Conformational exploration

Conformational Exploration of Peptides Using Molecular Dynamics... 

It is highly probable that most of the conformational exploration of the BR s occurs while they are triplets. Ultimately, the triplets will convert to singlets which probably react (by cyclization, fragmentation, or reverse hydrogen transfer to the parent molecule) before significant conformational change occurs. 

A study on the chiral complexation preferences of three series of cyclic a-hydroxy carbonyl compounds (Scheme 3.26) has been carried out using DFT and MP2 calculations. The dimer formation study has been preceded by a conformational exploration of the isolated monomers of the parent compounds. In addition, three possible dimers have been considered initially in the dimers of the parent compound, discarding those with the highest energies for the rest of the derivatives. 

Rigid 3D-fingerprints consider only a single conformation of the molecule, while flexible 3D-fingerprints account for all the geometric features that can be achieved, based on a conformational exploration of the considered molecule, usually based on the incremental rotation of all the rotatable bonds. 

However compelling, the scenario described above requires a rigorous justification that entails an understanding of the crossover behavior at a local level. This understanding prompts us to focus on the solvent environment of individual hydrogen bonds during the conformational exploration performed by the protein chain as the hydrophobic collapse takes place [12, 16, 17]. 

A final goal is to apply the same methods to generate alternative reasonable conformers of a compound in other words, to develop a symbolic conformational exploration capabiUty. 

---