Determination of the Handedness of Urea Inclusion Compounds.

Since the discovery of urea inclusion compounds (UICs) in 1940, the handedness of this chiral helical system has not been established experimentally. Here three UIC systems containing only light atoms were studied. The optical rotations were first measured, and the absolute structures of the enantiomorphic domains of three UICs were determined by single crystal X-ray diffraction (SCXRD). The correlation between the optical rotation and the absolute configuration of the UICs was finally established, showcasing the power of absolute structure determination by SCXRD, which is essential in structural chemistry and pharmaceutical research.

Reply to comment on Couzi et al. (2018): a phenomenological model for structural phase transitions in incommensurate alkane/urea inclusion compounds.

In a recent paper (Couzi et al. 2018 R. Soc. open sci. 5, 180058. (doi:10.1098/rsos.180058)), we proposed a new phenomenological model to account for the I↔II↔"III" phase sequence in incommensurate n-alkane/urea inclusion compounds, which represents an alternative interpretation to that proposed in work of Toudic et al. In a Comment (Toudic et al. 2019 R. Soc. open sci. 6, 182073. (doi:10.1098/rsos.182073)), Toudic et al. have questioned our assignment of the superspace group of phase II of n-nonadecane/urea, which they have previously assigned, based on a (3 + 2)-dimensional superspace, as C2221(00γ)(10δ). In this Reply, we present new results from a comprehensive synchrotron single-crystal X-ray diffraction study of n-nonadecane/urea, involving measurements as a detailed function of temperature across the I↔II↔"III" phase transition sequence. Our results demonstrate conclusively that "main reflections" (h, k, l, 0) with h+k odd are observed in phase II of n-nonadecane/urea (including temperatures in phase II that are just below the transition from phase I to phase II), in full support of our assignment of the (3+1)-dimensional superspace group P212121(00γ) to phase II. As our phenomenological model is based on phase II and phase "III" of this incommensurate material having the same (3+1)-dimensional superspace group P212121(00γ), it follows that the new X-ray diffraction results are in full support of our phenomenological model.

A phenomenological model for structural phase transitions in incommensurate alkane/urea inclusion compounds.

n-Alkane/urea inclusion compounds are crystalline materials in which n-alkane 'guest' molecules are located within parallel one-dimensional 'host' tunnels formed by a helical hydrogen-bonded arrangement of urea molecules. The periodic repeat distance of the guest molecules along the host tunnels is incommensurate with the periodic repeat distance of the host substructure. The structural properties of the high-temperature phase of these materials (phase I), which exist at ambient temperature, are described by a (3 + 1)-dimensional superspace. Recent publications have suggested that, in the prototypical incommensurate composite systems, n-nonadecane/urea and n-hexadecane/urea, two low-temperature phases II and 'III' exist and that one or both of these phases are described by a (3 + 2)-dimensional superspace. We present a phenomenological model based on symmetry considerations and developed in the frame of a pseudo-spin-phonon coupling mechanism, which accounts for the mechanisms responsible for the I ↔ II ↔ 'III' phase sequence. With reference to published experimental data, we demonstrate that, in all phases of these incommensurate materials, the structural properties are described by (3 + 1)-dimensional superspace groups. Around the temperature of the II ↔ 'III' transition, the macroscopic properties of the material are not actually associated with a phase transition, but instead represent a 'crossover' between two regimes involving different couplings between relevant order parameters.

The structural and dynamic properties of 1-bromodecane in urea inclusion compounds investigated by solid-state (1)H, (13)C and (2)H NMR spectroscopy.

For asymmetric guest molecules in urea, the end-groups of two adjacent guest molecules may arrange in three different ways: head-head, head-tail and tail-tail. Solid-state (1)H and (13)C NMR spectroscopy is used to study the structural properties of 1-bromodecane in urea. It is found that the end groups of the guest molecules are randomly arranged. The dynamic characteristics of 1-bromodecane in urea inclusion compounds are probed by variable-temperature solid-state (2)H NMR spectroscopy (line shapes, spin-spin relaxation: T2 , spin-lattice relaxation: T1Z and T1Q) between 120 K and room temperature. The comparison between the simulation and experimental data shows that the dynamic properties of the guest molecules can be described in a quantitative way using a non-degenerate three-site jump process in the low-temperature phase and a degenerate three-site jump in the high-temperature phase, in combination with the small-angle wobbling motion. The kinetic parameters can be derived from the simulation.