Molecules structural similarity

A very common reaction during processing is the polymerization or crosslinking reaction of thermoset materials to form a final polymeric product. This is a common, heat- induced reaction in the epoxy resins and phenol/methanal polymers discussed in this book. It is also common in mbbers undergoing vulcanization and in isocyanates undergoing transformation to urethanes. These reactions form molecules structurally similar to the crosslinked hydrocarbon shown in Figure 4. 

Cd(CN)2, is isomorphous. To prevent the interpenetration, relatively large species must be hosted into the diamondoid network. Indeed, the mixed metal complex NMe4[Cu Zn CN)4] shows no interpenetration because the tetra-methylammonium cations, whose size fits to that of the adamantane-like cavity, occupy half of these cavities (both Cu and Zn ions are tetracoordinated). The interpenetration of neutral M(CN)2 nets (M = Zn, Cd) can be hindered by hosting neutral molecules, structurally similar to NMe4. The solution of this problem is obvious and elegant The crystallization of Cd(CN)2 in the presence of Me4C leads to a single diamond-like net. ... 

The above approximation, however, is valid only for dilute solutions and with assemblies of molecules of similar structure. In the event that concentration is high where intemiolecular interactions are very strong, or the system contains a less defined morphology, a different data analysis approach must be taken. One such approach was derived by Debye et al [21]. They have shown tliat for a random two-phase system with sharp boundaries, the correlation fiinction may carry an exponential fomi. 

Structurally similar molecules are expected to exhibit similar physical properties or, similar biological activities. ... 

We can descnbe the major elements of fatty acid biosynthesis by considering the for mation of butanoic acid from two molecules of acetyl coenzyme A The machinery responsible for accomplishing this conversion is a complex of enzymes known as fatty acid synthetase Certain portions of this complex referred to as acyl carrier protein (ACP), bear a side chain that is structurally similar to coenzyme A An important early step m fatty acid biosynthesis is the transfer of the acetyl group from a molecule of acetyl coenzyme A to the sulfhydryl group of acyl carrier protein... 

A similarity measure is required for quantitative comparison of one strucmre with another, and as such it must be defined before the analysis can commence. Structural similarity is often measured by a root-mean-square distance (RMSD) between two conformations. In Cartesian coordinates the RMS distance dy between confonnation i and conformation j of a given molecule is defined as the minimum of the functional... 

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

Figure 3.13 The hemoglobin molecule is built up of four polypeptide chains two a chains and two (3 chains. Compare this with Figure 1.1 and note that for purposes of clarity parts of the a chains are not shown here. Each chain has a three-dimensional structure similar to that of myoglobin the globin fold. In sicklecell hemoglobin Glu 6 in the (3 chain is mutated to Val, thereby creating a hydrophobic patch on the surface of the molecule. The structure of hemoglobin was determined in 1968 to 2.8 A resolution in the laboratory of Max Perutz at the MRC Laboratory of Molecular Biology, Cambridge, UK.

The close structural similarities between polychloroprene and the natural rubber molecule will be noted. However, whilst the methyl group activates the double bond in the polyisoprene molecule the chlorine atom has the opposite effect in polychloroprene. Thus the polymer is less liable to oxygen and ozone attack. At the same time the a-methylene groups are also deactivated so that accelerated sulphur vulcanisation is not a feasible proposition and alternative curing systems, often involving the pendant vinyl groups arising from 1,2-polymerisation modes, are necessary. 

Crystal structure determination has also been done with -butyllithium. A 4 1 n-BuLi TMEDA complex is a tetramer accommodating two TMEDA molecules, which, rather than chelating a lithium, link the tetrameric units. The 2 2 -BuLi TMEDA complex has a structure similar to that of [PhLi]2 [TMEDA]2. Both 1 1 -BuLi THF and 1 1 -BuLi DME complexes are tetrameric with ether molecules coordinated at each lithium (Fig. 7.2). These and many other organolithium structures have been compared in a review of this topic. ... 

One of the goals of Localized Molecular Orbitals (LMO) is to derive MOs which are approximately constant between structurally similar units in different molecules. A set of LMOs may be defined by optimizing the expectation value of an two-electron operator The expectation value depends on the n, parameters in eq. (9.19), i.e. this is again a function optimization problem (Chapter 14). In practice, however, the localization is normally done by performing a series of 2 x 2 orbital rotations, as described in Chapter 13. 

Molecular similarity searching provides the possibility of finding unrelated but functionally analogous molecules. This is a very nice feature because many distinct structures in contact with a CSP often share the same active sites. The compounds which have a structure similar to the structure of the sample query can be displayed automatically in order of their similarity. The degree of similarity is measured by a numerical value on a scale of 0 to 100 that may be included in the output form. An example of a similarity search is shown in Fig. 4-3. In this example, a search is being performed for the AZT with a similarity value >65 %. 

As noted previously, RNA is structurally similar to DNA but contains ribose rather than deoxyribose and uracil rather than thymine. There are three major kinds of RNA, each of which serves a specific function. All three are much smaller molecules than DNA, and all remain single-stranded rather than double-stranded. 

In a similar manner, ethanol can be oxidized by the dichromate ion to form a compound called acetaldehyde, CHaCHO. The molecular structure of acetaldehyde, which is similar to that of formaldehyde, is shown at the bottom in Figure 18-6. We see that the molecule is structurally similar to formaldehyde. The methyl group, —CH3, replaces one of the hydrogens of formaldehyde. The balanced equation for the formation of acetaldehyde from ethanol is... 

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