Topological isomerism

A large number of terms have been used to describe forms of isomerism in extended supramolecular arrays observed in the solid state. These include architectural isomerism,topological isomerism,and older terms that have specific and often well-defined meanings, in-... 

The earlier sections have only considered the way atoms are bonded to each other in a molecule (topology) and how this is translated into a computer-readable form. Chemists define this arrangement of the bonds as the constitution of a molecule. The example in Figure 2-39, Section 2.5.2.1, shows that molecules with a given empirical formula, e.g., C H O, can have several different structures, which are called isomers [lOOj. Isomeric structures can be divided into constitutional isomers and stereoisomers (see Figure 2-67). 

Dl A. Supercoiling. Supercoiling is a topological property of closed-circular DNA molecules. Circular DNA molecules can exist in various conformations differing in the number of times one strand of the helix crosses the other. These different isomeric conformations are called topoisomers and maybe characterized in terms of the linking number, Ek. A linear DNA molecule having Nbase pairs and h base pairs per turn of the helix, if joined end to end, has the following ... 

In the case of n-butene isomerization it was demonstrated (Figure 2) that the ideal micro-pore topology led to retardation of the C8 dimer intermediate and that the catalyst based on the ferrierite structure was close to optimal in this respect [1). For selective isodewaxing a one-dimensional pore structure which constrained the skeletal isomerization transition state and thereby minimized multiple branching such as the SAPO-11 structure was found to meet these criteria. Clearly, these are ideal systems in which to apply computational chemistry where the reactant and product molecules are relatively simple and the micro-porous structures are ordered and known in detail. 

Our definitions of the stereoisomeric center, line, and plane all stipulate the existence of bonds between the ligating element and its ligands. The exclusive use of these elements limits our analysis to classical stereochemistry and thus does not encompass the so-called topological isomerism (47) of interlocked rings—catenanes (48)—or of knots. As there is no bond between the rings of the catenanes we cannot expect to handle such compounds with a system based on connectedness. At the present stage of development, this limitation in scope... 

Amino-acul complexes. frans-(0,X)-[CoX(aminoacidato)(dien)]Y (X == CN, NO2, or Cl Y = Br, Cl, or ClO aminoacid === Gly, a-aminobutyric acid, L-Ala. L-Val, L-Thr, or L-Pro) complexes have been isolated. The cyano-complexes were shown to exist in the new conformational isomeric endo- and cxo-forms. This refers to the position of the hydrogen atom bonded to the central N of dien w ith respect to the cyanide group. The tetramine ligands 1,3-diaminopropane, 3,7-diaza-l,9-nonanediamine (2,3,2-tet), and 4,7-diaza-1.10-decanediamine (2,2,3-tet) exhibit marked topological specificity in the complexes [Co(tetramine)(aa)] (aa = Gly. Ala, Val. or Sar). Thus a-[Co-(3,2,3-tet)aa] and P2-[Co(2,3,2-tet)aa] appear to be formed exclusively under the synthetic conditions employed. 

The study of chemical reactions requires the definition of simple concepts associated with the properties ofthe system. Topological approaches of bonding, based on the analysis of the gradient field of well-defined local functions, evaluated from any quantum mechanical method are close to chemists intuition and experience and provide method-independent techniques [4-7]. In this work, we have used the concepts developed in the Bonding Evolution Theory [8] (BET, see Appendix B), applied to the Electron Localization Function (ELF, see Appendix A) [9]. This method has been applied successfully to proton transfer mechanism [10,11] as well as isomerization reaction [12]. The latter approach focuses on the evolution of chemical properties by assuming an isomorphism between chemical structures and the molecular graph defined in Appendix C. 

Topological resonance energy studies of the three isomeric thienopyrimidines show that while all of the ring systems are aromatic, the thieno[3,4-, pyrimidine class of compounds is less aromatic by approximately 20%. Correspondingly this system is believed to be considerably more reactive than its isomers <1997CCA841>. 

Figure 21. The equilibrium between the helical interlaced system precursor of the trefoil knot and its face-to-face analogous complex leading to the face-to-face complexes. Interconversion between the two isomeric cyclic products is, of course, not possible. For the cyclic compounds, the total number of atoms x connecting two phenolic oxygen atoms is 16 if n=4 (pentakis(ethyleneoxy) fragment) or 19 if n = 5 (hexakis(ethyleneoxy) linker). Each knot is represented by the letter k accompanied by the overall number of atoms included in the cycle. The face-to-face complexes contain two monocycles (letter m), the number of atoms in each ring also being indicated. It can be noted that each knot has a face-to-face counterpart. For instance [Cu2(k-90)]2+ and [Cu2(m-45)2]2+ are constitutional isomers. They are by no means topological stereoisomers [34, 35].

A. Molecular topology and photochemical reactions of cis-trans isomeric I,2-di-9-anthrylethylenes and related di-9-anthrylalkenes... 

The importance of molecular topology for the course of photochemical isomerizations is evident from the different modes of cycloaddition for seemingly similar linked anthracenes. For example, the photochemical isomerization of methyl 9-anthrilate 3, different from that of lb, proceeds with... 

A. Molecular Topology and Photochemical Reactions of cis-trans Isomeric l,2-Di-9-anthrylethylenes and Related Di-9-anthrylalkenes... 

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