Ligand conformational energy

Bostrom J, P-O Norrby and T Liljefors 1998, Conformational Energy Penalties of Protein-boun Ligands. Journal of Computer-A ided Molecular Design 12 383-396. 

Fig. 8.3 Calculated conformational energy display values less than 2kcalmol ligands penalties of the protein-bound ligands 1-36. with five to eight rotors display values less The energy penalty increases with the number than 4kcalmol and ligands with eight to 11 of rotors. Ligands with one to four rotors rotors display values less than 6kcal mol. ...

Bostrom, J., Norrby, P.-O., Liljefors, T. Conformational energy penalties of protein-bound ligands. /. Comput.-Aided. Mol. Des. 1998, 12, 383-396. 

Details of the conformational energies of the ConA-ligand complexes are given in Table II. The difference in energy between the two binding modes for aMeMan in the binding site of ConA is due mainly to the difference in the interaction energy component. 

Table II. Conformational energies of ConA-ligand complexes...

Conformational energy of the ligand in the end bound form. Conformational energy of the binding site residues of the protein. Interaction energy between the protein and the ligand. 

Use of Rh2(OAc)4 suggested that there was no inherent selectivity attributable to the coordinated carbene or to rhodium(ll). However, modification of dirhodium(ll) ligands to imidazolidinones provided exceptional diastereocontrol, obtained by influencing the conformational energies of the intermediate metal carbene [19, 23], as well as high enantiocontrol. Representative examples of products from these highly selective intramolecular C-H insertion reactions with cyclic systems is given in Scheme 15.6. Additional examples of effective insertions in systems from which diastereomeric products can result are illustrated in processes of the synthesis of 2-deoxyxylolactone (Scheme 15.7) [64, 65]. Here the conformation of the reactant metal carbene that is responsible for product formation is 32 rather than 33. Other examples in non-heteroatom-bound systems (for example, as in Eq. 15) confirm this preference. 

Conformations conformational energies and changes The ligand may be able to exist in several conformations, one of which may have more suitable features this is true for G for instance, whose endo-endo form (see figure 8 below) contains a cavity that is nearer to a sphere than the cavities of the two other forms. Monocyclic ligands of type D may exist in folded conformations or may acquire such a conformation in the complexes (see below). The equilibrium conformation of a ligand depends... 

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