Back-folded conformation

Keywords silyl radicals, poly silanes, back-folded conformation, dissociation energy of Si-Si bonds... 

Bonzom et al., 1997 Corey et al., 1983 Corey et al., 1979 Leach and Front, 1990 Rabinovich and Ripatti, 1991 Rich, 1993 Wilson et al., 1988). These computational studies of AA have primarily found looped or back-folded conformations to be low-energy conformers of AA. Rich conducted a quenched MD smdy of AA in vacuo (Rich, 1993). The two lowest enthalpy conformers found for AA were J-shaped conformers in which the carboxylic acid group is in close proximity to the C14—C15 Jt bond. This same J-shape was reported by Corey and co-workers (1983) as one type of low-energy minimum identified in their conformational analysis of AA. Corey suggested that such a J-shaped conformation in solution would be energetically favorable and would be consistent with the chemistry of peroxyarachidoiuc acid for which an internal epoxidation leads to 14, 15-epoxyarachidonic acid (Corey et al., 1979). 

In the simple sampling procedure of generating chain conformations all successfully generated walks have equal probabihty. Walks are grown purely stochastically. Each time an attempted new bond hits a site which is already occupied, one has to start at the very beginning. Otherwise different conformations would have different probabihties and this would introduce an effective attraction among the monomers [54]. With this method, each conformation is taken randomly out of the q q — 1) possible random paths which do not include direct back-folding. However, the total number of SAW on a lattice is known [26] to be ... 

A very important question in the context of dendrimers and their utility as host molecules relates to the existence of cavities within these macromolecules. The presence of internal voids in dendrimers is closely related to their conformational behaviour and to the degree of back-folding of the terminal branches into the interior of the dendrimer. The issue of back folding was already briefly touched upon in section 16.2.1. Next to the purely theoretical calculations mentioned there, several calculations have been performed on specific dendrimer types. 

Figure 16.11 The pH-dependent conformational behaviour of polypropylene imine) dendrimers. At low pH (left) the occurrence of a soft-core, dense-shell dendrimer, whereas at high pH (right) severe back-folding occurs leading to a dense-core structure [57]...

Poly(benzyl ether) dendrimers synthesized by Frechet el al. have been studied with many techniques in order to reveal their conformational properties. Size exclusion measurements performed by Mourey et al. [154], rotational-echo double resonance (REDOR) NMR studies by Wooley et al. [155] and spin lattice relaxation measurements by Gorman et al. [156] reveal that back-folding takes place and the end-groups can be found throughout the molecule. The observed trends are in qualitative agreement with the model of Lescanec and Muthukumar [54],... 

Using conformational searching/quench dynamics and 7) relaxation measurements, each back-folded isomer was determined to be smaller than its extended counterpart. Thus, the effective distance of electron transfer was not reflected in the hydrodynamic radius of the molecule. Rather, the back-folded isomers were argued to be less mobile with the iron-sulfur core buried more deeply within them. The extended isomers were more mobile with the iron-sulfur core more able to come closer to the molecular surface. By this reasoning, the back-folded isomers had a larger effective electron transfer distance than the extended isomers. 

The biologiccJ function of a protein or peptide is often intimately dependent upon the conformation(s) that the molecule can adopt. In contrast to most synthetic polymers where the individual molecules can adopt very different conformations, a protein usually exists in a single native state. These native states are found rmder conditions typically found in Uving cells (aqueous solvents near neutred pH at 20-40°C). Proteins can be unfolded (or denatured) using high-temperature, acidic or basic pH or certain non-aqueous solvents. However, this unfolding is often reversible cind so proteins can be folded back to their native structure in the laboratory. 

---