Nomenclature, conformational angles

A. According to the nomenclature proposed by Balaram and by analogy with j8-pep-tides [158], the conformational space of oli-go(a-aminoxy acid) can be described by the following torsion angles to, ifi, O-i, and y/. 

The metal salts of peroxynitrite have also been studied using ab initio methods. We use the same nomenclature as McGrath and Powland s early paper on ONO—OH , which distinguishes different conformers by their dihedral angles. For example, the structure with a cis ONO—O arrangement and the alkali atom bonded to the terminal oxygen with a perpendicular orientation is called cis,perp Figure 1 describes the conformational aspects of the conformers studied. 

In each family, there are two different genera. To each genus can be assigned a quintet letter code (Table I) which sequentially refers to the conformational domain of the angles ot, 3, Y, S and e. In this nomenclature, t, g+ and g refer to the domains centered around 180°, 60° and -60° respectively and spanning a range of +60°. The first genus in the 4-family,... 

Let US first examine current practice in nomenclature of the phenom-menon of internal rotation. Standard textbooks on conformational analysis on the one hand and those on spectroscopy on the other hand deal differently with the basic definitions. Internal rotation is measured by one or more torsion angles (dihedral angles, azimuthal angles). In the simple cases of e.g. a 1,2-disubstituted ethane the potential energy associated with the internal rotation may be written in a formal sense as a truncated Fourier expansion ... 

Figure 7.2 Conformational interconversion ofthe five-membered diamine chelate ring of [Co(en)(NH3)4] +. (a) Nomenclature of the torsional angles, (b) Representation of the extreme, intermediate and transition state conformations, (c) Graphical representation ofthe potential energy surface (see Text). (Reproduced from Ref [237] John Wiley and Sons, Inc., 1987.)...

When molecules are composed of several peptide units, they may adopt the extended conformation, in which the entire backbone is nearly planar and each peptide unit is in the trans form. More often, however, peptides, whether they are linear or cyclic, are folded. The folding is accomplished by rotations about the N—C bonds and the C —C bonds. An international commission has established a convention for the nomenclature (lUPAC-IUB Commission on Biochemical Nomenclature, 1970) for torsional angles (Fig. 1). According to this convention, the torsional angles f, and a>i equal 180° for a fully extended chain. For a planar trans peptide unit, a>i = 180°, whereas... 

The most common crown ethers are shown in Fig. 22. Since application of lUPAC rules to polyethers leads to somewhat cumbersome designations, we will follow the simple crown nomenclature proposed by Pedersen Polyethers are built up from 1,4-dioxa units, O—CH —CH —O. The minimum energy conformation of these units is staggered with torsion angles about C-C bonds being synclinal (60°) and about C-O bonds being antiperiplanar ( 180 °C) (for definitions see Fig. 23). These preferences, however, do not preclude deviations if required by ring formation or cation complexation. 

Besides these qualitative nomenclatural systems, quantitative systems are available to describe the ring. shape, or puckering. Two puckering parameters. suffice for five-membered rings, where three are needed for pyranoses. For furanoses, the phase angle 4> is related to where the ring is most puckered, and specifically points to a position on the conformational wheel. The information on extent of deviation from planarity is furnished by the amplitude. 

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