. Segments or some side-chain components in the structures are substantially hydrophobic. In general, however, the... 

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