Conformation half-chain

Fig. 20. The variation in strain energy, V, for various conformations of [M(18-crown-6)]n+ complex, as a function of strain-free M-0 bond length. The M—O bond lengths of various metal ions are indicated on the M-0 bond length axis. The curves are for the planar D3d (+-+-+-), half-buckled (+-+--), and buckled (++-+ +-) conformers shown in Fig. 21, and for the complex of the open chain complex of pentaethylene glycol. The calculations were carried as described in the text, and in Refs. (4 and 60). Redrawn after Ref. (60). 

For a simulation of PP, the relationship between the 2nnd lattice and its underlying diamond lattice must be established at the beginning of the simulation, in order to preserve the stereochemical sequence and its influence on the conformations of the chains. The half of the equilateral triangles of area L2/2 that produce local collapsed beads is therefore known at the start, and the simulation can be performed in a manner which avoids the formation of these unphysical structures [158]. 

An important property of chain molecules is that a major contribution to the standard entropy is conformational in nature, i.e. is due to hindered internal rotations around single bonds. This property is most relevant to cyclisation phenomena, since a significant change of conformational entropy is expected to take place upon cyclisation. Pitzer (1940) has estimated that the entropy contribution on one C—C internal rotor amounts to 4.43 e.u, A slightly different estimate, namely, 4.52 e.u. has been reported by Person and Pimentel (1953). Thus, it appears that nearly one-half of the constant CH2 increment of 9.3 e.u. arises from the conformational contribution of the additional C—C internal rotor. 

A difference in conformation of molecules in the ervafolene and ervafolidine series emerged from X-ray analysis. In ervafolene (246), where C-3 is linked to N1, a cis relationship between N4 lone pair and the bond between C-14 and C-17 was observed. Also the lone pair of N4 was cis to the ethyl chain at C-20. In 3-epiervafolidine and (19 R)-19 -hydroxyervafolidine, the molecule adopted an identical conformation with the lone pair of N4 and N4, trans with respect to the C-14—C-17 bond and the ethyl chain, respectively. The absolute configurations depicted in formulas 242-249 were deduced from relative configurations and based on the assumption that the ibogan half of the molecule was derived from 20-epipandoline (165) whose absolute configuration is known. 

Many conformations were sampled by the usual MC procedure. The result is of course that there is no preferred orientation of the molecule. Each conformation can, however, be characterised by an instantaneous main axis this is the average direction of the chain. Then this axis is defined as a director . This director is used to subsequently determine the orientational order parameter along the chain. The order is obviously low at the chain ends, and relatively high in the middle of the chain. It was found that the order profile going from the centre of the molecules towards the tails fell off very similarly to corresponding chains (with half the chain length) in the bilayer membrane. As an example, we reproduce here the results for saturated acyl chains, in Figure 10. The conclusion is that the order of the chains found for acyl tails in the bilayer is dominated by intramolecular interactions. The intermolecular interactions due to the presence of other chains that are densely packed around such a chain,... 

Contrasting with these, the CH3-terminated 99 did show a Cotton effect. This is because the chiral side chain is / -branched, so that the chiral locking effect is sufficient to afford a stable PSS conformation. CF3-terminated 98 also showed a Cotton effect, though the CD and also UV intensity were about half those of 99, presumably due to some competition between the C-F- -Si interaction and chiral side-chain packing effects. 

There are two distinct stereochemical possibilities for the helix which are consistent with the intensity distribution. One of them is a 2-fold single-helix of pitch 19.6A and the other a 4-fold, half-staggered, parallel, double-helix of pitch 39.2A. The doublehelix could be right- or left-handed. In all cases, there is considerable conformational mobility about the (1- 6) linkage of the disaccharide side chain. Preliminary models have been built for each possibility and, due to insufficient diffraction data, detailed x-ray refinements have not been conducted for any of them. 

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