TOPICAL three-dimensional structure

Much of what we need to know abont the thermodynamics of composites has been described in the previous sections. For example, if the composite matrix is composed of a metal, ceramic, or polymer, its phase stability behavior will be dictated by the free energy considerations of the preceding sections. Unary, binary, ternary, and even higher-order phase diagrams can be employed as appropriate to describe the phase behavior of both the reinforcement or matrix component of the composite system. At this level of discussion on composites, there is really only one topic that needs some further elaboration a thermodynamic description of the interphase. As we did back in Chapter 1, we will reserve the term interphase for a phase consisting of three-dimensional structure (e.g., with a characteristic thickness) and will use the term interface for a two-dimensional surface. Once this topic has been addressed, we will briefly describe how composite phase diagrams differ from those of the metal, ceramic, and polymer constituents that we have studied so far. 

In this chapter we have covered a great deal of material relating to the preparation of macrocyclic complexes. The basic reactions that we have introduced in earlier chapters have now found a synthetic use. At the very end of the chapter we began to ponder ways of introducing three dimensional structure into macrocyclic systems. This is the topic that we consider in the next chapter. 

Disulfide bonds These covalent bonds form between Cys residues that are close together in the final conformation of the protein (see Fig. 4) and function to stabilize its three-dimensional structure. Disulfide bonds are really only formed in the oxidizing environment of the endoplasmic reticulum (see Topic A2), and thus are found primarily in extracellular and secreted proteins. 

The structures of carbohydrates have fascinated chemists since the dawn of modem organic chemistry with the work of Fischer. " While Fischer determined the stereochemical relationship of the simple sugars, controversy still remains as to some of the more subtle features of their three-dimensional structures. In particular, the origins of the anomeric and exo-anomeric effects remain topics of debate. Complicating these discussions is the role that solvent may play in perhaps preferentially stabilizing some conformer(s) over others. We will concentrate our attention in this section to stmcture of D-glucose and the role that aqueous solvent has in altering its eonformational preference. 

Thanks to genomics, it is now much easier to deduce the amino acid sequence of a protein than by the older method of direct chemical analysis ( protein sequencing ). It is much harder to get a protein s three-dimensional structure than to get its sequence (i.e., essentially its chemical formula). The latter can be simply be deduced from the sequence of DNA, while the former is a major topic in other grand projects that will impact... 

The emerging understanding that the coding of information into the three-dimensional structure of all biomolecules is emphasized in this edition (see page 229). This approach introduces students to the most basic and accessible features of biological information theory and makes several topics (e.g., cell signaling mechanisms) more comprehensible. 

Links. PDB s search engine, the Structme Explorer, can be used to retrieve PDB records, as shown in Figure 5.2. The Structure Explorer is also the primary database of links to third-party aimotation of PDB structure data. There are a number of links maintained in the Structure Explorer to Internet-based three-dimensional structure services on other Web sites. Figme 5.2 shows the Structure Summary for the protein bamase (IBNR Bycroft et al., 1991). The Structure Explorer also provides links to special project databases maintained by researchers interested in related topics, such as structural evolution (FSSP Holm and Sander, 1993), structure-structure similarity (DALI Holm and Sander, 1996), and protein motions (Gerstein et al., 1994). Links to visualization tool-ready versions of the structure are provided, as well as authored two-dimensional images that can be very helpful to see how to orient a three-dimensional structure for best viewing of certain features such as binding sites. 

Both the theoretical background of x-ray crystallography and its apphcation for the elucidation of three dimensional structure of peptides transcend the boundaries of peptide chemistry. Some special articles written on this subject are cited at the end of this chapter to provide sources for those who wish to pursue this topic in more detail. Here we can merely comment on the scope and significance of the method. 

The molecule was of course there aU along, but how to construct it from atoms, how to understand the three-dimensional structure of molecules, and what is beautiful and enchanting about their structure All this was reached quite late in some cases you had to go through 300-400 pages of the book to find this topic. I felt that the beauty of chemistry ought to be revealed right at the onset of the course to attract the students and motivate them to be engaged in the rest of the course. 

Symmetry is a powerful and useful tool in chemistry. In this chapter, we have seen some examples of how symmetry ideas and group theory can be applied to quantum mechanics. Other topics involving symmetry will be introduced in future chapters. As illustrated in Example 13.12, symmetry considerations will be very important in our consideration of the spectroscopy of atoms and molecules. Symmetry will also be important when considering crystals and surfaces, topics covered near the end of the text. Any advanced study of chemistry must include symmetry and group theory, not only because it can be applied to wavefunctions, as we did here, but to the three-dimensional structures of all molecules. 

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