Structure representation interconversion

The intrinsic language of chemistry is formed by the vocabulary of chemical formulae and structural representations connected by the syntax of their interconversions. It describes a tangible reality it is a reification of the word and the text its signs are engraved into matter [1.18,1.19]. 

The wide variety of chemical structure representations in use has inevitably resulted in a need to interconvert them some of these interconversions are fairly trivial, while others are nearly or completely impossible. 

The chemical constitution of a molecule or an ensemble of molecules (EM) of n atoms is representable by a symmetric n X n BE-matrix and corresponds accordingly to a point P in TR ( +D/a an n(n +1)/2 dimensional Euclidean space, the Dugundji space of the FIEM(A). The "city block distance of two points P i and P 2 is twice the number of electrons that are involved in the interconversion EMi EM2 of those EM that belong to the points Pi and P2. This chemical metric on the EM of an FIEM provides not only a formalism for constitutional chemistry, but also allows us to use the properties of Euclidean spaces in expressing the logical structure of the FIEM, and thus of constitutional chemistry 3e>32c>. 

A universal, computer oriented representation of the relevant structural features of molecular systems and their interconversion by chemical reactions is possible with the pairwise combinations (E, C) of BE-matrices and CC-matrices. The transformation... 

Figure 24. Schematic representation of conformational interconversions in carcer-ands and structurally similar self-assembled capsules. Left. Interconversion of "twistomers" with a still freely rotation guest. Right Rotation of the guest (symbolized by an arrow) in a frozen twistomer.

Fig. 2.94. Schematic representation of the potential energy surface for the interconversion of various [RhTp(CO)2] structures.

Figure 7.2 shows the relevant structural parameters, schematic representations of the extreme, intermediate and transition-state conformations of the chelate ring, and the calculated energy profile. Heavy equipotential lines are spaced by 10 kj mol , and light lines by 2 kJ moP (see the labeling of some of the equipotential lines). Also shown in Figure 7.2 are the two symmetrically related lowest-energy pathways for the 5- i interconversion. 

FIGURE 2.15 Molecular structure of amphiphilic dumbbell-shaped molecule 14 and representation of the reversible interconversion of helical fibers into nanocapsules. Reprinted with permission from Reference 55. Copyright 2006 John Wiley Sons, Inc. 

If you have access to a set of molecular models, converting between perspective formulas, Fischer projections, and skeletal structures is rather straightforward. If, however, you are interconverting these three-dimensional structures on a two-dimensional piece of paper, it is easy to make a mistake, particularly if you are not good at visualizing structures in three dimensions. Fortunately, there is a relatively foolproof method for these interconversions. All you need to know is how to determine whether an asymmetric center has the / or the 5 configuration (Sections 4.7 and 4.14). Look at the following examples to learn how easy it is to interconvert the various stractural representations. 

Prediction of properties affected by vibrational averaging can only be accomplished if an accurate representation of the molecular PES is available at least around the equilibrium position(s). Anharmonic force fields provide the most convenient source for such a representation on which most interconversions of the many distance types are based. Thus, the use of anharmonic force fields in accurate structural studies of small molecules has a long hi story Furthermore, a... 

Figure 7. Schematic representation of oligomeric structure of type Abotulinum and tetanus neurotoxins. Based on results in Ledoux et al. (1994) and modified after Singh (1993), it is assumed that botulinum neurotoxin exists as trimer and tetramer whereas tetanus neurotoxin exists as dimer and trimer. The arrows indicate possible interconversion between two oligomeric form. The shaded areas indicate the location of amphiphilic/trans-membrane region of the monomeric units.

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