The crystal structure and the conformational analysis of carbobenzoxyl-L-leucyl-p-nitrophenyl ester

Bioorganic stereochemistry. A study of the peptide oxazolones from Z-(Aib)n-OH (n = 2-4) in the solid state

An investigation of the preferred conformations and modes of self-association of the peptide oxazolones from Z(-Aib-)n-OH (n = 2-4) in the solid state has been performed by infrared absorption. More detailed information on the peptide oxazolone from Z(-Aib-)3OH(2) has been obtained using X-ray diffraction. In this compound the conformations of the first two Aib residues differ substantially, only the N-terminal one being found in the usual 3(10)-(or alpha-) helical region of the Ramachandran map. The C = N-bond of the oxazolone group is not conjugated with the lactone moiety. A very weak intermolecular interaction occurs between the urethane N-H and the carbonyl group of the oxazolone ring.

Preferred conformation of the benzyloxycarbonyl-amino group in peptides

Structural parameters, derived from X-ray crystallographic data, have been compiled for 35 derivatives of amino acids, peptides, and related compounds, which contain the N-terminal benzyloxycarbonyl (Z) group. The geometry of the urethane moiety of this end group is closely similar to that of the tert-butoxycarbonyl (Boc) group, except for a relaxation of some bond angles because the Z group is sterically less crowded than the Boc group. For the same reason, the Z group has greater conformational flexibility. As a result, packing forces in the crystal may cause greater deformations of bond angles, resulting in larger variations of observed bond lengths and bond angles than in Boc-peptide crystals. The aromatic rings of the Z end groups tend to stack in crystals. Conformational energy calculations indicate that most conformations of Z-amino acid-N'-methylamides and of corresponding Boc derivatives have similar dihedral angles and relative energies, i.e. the nature of the N-terminal end group has little effect on the conformational preferences of the residue next to it. In particular, the computed fraction of molecules with a cis urethane (C-N) bond is similar for the two derivatives: 0.51 and 0.42 in Boc-Pro-NHCH3 and Z-Pro-NHCH3, respectively, and 0.02 in the two Ala derivatives. There exist several computed conformations of Z-Ala-NHCH3 and Z-Pro-NHCH3 in which the phenyl ring and the C-terminal methylamide group are close to each other. Because of favorable nonbonded interactions, such conformations are of low energy.