Refined crystal structure and absolute configuration of the di-amino acid peptide cyclo(L-Aspartyl-L-Aspartyl): comparison with the DFT calculated structure

Rex A. Palmer, Brian S. Potter, Andrew P. Mendham, Trevor J. Dines, Babur Z. Chowdhry

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    The X-ray crystal structure of the di-amino acid peptide cyclo(L-Asp-L-Asp), C6H10N2O4, has been re-determined at 20 degrees C usingCuK alpha radiation, lambda = 1.54180 angstrom. The crystals are triclinic P1 with unit cell dimensions a = 5.0829(3), b = 5.0285(4), c = 18.8765(10) angstrom, alpha = 88.95(2)degrees, beta = 83.72(2)degrees, gamma = 74.79(2)degrees, unit cell volume 462.75(5) angstrom(3), and Z = 2 independent molecules A and B per asymmetric unit. Final R indices [I > 2sigma(I)] are R1 = 0.0492, wR2 = 0.1039 for 2,540 independent reflections; R1 = 0.0686 and wR2 = 0.1112 for all 3,193 data; Goodness of Fit, S = 0.979, and the Flack x parameter = 0.1(3). In both molecules the overall shape of the diketopiperazine (DKP) ring displays an almost identical slightly distorted boat conformation with pseudo symmetry C-2v (mm2). The two side chains of the cyclic peptide on opposite sides of both molecules differ in their conformations, one side being extended and the other coiled. The coiled chains are located away from the DKP ring plane while the extended chains lie approximately parallel to it. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. The geometry of cyclo(L-Asp-L-Asp) derived from Ab initio calculations is compared with those of molecules A and B derived from the X-ray structure reported here. In this calculated model the DKP ring is in a pseudo twist boat conformation; both side chains are extended and lie approximately parallel to the DKP ring face as opposed to molecules A and B in the X-ray structure in each of which one side chain is approximately parallel and the other is folded away from the DKP ring face.

    Original languageEnglish
    Pages (from-to)608-615
    Number of pages8
    JournalJournal of Chemical Crystallography
    Issue number7
    Publication statusPublished - Jul 2010


    • Cyclic dipeptide
    • Crystal structure
    • Absolute configuration
    • Ring geometry

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