Chain structure conformation

Side chain generation is often a source of error. It will be most reliable if certain rules of thumb are obeyed. Start with structurally conserved side chains and hold them fixed. Then look at the energy and entropy of rotamers for the remaining side chains. Conventional conformation search techniques are often used to place each side chain. 

Bovcy, F.A. Chain Structure ami Conformation of Macromolecules, Wiley New York, 1982. 

While conformation II (Fig. 2.34) of Uke-y -amino acids is found in the 2.614-helical structure, conformation I, which similarly does not suffer from sy -pen-tane interaction, should be an appropriate alternative for the construction of sheet-like structures. However, sheet-like arrangement have not been reported so far for y-peptides composed of acyclic y " -amino acid residues. Nevertheless, other conformational biases (such as a,/9-unsaturation, cyclization between C(a) and C(y)) have been introduced into the y-amino acid backbone to restrict rotation around ethylene bonds and to promote extended conformation with formation of sheets in model peptides. Examples of such short chain y-peptides forming antiparallel (e.g. 152 [208]) and parallel (e.g. 153-155 [205, 208]) sheet-hke structures are shown in Fig. 2.38. 

The most likely way for pardaxin molecules to insert across the membrane in an antiparallel manner is for them to form antiparallel aggregates on the membrane surface that then insert across the membrane. We developed a "raft"model (data not shown) that is similar to the channel model except that adjacent dimers are related to each other by a linear translation instead of a 60 rotation about a channel axis. All of the large hydrophobic side chains of the C-helices are on one side of the "raft" and all hydrophilic side chains are on the other side. We postulate that these "rafts" displace the lipid molecules on one side of the bilayer. When two or more "rafts" meet they can insert across the membrane to form a channel in a way that never exposes the hydrophilic side chains to the lipid alkyl chains. The conformational change from the "raft" to the channel structure primarily involves a pivoting motion about the "ridge" of side chains formed by Thr-17, Ala-21, Ala-25, and Ser-29. These small side chains present few steric barriers for the postulated conformational change. 

In principle, polymers equivalent to those obtained from vinyl and divinyl monomers may be synthesized by this method. The product in the above example possesses the same chain structure as polyethylene. The polymerization process, notwithstanding the likelihood of a metal alkyl intermediate, should conform satisfactorily to stepwise condensation. However, the product, and those obtained by Friedel-Crafts condensation as well, lack the recurrent functional groups which generally characterize condensation polymers. 

Macromolecules differ from small molecules in a number of critical properties. First, the linear chain structure confers elasticity, toughness, and strength on the solid state system. This is a consequence of the reorientational freedom of the skeletal bonds and of their ability to absorb impact or undergo elastic deformation by means of conformational changes rather than bond cleavage. 

In order to study this question in a more systematic way, we have recently optimized 144 different structures of ALA at the HF/4-21G level, covering the entire 4>/v )-space by a 30° grid (Schafer et al. 1995aG, 1995bG). From the resulting coordinates of ALA analytical functions were derived for the most important main chain structural parameters, such as N-C(a), C(a)-C, and N-C(a)-C, expanding them in terms of natural cubic spline parameters. In fact, Fig. 7.18 is an example of the type of conformational geometry map that can be derived from this procedure. 

The case of isotactic polypropylene (iPP) presents some differences with respect to those just discussed. While both sPP and PET adopt in their mesophases disordered, extended, essentially non-helical conformations, iPP is characterized by a unique, relatively well ordered, stable chain structure with three-fold helical symmetry [18,19,36]. More accurately we can state that an iPP chain segment can exist in the mesophase either as a left handed or as the enantiomeric right-handed three-fold helix. The two are isoener-getic and will be able to interconvert only through a rather complex, cooperative process. From a morphological point of view Geil has reported that thin films of mesomorphic iPP quenched from the melt to 0 °C consist of... 

The shift of the amide I mode (FTIR spectra) from 1657 to 1646 cm-1 was attributed to a change in the a-helix native structure to fl-sheets, secondary structure conformations. Atomic Force Microscopy (AFM) images display the coating of the manganese oxide surface as well as the unfolding in a ellipsoidal chain of the protein molecules after adsorption and immobilization on the surface. 

The transition state was shown to have a four-centered nonplanar structure and the product showed a strong jS-agostic interaction.59 Molecular-mechanics (MM) calculations based on the structure of the transition state indicated that the regioselectivity is in good agreement with the steric energy of the transition state rather than the stability of the 7r-complex. The MM study also indicated that the substituents on the Cp rings determine the conformation of the polymer chain end, and the fixed polymer chain end conformation in turn determines the stereochemistry of olefin insertion at the transition state.59... 

A particular kind of disorder, characterized by maintaining three-dimensional long-range periodicity only for some points of the structure, has been found in samples of syndiotactic polypropylene having a relatively low degree of stereoregularity.189 190 In these samples the chains present conformational disorder, which produces defects frozen in the crystals. 

The substituents on the phenyl group can also sterically influence the chiral recognition ability. The main-chain structures of 23a and 23x look similar, but the conformations of side groups are not the same. Three aromatic groups of... 

Although the main-chain conformations of polysilanes have been described as random coil, 73- (deviant helical), 157 (transoid helical), and 2i (all anti, planar) structures, it is now generally accepted that most polysilanes tend to adopt helical main-chain structures, regardless of side groups and temperature.39 It... 

In this part, two series of 44 copolymers with coiled main-chain structures and 45 copolymers with stiff main-chain conformations were described. It was concluded that both optically inactive 42 and 43 adopt helical conformations with an equal proportion of P and M screw senses by means of UV and CD spectra as well as molecular mechanics calculations. A marked positive cooperative induction effect of the preferential screw sense in 44 and 45 copolymers was found. However, there is a marked difference in the helical cooperativity between 44 and 45, probably because of the differences in their global and local conformations. This difference can be related to the persistence of the helical conformation against defects allowing change of... 

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