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

Circumventing a challenging aspect of crystal structure determination from powder diffraction data

Schmidt and co-workers [Acta Cryst. (2022), B78, 195–213], report a strategy for structure determination from powder XRD data in which unit-cell determination and structure solution are combined within a single process, rather than handling them as sequential stages on the structure determination pathway. This strategy offers the prospect to achieve successful structure determination in cases for which conventional approaches for indexing powder XRD data prove to be challenging

NMR crystallography as a vital tool in assisting crystal structure determination from powder XRD data

Powder X-ray diffraction (XRD) and solid-state NMR spectroscopy are complementary techniques for investigating the structural properties of solids, and there are considerable opportunities and advantages to applying these techniques synergistically together in determining the structural properties of crystalline solids. This article provides an overview of the potential to exploit structural information derived from solid-state NMR data to assist and enhance the process of crystal structure determination from powder XRD data, focusing in particular on the structure determination of organic molecular materials

Polymorphic phase transformations of 3-chloro-trans-cinnamic acid and its solid solution with 3-bromo-trans-cinnamic acid

We have investigated the polymorphic phase transformations above ambient temperature for 3-chloro-trans-cinnamic acid (3-ClCA, C9H7ClO2) and a solid solution of 3-ClCA and 3-bromo-trans-cinnamic acid (3-BrCA, C9H7BrO2). At 413 K, the γ polymorph of 3-ClCA transforms to the β polymorph. Inter­estingly, the structure of the β polymorph of 3-ClCA obtained in this transformation is different from the structure of the β polymorph of 3-BrCA obtained in the corresponding polymorphic transformation from the γ polymorph of 3-BrCA, even though the γ polymorphs of 3-ClCA and 3-BrCA are isostructural. We also report a high-temperature phase transformation from a γ-type structure to a β-type structure for a solid solution of 3-ClCA and 3-BrCA (with a molar ratio close to 1:1). The γ polymorph of the solid solution is isostructural with the γ polymorphs of pure 3-ClCA and pure 3-BrCA, while the β-type structure produced in the phase transformation is structurally similar to the β polymorph of pure 3-BrCA

Evolutionary aspects of urea utilization by fungi

The higher fungi exhibit a dichotomy with regard to urea utilization. The hemiascomycetes use urea amidolyase (DUR1,2), whereas all other higher fungi use the nickel-containing urease. Urea amidolyase is an energy-dependent biotincontaining enzyme. It likely arose before the Euascomycete/Hemiascomycete divergence c. 350 million years ago by insertion of an unknown gene into one copy of a duplicated methylcrotonyl CoA carboxylase (MccA). The dichotomy between urease and urea amidolyase coincides precisely with that for the Ni/Co transporter (Nic1p), which is present in the higher fungi that use urease and is absent in those that do not. We suggest that the selective advantage for urea amidolyase is that it allowed the hemiascomycetes to jettison all Ni2+- and Co2+- dependent metabolisms and thus to have two fewer transition metals whose concentrations need to be regulated. Also, the absence of MccA in the hemiascomycetes coincides with and may explain their production of fusel alcohols

Structural properties of methoxy derivatives of benzyl bromide, determined from powder X-ray diffraction data

Structure determination of 3,5-dimethoxybenzyl bromide and 3,4,5-trimethoxybenzyl bromide has been carried out from laboratory powder X-ray diffraction data using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. These two compounds are of interest for their potential use as building blocks for the synthesis of dendritic materials. Although the two molecules differ only in the presence/absence of the methoxy group at the 4-position of the aromatic ring, the structural properties of the two materials are significantly differen

High-dimensional cluster analysis with the masked EM algorithm

This is an Open Access article published under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license https://creativecommons.org/licenses/by/3.0/Cluster analysis faces two problems in high dimensions: the "curse of dimensionality" that can lead to overfitting and poor generalization performance and the sheer time taken for conventional algorithms to process large amounts of high-dimensional data. We describe a solution to these problems, designed for the application of spike sorting for nextgeneration, high-channel-count neural probes. In this problem, only a small subset of features provides information about the cluster membership of any one data vector, but this informative feature subset is not the same for all data points, rendering classical feature selection ineffective.We introduce a "masked EM" algorithm that allows accurate and time-efficient clustering of up to millions of points in thousands of dimensions. We demonstrate its applicability to synthetic data and to real-world high-channel-count spike sorting data.Peer reviewe

"Classic NMR": an in-situ NMR strategy for mapping the time-evolution of crystallization processes by combined liquid-state and solid-state measurements

A new in-situ NMR strategy (termed CLASSIC NMR) for mapping the evolution of crystallization processes is reported, involving simultaneous measurement of both liquid-state and solid-state NMR spectra as a function of time. This combined strategy allows complementary information to be obtained on the evolution of both the solid and liquid phases during the crystallization process. In particular, as crystallization proceeds (monitored by solid-state NMR), the solution state becomes more dilute, leading to changes in solution-state speciation and the modes of molecular aggregation in solution, which are monitored by liquid-state NMR. The CLASSIC NMR experiment is applied here to yield new insights into the crystallization of m-aminobenzoic acid

Conformational properties of monosubstituted cyclohexane guest molecules constrained within zeolitic host materials. A solid-state NMR investigation

The conformational properties of monosubstituted cyclohexane guest molecules (C6H11X with X = CH3, OH, Cl, Br and I) included within microporous solid host materials (silicalite-I, H-ZSM-5, NH4-mordenite and zeolite NH4-Y) have been elucidated via high-resolution solid-state 13C NMR spectroscopy. For all of the inclusion compounds investigated, the fraction of monosubstituted cyclohexane molecules in the equatorial conformation is similar to that in solution, suggesting that these host materials do not impose any significant constraints upon the conformational properties of the monosubstituted cyclohexane guest molecules. For the monohalogenocyclohexane guest molecules (C6H11X with X = Cl, Br and I), this result is in marked contrast to the situation for the same guest molecules in the thiourea host structure, for which the conformational properties of the guest molecules are substantially different from those of the same molecules in solution. For cyclohexanol (C6H11OH) in H-ZSM-5, some amount of dicyclohexyl ether (C6H11OC6H11) is observed, and is analogous to the proposed production of dimethyl ether in the first stage of methanol-to-gasoline conversion on this zeolite. The comparatively low temperature (ambient temperature) at which this conversion from cyclohexanol to dicyclohexyl ether occurs is noteworthy. In addition to our high-resolution solid-state 13C NMR studies of these materials, 1H MAS and 27AI MAS NMR spectra have also been recorded, and are discussed