The urea molecule is planar when in a solid crystal because of sp hybridization of the N orbitals. It is non-planar with C symmetry when in the gas phase or in aqueous solution, with C–N–H and H–N–H bond angles that are intermediate between the trigonal planar angle of 120° and the tetrahedral angle of 109.5°. In solid urea, the oxygen center is engaged in two N–H–O hydrogen bonds. The resulting dense and energetically favourable hydrogen-bond network is probably established at the cost of efficient molecular packing: The structure is quite open, the ribbons forming tunnels with square cross-section. The carbon in urea is described as sp hybridized, the C-N bonds have significant double bond character, and the carbonyl oxygen is relatively basic. Urea's high aqueous solubility reflects its ability to engage in extensive hydrogen bonding with water.
By virtue of its tendency to form porous frameworks, urea has the ability to trap many organic compounds. In these so-called clathrates, the organic "guest" molecules are held in channels formed by interpenetrating helices composed of hydrogen-bonded urea molecules.
As the helices are interconnected, all helices in a crystal must have the same molecular handedness. This is determined when the crystal is nucleated and can thus be forced by seeding. The resulting crystals have been used to separate racemic mixtures.