Journal of Applied Crystallography最新文献

Flow cells are ubiquitous in laboratories and automated instrumentation, and are crucial for ease of sample preparation, analyte addition and buffer exchange. The assumption that the fluids have exchanged completely in a flow cell is often critical to data interpretation. This article describes the buoyancy effects on the exchange of fluids with differing densities or viscosities in thin, circular flow cells. Depending on the flow direction, fluid exchange varies from highly efficient to drastically incomplete, even after a large excess of exchange volume. Numerical solutions to the Navier–Stokes and Cahn–Hilliard equations match well with experimental observations. This leads to quantitative predictions of the conditions where buoyancy forces in thin flow cells are significant. A novel method is introduced for exchanging fluid cells by accounting for and utilizing buoyancy effects that can be essential to obtain accurate results from measurements performed within closed-volume fluid environments.

The objective of crystal structure prediction (CSP) is to predict computationally the thermodynamically stable crystal structure of a compound from its stoichiometry or its molecular diagram. Crystal similarity indices measure the degree of similarity between two crystal structures and are essential in CSP because they are used to identify duplicates. Powder-based indices, which are based on comparing X-ray diffraction patterns, allow the use of experimental X-ray powder diffraction data to inform the CSP search. Powder-assisted CSP presents two unique difficulties: (i) the experimental and computational structures are not entirely comparable because the former is subject to thermal expansion from lattice vibrations, and (ii) experimental patterns present features (noise, background contribution, varying peak shapes etc.) that are not easily predictable computationally. This work presents a powder-based similarity index (GPWDF) based on a modification of the index introduced by de Gelder, Wehrens & Hageman [J. Comput. Chem. (2001), 22, 273–289] using cross-correlation functions that can be calculated analytically. Based on GPWDF, a variable-cell similarity index (VC-GPWDF) is also proposed that assigns a high similarity score to structures that differ only by a lattice deformation and which takes advantage of the analytical derivatives of GPWDF with respect to the lattice parameters. VC-GPWDF can be used to identify similarity between two computational structures generated using different methods, between a computational and an experimental structure, and between two experimental structures measured under different conditions (e.g. different temperature and pressure). VC-GPWDF can also be used to compare crystal structures with experimental patterns in combination with an automatic pre-processing step. The proposed similarity indices are simple, efficient and fully automatic. They do not require indexing of the experimental pattern or a guess of the space group, they account for deformations caused by varying experimental conditions, they give meaningful results even when the experimental pattern is of very poor quality, and their computational cost does not increase with the flexibility of the molecular motif.

A numerical framework based on the integral solution of the Takagi–Taupin equations has been developed for cylindrically bent Laue crystals. On the basis of this framework, diffraction geometries that satisfy the `magic condition' have been studied from the perspective of dynamical theory. The numerical findings indicate that, in certain diffraction geometries, the focusing behaviour of cylindrically bent Laue crystals will be notably influenced by dynamical effects and the foci of different energies will not converge as predicted by the `magic condition', which is derived from geometric optics theory. These dynamical effects are further explained through a direct numerical analysis of the influence function.

The effect of specimen displacement in X-ray powder diffraction experiments with laboratory diffractometers has been revisited and new expressions have been derived for several commonly used experimental configurations, including Bragg–Brentano parafocusing geometry and flat-plate transmission geometry. The results presented in this work allow the analysis of data from samples with relatively large displacements. This may open the possibility to study samples with dimensions that are difficult to accommodate with the sample-handling capabilities of standard laboratory diffractometers.