Reduced conformational space

Would it not be advantageous to have a bidentate dienophilic ligand on hand After complexation, a reduced conformational space for the transition structure of the Diels/Alder reaction would be available. In consequence, stereoselection might improve. 

Approaches to structure prediction using different flavors of secondary structure constraints have been recently reported. This renewed interest in the use of secondary structure information as a way of reducing conformational space when building molecular models is the result of the recent improvement in accuracy of secondary structure prediction methods due to the introduction of evolutionary information. 

Molecular dynamics simulations are el ficient for searching the conformational space of medium-sized molecules and peptides. Different protocols can increase the elTicieiicy of the search and reduce the computer time needed to sample adequately the available conformations. 

Aproblem in searching conformational space using molecular dynamics simulations is repeating a trajectory that generates the same structures. To reduce this possibility, you can randomize the velocities of the atoms. 

Although cyclization significantly reduces the accessible conformational space, cyclic peptides often maintain considerable flexibility. 36,37 The more the backbone prefers a single conformation, the more the side chains do the same, at least for the %rangle. The preferred backbone conformation is primarily determined by the tendency to minimize the allylic strain, 24,38 as shown in Scheme 2. If possible, the Ca-proton is syn to the carbonyl oxygen of... 

In the case of homoantiaromaticity, characterization is more difficult. Antiaromaticity describes a situation in which electron delocalization leads to destabilization. Clearly, if through-space interactions would close a cyclic system to form an antiaromatic electron ensemble, the molecule would adopt another conformation that would help to avoid antiaromatic electron delocalization. Of course, steric factors may enforce through-space interactions as in 40 (Figure 5). However, simple deformations of the molecule can reduce through-space interactions to an insignificant level. 

As a result of the branched chain architecture, TASP molecules exhibit some unique conformational properties)5 12-14 47 75 76 148 For example, the folding to a compact state proceeds via two distinct steps the onset of secondary structure in the attached peptide blocks followed by their template-directed self-assembly to a three-dimensional packing topology. Due to its characteristic branched chain connectivity, the conformational space accessible in the unfolded state is considerably reduced compared to a linear chain of similar size (excluded volume effect), resulting in a smaller chain entropy. Thus, folded TASP molecules are expected to show higher thermodynamic stability compared to unbranched polypeptides of comparable size. 

---