Three-Dimensional Molecular Structure Tables

Chapter 11 Three-Dimensional Molecular Structure Tables... 

Many biological, physical and chemical properties are clearly functions of the three-dimensional (3D) structure of a molecule. Thus, the understanding of receptor-ligand interactions, molecular properties or chemical reactivity requires not only information on how atoms are connected in a molecule (connection table), but also on their 3D structure. 

The prediction of three-dimensional chemical structure from a list of atoms in a molecule and their connectivity is a good example of a chemical problem that may be solved by an expert system. We have already seen (Fig. 9.2) how the SMILES interpreter can construct a two-dimensional representation of a structure from its one-dimensional representation as a SMILES string. The CONCORD program (CONnection table to CoORDinates) takes a SMILES string and, very rapidly, produces a three-dimensional model of an input molecule. This system is a hybrid between an expert system and a molecular mechanics program, molecular mechanics being the method by which molecular structures are minimized in most molecular modelling systems. The procedure operates as follows. 

Fig. 6.11 Two-dimensional and three-dimensional CPK structural features identified for cross-reactivity are an N space-fiUing molecular models of sulfamethoxazole and aromatic heterocyclic ring containing at least one nitrogen three aUergenically cross-reactive sulfonamides, sulfa- and with a methyl substituent arrowed) p to the point of moxole, sulfamerazine, and sulfamethazine. Important attachment of the ring to the nitrogen (see also Table 6.2)...

The classic database of three-dimensional molecular struaures is the Cambridge Structural Database. It contains evaluated small-molecule and polymer X-ray and neutron diffraction data for more than 70,000 compounds. The database grows at the rate of 10% per year. It contains the connection table of each structure (frequently a complex or solvate), the bibliographic... 

The structure of each compound is stored as a connection table. A molecular models is generated for each stored structure using molecular mechanics model building such as MM2, the semiempirical method MOPAC 6.0, or specialized methods such as a recently developed extended Hiickel method. Three-dimensional structures can also be generated directly from their connection tables by structure generators (see Three-dimensional Structure Generation Automation) such as concord or CORINA. Some approaches to QSPR use only descriptors derived from the topological representation of the molecular structures, and in this case the development of three-dimensional molecular models is not necessary. 

The monomers discussed thus far have an active bond that may react to form two covalent bonds with other monomers forming a two-dimensional chamUke molecular structure, as indicated earlier for ethylene. Such a monomer is termed bifimctional. In general, the functionality is the number of bonds that a given monomer can form. For example, monomers such as phenol-formaldehyde (Table 14.3) are trifiinctional they have three active bonds, from which a three-dimensional molecular network structure results. 

Thermoset moldable compounds can be mixed with a very wide variety of fillers to modify their properties to meet the requirements for a given application. Adding suitable fillers can produce coefficients of thermal expansion and elongation behavior virtually identical to those of copper. Once thermoset materials have cured, moreover, their three-dimensional molecular network structure gives them a very high level of dimensional stability. Consequently, in terms of temperature resistance to soldering many of the materials in this class are potentially suitable as MID substrates. Table 2.5 summarizes some of the important thermal properties of commercially available thermoset moldable compounds. Thermoset moldable compounds, moreover, have economic potential because in some cases the cost of the material Is low. Phenolic resin moldable compounds in particular are available at a price of less than about 7 (EUR 5) per kg and could therefore be considered an economical alternative to LDS high-temperature thermoplastics. 

So far we have emphasized structure in terms of electron bookkeeping We now turn our attention to molecular geometry and will see how we can begin to connect the three dimensional shape of a molecule to its Lewis formula Table 1 6 lists some simple com pounds illustrating the geometries that will be seen most often m our study of organic chemistry... 

Structural classifications of oxides recognize discrete molecular species and structures which are polymeric in one or more dimensions leading to chains, layers, and ultimately, to three-dimensional networks. Some typical examples are in Table 14.14 structural details are given elsewhere under each individual element. The type of structure adopted in any particular case depends (obviously) not only on the... 

The demulsification data with four different demulsifiers for a crude oil-water system (Table I) support this conclusion. Structurally, the demulsifier PI and R0 are of moderate (MW 2,000-5,000) molecular weights, whereas PI and P2 are large (MW >50,000) three dimensional structures. 

A number of different molecular mechanisms can underpin the loss of biological activity of any protein. These include both covalent and non-covalent modification of the protein molecule, as summarized in Table 6.5. Protein denaturation, for example, entails a partial or complete alteration of the protein s three-dimensional shape. This is underlined by the disruption of the intramolecular forces that stabilize a protein s native conformation, namely hydrogen bonding, ionic attractions and hydrophobic interactions (Chapter 2). Covalent modifications of protein structure that can adversely affect its biological activity are summarized below. 

One of the most signiflcant variables affecting zeolite adsorption properties is the framework structure. Each framework type (e.g., FAU, LTA, MOR) has its own unique topology, cage type (alpha, beta), channel system (one-, two-, three-dimensional), free apertures, preferred cation locations, preferred water adsorption sites and kinetic pore diameter. Some zeolite characteristics are shown in Table 6.4. More detailed information on zeolite framework structures can be found in Breck s book entitled Zeolite Molecular Sieves [21] and in Chapter 2. 

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