Helical conformation conformational energy calculations

The helical parameters corresponding to the various skeletal conformations of the blsphenol A polycarbonate chain are calculated. Combining these results with the conformational energy calculations shows that flat-helical and extended conformations are of equal energy for this chain. In addition, cyclic structures are also found to be stereochemically possible. The small values of the characteristic ratio of the unperturbed end-to-end distance and its temperature coefficient are attributed to the equal energy of the flat-helical and extended-helical, as well as the nonhelical, conformers. 

Empirical conformational energy calculations are performed on helical poly(2,3-quinoxaline)s to predict stable conformations. Two energy minimum conformations are found by varying the dihedral angle, y, between two adjacent quinoxaline units from 5 to 180°. Circular dichroism spectra are calculated for the two stable conformations (v - 45 and 135°) on the basis of exciton theory. 

Besides this statistical mechanical approach to the question of helix stability, the problem has also been addressed by conformational energy calculations. First, the helix-breaking tendencies of such residues as serine and aspartic acid can be accounted for by the tendency toward formation of side chain-backbone hydrogen bonds in nonhelical conformations163 (Figures 20 and 21). Second, the free energies of the helical and statistical coil forms in water have... 

In addition to the order-disorder transition, observed for a helices, helical structures can also be induced to undergo transitions from one ordered form to another. For example, a crystalline form of poly[p-(p-chlorobenzyl)-L-aspartate] can be made to undergo a phase transition from an a-helical to an co-helical form by heating rotational entropy is computed to play a role in this process.68 Another order-order transition is the solvent-induced interconversion between polyproline 1 (with cis peptide bonds) and polyproline 11 (with trans peptide bonds), a process that has also been subjected to conformational energy calculations.85 The transition has been accounted for in terms of differences in the binding of solvent components to the peptide 0=0 groups. 

An empirical conformation energy calculation based on the ECEPP functions indicated two stable side-chain orientations (A and B) are possible for a-helical main chain. A theoretical CD computation, however, suggested that orientation B = 290°, X2 285°) is more populated than A. 

Geometrical and conformational energy calculations have shown that nearly extended conformations are energetically feasible both for diisotactic and disyndiotactic EN chains [121,207] they correspond to two-fold helical s(2/l)m and glide plane tern symmetries for the diisotactic and disyndiotactic configurations, respectively [67]. Moreover, both conformations account for the experimental chain axis period c = 8.9 A and present distances be-... 

The semi-empirical conformational energy calculations of poly-cis-5-ethylproline (PC5EP) predict that the helical structure may exist in two conformational forms such as I and II. Experimental results confirmed that in solution two major conformations may be assumed by the poly-cis-5-ethyl-D-proline. However, the calculations for poly-trans-5-ethyl-D-proline indicated that only one form may be allowed.Spectroscopic data (Circular Dichroism, NMR) showed the polypeptide exists in a poly-L-proline form-I-type helix and changes slowly to some intermediate conformation. The slow muta-rotation is partially due to the steric interactions of the ethyl group with the carbonyl group of the amide during the mutarotation. 

This pardaxin model is not unique. We have developed several similar models that are equally good energetically and equally consistent with present experimental results. It is difficult to select among these models because the helices can be packed a number of ways and the C-terminus appears very flexible. Our energy calculations are far from definitive because they do not include lipid, water, ions, membrane voltage, or entropy and because every conformational possibility has not been explored. The model presented here is intended to illustrate the general folding pattern of a family of pardaxin models in which the monomers are antiparallel and to demonstrate that these models are feasible. 

The idea that the most stable conformation of 42 and 43 may be helical is supported by a molecular mechanics calculation using Discover III with a PCFF force held (MSI, ver. 3.00). Figure 4.31a shows the total energy of a 42 oligomer with 21 Si repeat units as a function of the Si-Si-Si-Si dihedral angle. The respective P- and M-helical conformations of 42 near dihedral angles of 160° and 200° are more stable than a trans planar conformation of... 

Isotactic poly(methyl methacrylate), also, is an intricate case, resolved only after a 20-year debate. The repetition period along the chain axis is 10.40 A corresponding to S monomer units the entire cell contains 20 monomer units (four chains). At first, the stmcture was resolved as a 5/1 helix (183) with = 180° and 62 — 108° but no reasonable packing was found using this assumption. Further conformational calculations showed that helices like 10/1 or 12/1 should be more stable than the 5/1 helix. The structure was solved by Tadokoro and co-workers (153b) who proposed the presence of a double helix. Two chains, with the same helical sense and the same direction but displaced by 10.40 A one from the other are wound on each other, each chain having 10 monomer units per turn [i(10/l)] and a 20.80-A repeat period. As a result, the double helix has a 10.40-A translational identity period, identical to that found in the fiber spectmm. The conformational parameters are Of = 179° and 2 = -148°. Energy calculations indicate that the double helix is more stable by 4.4 kcal per-mole of monomer units than two isolated 10/1 helices, a result that is in line with the well-known capacity of this polymer to form complexes in solution (184). 

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