Structure of the Stacked Cyclic Oligoamides: 1,6-Diaza-2,7-cyclodecadione and 1,5,9-Triaza-2,6,10-cyclododecatrione. A Ring Model of the α-Helix

Article abstract of DOI:10.1107/S0108768193008924

The structure of two cyclic amides, comprised of methylene and peptide groups, is described.The cyclic amides form parallel columns of stacked hydrogen-bonded rings.The cyclic dimer of butyramide (1,6-diaza-2,7-cyclodecadione) (I), C8H14N2O2, forms monoclinic crystals, space group P2₁/n, a = 4.874(2), b = 11.714(4), c = 8.088(2) Angstroem, β = 107.3(3) deg, R = 0.125 for 536 observed reflections, I > 3?(I), Z = 2, D_x = 1.28 g cm^-3, λ(Cu Kα) = 1.5418 Angstroem,μ = 7.26 cm^-1, T = 298 K.Extra peaks were found near the peptide groups, but the R factor could not be reduced by introducing additional parameters to account for disorder.The ten-membered ring skeleton adopts a centrosymmetric crown conformation which is rarely found in other ten-atom rings, but had been described for its isomer 1,5-diaza-6,10-cyclodecadione.A cyclic trimer of β-alanine (1,5,9-triaza-2,6,10-cyclododecatrione) (2), C9H15N3O3, is also studied.It forms trigonal crystals, a = b = 13.74(2), c = 4.82(1) Angstroem, space group R3m, R = 0.060 for 161 observed reflections, I > 2.5?(I), Z = 3, D_x = 1.35 g cm^-3, λ(Cu Kα) = 1.5418 Angstroem, μ = 8.16 cm^-1, T = 298 K.The 12-atom ring has two conformations which are mirror images and co-exist in the crystal.They appear superimposed in the solved structure.The peptide groups are planar and the organization of the stacked rings is very similar to that of an α-helix.