Three-dimensional structural notations

Chemical identity may appear to present a trivial problem, but most chemicals have several names, and subtle differences between isomers (e.g., cis and trans) may be ignored. The most commonly accepted identifiers are the IUPAC name and the Chemical Abstracts System (CAS) number. More recently, methods have been sought of expressing the structure in line notation form so that computer entry of a series of symbols can be used to define a three-dimensional structure. For environmental purposes the SMILES (Simplified Molecular Identification and Line Entry System, Anderson et al. 1987) is favored, but the Wismesser Line Notation is also quite widely used. 

The selective oxidation of ra-butane to give maleic anhydride (MA) catalyzed by vanadium phosphorus oxides is an important commercial process (99). MA is subsequently used in catalytic processes to make tetrahydrofurans and agricultural chemicals. The active phase in the selective butane oxidation catalyst is identified as vanadyl pyrophosphate, (V0)2P207, referred to as VPO. The three-dimensional structure of orthorhombic VPO, consisting of vanadyl octahedra and phosphate tetrahedra, is shown in Fig. 17, with a= 1.6594 nm, b = 0.776 nm, and c = 0.958 nm (100), with (010) as the active plane (99). Conventional crystallographic notations of round brackets (), and triangular point brackets (), are used to denote a crystal plane and crystallographic directions in the VPO structure, respectively. The latter refers to symmetrically equivalent directions present in a crystal. 

In the remainder of this chapter, specific examples of fibrous minerals are presented. The chemical formulas are given as well as the mineral names. A formula is a shorthand notation that describes the elemental composition of the compound plus the specific ion associations, as determined by three-dimensional structure analysis of the species. Because every mineral sample is not completely analyzed, an ideal formula—one that summarizes the chemistry and associations of the ions—is usually presented. 

A convenient short-hand representation of such three dimensional structures introduced by Zimmerman I 4,7) is often convenient when one is following complex photochemical reactions. This two dimensional notation is shown in Equation 6 31). Thus Equation 6 in two dimensions represents the three dimensions of Equation 5. 

When it comes to physicochemical (biological) properties the common structural formulae obscure rather than explain the problem. One of the most convincing examples may be the anaesthetic activity of chemicals. Among general anaesthetics one can identify such diverse chemical families like hydrocarbons, alcohols, ethers, barbiturates, nitrous oxide, steroids, etc. Each one must have anaesthetic activity encoded in its structure but how is it discovered using conventional chemical symbolic The planar or three-dimensional chemical notation can be an obstacle to making a breakthrough in chemistry. 

Now that the three-dimensional structure of the molecule is important, the dot and cross notation, which was so useful when counting electrons around each atom, is of less utility. First, it is rather cumbersome and secondly, it does not... 

All structural notations attempt to give some indication of the real-life arrangement of the atoms within the molecule in question. The notations fall into two categories two-dimensional and three-dimensional. The former type portrays the molecule as though it were flat, and leaves unresolved any explicit information about the three-dimensional structure. This type only indicates the connectivities of the component atoms to each other. In contrast, the latter type sets out to give as much information as is possible on a flat sheet of paper of the spatial configuration of the constituent parts of the molecule in question. 

This variation is of very limited use, and, in order to convey more fully the three-dimensional structure of the molecule, more sophisticated notations must be employed. 

Rule scripts operate on substances defined in a data file in either SMILES (simplified molecular input line entry specification) or CMP (compound) format. The conventional SMILES notation as developed by Weininger [28] provides a basic description of molecules in terms of two-dimensional chemical graphs. The CMP file format developed with the OASIS system [29] provides separate logical records for information about connectivity, three-dimensional structure, electronic structure from quantum-chemical molecular-orbital computations, as well as physicochemical and experimental toxicological data. 

Since molecular geometries are three-dimensional, they are often difficult to represent on two-dimensional paper. Many chemists use tiiis notation for bonds to indicate three-dimensional structures on two-dimensional paper. 

Fig. 31 The three-dimensional structures of the two observed conformers of D-erythrose showing the intramolecular hydrogen bond networks. The notation used to label the conformers includes the symbols o and p to denote the anomer type, E and T with lower and upper subscripts indicate the ring puckerings, and the symbols c or cc to indicate the clockwise or counterclockwise coniiguratitm of the adjacent OH bonds, respectively. (From [222])...

An electrostatic potential map for acetonitrile (CH3CN), which is polar, is shown at left. From this map, determine the geometry for how two acetonitrile molecules would interact with each other. Draw structural formulas, using the three-dimensional bond notation introduced in Section 10.4, to illustrate the geometry of the interaction. 

Zeolite structures are designated by a three capital-letter code, for example, FAU stands for the faujasite structure, to which the well-known X and Y zeolites belong. A very useful short notation is used for the description of the pore system(s) each pore network is characterized by the channel directions, the number of atoms (in bold type) in the apertures, the crystallographic free diameter of the apermre (in A), asterisks (1, 2, or 3) indicating whether the systems is one-, two-, or three-dimensional. To completely specify the pore system, the eventual presence of cages (or channel intersections) should be indicated, along with their... 

Organic molecules are three-dimensional, so showing structures on paper in two dimensions can give a misleading picture of what the molecule actually looks like. This has led to the use of wedged line notation, which provides a simple way of showing organic molecules to Indicate their three-dimensional nature. 

Three examples will suffice to demonstrate this information Figure 3 shows the polyhedral units in the synthetic zeolite Linde Type A, which link to provide a three-dimensional interconnecting array of channels, Figure 4 illustrates the essentially two-dimensional system of channels in the mordenite framework, and Figure 5 shows the major channels in synthetic zeolite Linde Type L arranged as parallel one-dimensional channels and shown as a stereo pair. Table 6 lists the Atlas notations for these structures with explanations, including the symbols used in Tables 2-5. 

Consult text books from the Further Reading section and, for each of the coordination geometries for coordination numbers from 2 to 8, identify at least one known compound which exemplifies that coordination geometry. Draw the structure of each using a notation which reveals the three-dimensional arrangement of the groups. 

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