Pseudorotation cycle

Figure 5.3 Each juncture of lines represents a configuration for which the pair of numbers represents the ligands that are located in apical positions. The lines connecting the number pairs correspond to cycles of pseudorotation. The "static" position for a particular pseudorotation cycle is that ligand of the five not represented by a number at either end of the connecting line. Reversals of number pairs (such as "24" and "42") represent pairs of enantiomers for a system with five nonidentical ligands about the central phosphorus (Pabxyz).

Figure 11.3. The pseudorotation cycle showing the relation between the pseudorotation angle P (0-360°) calculated from the five torsional angles of the furanose.

FIGURE 24. Pseudorotation cycle of the cyclopropyl radical cation. Relative energy [CISD/6-31 G(d)] of the2 A, ground state and the B2 transition state from Reference 231... 

First, given the wide range of prebiotic nucleic acids, ribose-based polymers may be the most eminently suited for catalysis. Eschenmoser has pointed out, for example, that nucleic acids constructed from hexose nucleotides form inflexible ribbon structures,61 poorly suited for convoluting into the complex shapes that are required for catalysis (e.g., the backbone of the projected tertiary structure of the Tetrahymena self-splicing intron folds back on itself a number of times).62 Conversely, backbones composed of acyclic nucleotides may be too flexible to adopt stable secondary structures (since a great deal of entropy would necessarily be lost on freezing into a given conformer). Ribose, on the other hand, has a limited flexibility because of its pseudorotation cycle, and RNA can adopt a variety of helical conformations. 

Figure 1 Each jimcture of lines represents a configuration for which the pair of numbers indicates the ligands that are in the apical positions. Lines interconnecting number pairs represent cycles of pseudorotation that ligand of the five not indicated by a number at either end of a given line is the static equatorial hgand for that particular pseudorotation cycle. The interchange of numbers (as 15 51 ) indicates a pair of enantiomers for the system Pabxyz...

Pseudorotation The progression of one conformer of a five-membered ring to another conformer. In the case of cyclopentane there is no planar intermediate all conformers have at least one carbon atom out of the plane of the other carbon atoms. The maximum pucker can, in this case, rotate with almost no potential energy barrier between conformers. Each of the multitude of possible conformers can be described in terms of the maximum pucker and the pseudorotation phase angle, that is, where the conformer lies on a pseudorotation cycle (with an arbitrarily chosen origin). 

In the pseudorotation cycle (O Fig. 21), a change of P by 180° reverses the signs of all torsion angles. At every phase angle P, the sum of the torsion angles is 0°. Envelope and twist conformations alternate every 18° and T conformations are found at even multiples of 18°. The section of the pseudorotation cycle with phase angles of 0 90° is referred to as the... 

Nucleosides with a bicyclic sugar ring are often called conformationaly restricted or looked. The two major conformations of natural nucleosides are C-3 -endo and C-2 -endo. The formation of a second ring induces a restriction of the pseudorotational cycle of the ribofuranose puekering. The application of bicyclic nucleosides goes from the synthesis of modified oligonueleotides to enzyme inhibitors. 

In the course of pseudorotation and ring inversion of boat-chair conformations, intermediate conformational minima of a different type, e.g. a chair, may be visited. This chair conformation will have its own pseudorotation cycle and ring inversion process, which is thus linked to the boat-chair cycle. There are likely to be further different, less stable conformational types, some of them little populated no doubt, but linked into the total conformational network by an interconversion process. 

The three terms interconversion, pseudorotation and ring inversion thus seem distinct, the first including both the latter, but every interconversion between different conformational types is part of some pseudorotation cycle perhaps not one of the obvious ones. For this reason I prefer to call all interconversions except ring inversions by the same name pseudorotation, to direct attention to the multitude of possibilities beyond those that are NMR visible. The reader may prefer to reserve pseudorotation for the interconversion of conformations of the same type. If aware of the alternatives, it is easy to recognise which usage any particular writer has adopted. 

N, near the north pole of the pseudorotation cycle roughly C3 -endo S, near the south pole of the... 

For a nucleoside in solution, despite the fact that the entire pseudorotation cycle would appear to be accessible, experimental evidence seems to indicate that both preferred regions identified in the solid structures are accessible in solution and that both coexist in a dynamic N / S equilibrium. This equilibrium is defined by the relative amounts of these two populated domains in which each N and S conformation is, respectively, a blend of near neighbors of a P = 0° conformer and a P = 180° conformer. In general terms, the N and S conformations are described as C-Y-endo and C-2 -endo, respectively. Endo (up) and exo (down) indicate the direction of displacement (puckering) of a specific atom in relation to the plane of the other atoms in the ribose ring. For the various twist (T) and envelope (E) forms this is described with numbers in the form of superscripts endo) and subscripts (exo) that indicate the atom being displaced above or below the plane (Figure 2). Finally, for the C-4 —C-5 torsion... 

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