Three-dimensional attachment

Hall, P. and Malik, M.R. (1986). On the instability of three-dimensional attachment-line boundary layer weakly non-linear theory and numerical approach. J. Fluid Mech., 395, 229-245. 

Figure 8. Three-dimensional mean-potential surface for the X IT state of HCCS, (Pi, Pa, y), presented in form of its ID sections. Curves represent the function given by Eq. (75). (with Ati — 0.0414, k2 — 0.952, tt 2 — 0.0184) for fixed values of coordinates p, and P2 (attached at each curve) and variable y — 4 2 4t Here y — 0 corresponds to cis-planar geometry and Y = ft to trans-planar geometry. Symbols results of explicit ab initio computations.

In most cases, the proteia is immobilized onto y-aminopropyl sUica and covalently attached usiag a cross-linking reagent such as -carbonyl diimidazole. The tertiary stmcture or three dimensional organization of proteias are thought to be important for their activity and chiral recognition. Therefore, mobile phase conditions that cause proteia "deaaturatioa" or loss of tertiary stmcture must be avoided. 

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

In this chapter, we will discuss the present status of CHIRBASE and describe the various ways in which two (2D) or three-dimensional (3D) chemical structure queries can be built and submitted to the searching system. In particular, the ability of this information system to locate and display neighboring compounds in which specified molecular fragments or partial structures are attached is one of the most important features because this is precisely the type of query that chemists are inclined to express and interpret the answers. Another aspect of the project has been concerned with the interdisciplinary use of CHIRBASE. We have attempted to produce a series of interactive tools that are designed to help the specialists or novices from different fields who have no particular expertise in chiral chromatography or in searching a chemical database. 

Haston, W.S., Shields, J.M., Wilkinson, P.C. (1982). Lymphocyte locomotion and attachment on two-dimensional surfaces and in three-dimensional matrices. J. Cell Biol. 92, 747—752. 

The ferrocene moiety is not just an innocent steric element to create a three-dimensional chiral catalyst environment. Instead, the Fe center can influence a catalytic asymmetric process by electronic interaction with the catalytic site, if the latter is directly coimected to the sandwich core. This interaction is often comparable to the stabilization of a-ferrocenylcarbocations 3 (see Sect. 1) making use of the electron-donating character of the Cp2Fe moiety, but can also be reversed by the formation of feirocenium systems thereby increasing the acidity of a directly attached Lewis acid. Alternative applications in asymmetric catalysis, for which the interaction of the Fe center and the catalytic center is less distinct, have recently been summarized in excellent extensive reviews and are outside the scope of this chapter [48, 49], Moreover, related complexes in which one Cp ring has been replaced with an ri -arene ligand, and which have, for example, been utilized as catalysts for nitrate or nitrite reduction in water [50], are not covered in this chapter. 

We have designed PBUILD, a new CHEMLAB module, for easy construction of random copolymers. A library of monomers has been developed from which the chemists can select a particular sequence to generate a polymeric model. PBUILD takes care of all the atom numbering, three dimensional coordinates, and knows about stereochemistry (tacticity) as well as positional isomerism (head to tail versus head to head attachment). The result is a model of the selected polymer (or more likely a polymer fragment) in an all trans conformation, inserted into the CHEMLAB molecular workspace in literally a few minutes. 

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