N-representable one-electron reduced density matrix reconstruction with frozen core electrons
Recent advances in quantum crystallography have shown that, beyond conventional charge density refinement, a one-electron reduced density matrix (1-RDM) satisfying N-representability conditions can be reconstructed using jointly experimental X-ray structure factors and directional Compton profiles (DCP) through semidefinite programming. So far, such reconstruction methods for 1-RDM, not constrained to idempotency, have been tested only on a toy model system (CO2). In this work, a new method is assessed on crystalline urea [CO(NH2)2] using static (0 K) and dynamic (50 K) artificial experimental data. An improved mod...
Source: Acta Crystallographica Section A - March 21, 2024 Category: Chemistry Authors: Yu, S. Gillet, J.-M. Tags: quantum crystallography reduced density matrix Compton scattering X-ray diffraction research papers Source Type: research
The single-atom R1: a new optimization method to solve crystal structures
A crystal structure with N atoms in its unit cell can be solved starting from a model with atoms 1 to j − 1 being located. To locate the next atom j, the method uses a modified definition of the traditional R1 factor where its dependencies on the locations of atoms j + 1 to N are removed. This modified R1 is called the single-atom R1 (sR1), because the locations of atoms 1 to j − 1 in sR1 are the known parameters, and only the location of atom j is unknown. Finding the correct position of atom j translates thus into the optimization of the sR1 function, with respect to its fractional coordinates, xj, yj, zj. Using expe...
Source: Acta Crystallographica Section A - March 18, 2024 Category: Chemistry Authors: Zhang, X. Donahue, J.P. Tags: structure solution global minimization single-atom R1 molecular replacement research papers Source Type: research
A digital distance on the kisrhombille tiling
The kisrhombille tiling is the dual tessellation of one of the semi-regular tessellations. It consists of right-angled triangle tiles with 12 different orientations. An adequate coordinate system for the tiles of the grid has been defined that allows a formal description of the grid. In this paper, two tiles are considered to be neighbors if they share at least one point in their boundary. Paths are sequences of tiles such that any two consecutive tiles are neighbors. The digital distance is defined as the minimum number of steps in a path between the tiles, and the distance formula is proven through constructing minimum p...
Source: Acta Crystallographica Section A - March 18, 2024 Category: Chemistry Authors: Kablan, F. Vizv á ri, B. Nagy, B. Tags: hexagonal grid digital geometry digital distance research papers Source Type: research
ClusterFinder: a fast tool to find cluster structures from pair distribution function data
A novel automated high-throughput screening approach, ClusterFinder, is reported for finding candidate structures for atomic pair distribution function (PDF) structural refinements. Finding starting models for PDF refinements is notoriously difficult when the PDF originates from nanoclusters or small nanoparticles. The reported ClusterFinder algorithm can screen 104 to 105 candidate structures from structural databases such as the Inorganic Crystal Structure Database (ICSD) in minutes, using the crystal structures as templates in which it looks for atomic clusters that result in a PDF similar to the target measured PDF. Th...
Source: Acta Crystallographica Section A - February 29, 2024 Category: Chemistry Authors: Anker, A.S. Friis-Jensen, U. Johansen, F.L. Billinge, S.J.L. Jensen, K.M. Ø . Tags: pair distribution function analysis nanoclusters nanomaterials screening research papers Source Type: research
Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning
Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data....
Source: Acta Crystallographica Section A - February 29, 2024 Category: Chemistry Authors: Monge, N. Deschamps, A. Amini, M.-R. Tags: machine learning nanoparticles SAXS small-angle X-ray scattering data analysis model selection research papers Source Type: research
Symmetry, Broken Symmetry, and Topology in Modern Physics: A First Course. By Mike Guidry and Yang Sun. Cambridge University Press, 2022. Hardback, pp. xv + 810. ISBN 9781316518618. Price USD 79.99.
(Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - February 22, 2024 Category: Chemistry Authors: Mala, F.A. Tags: book review symmetry topology book reviews Source Type: research
Report of the Executive Committee for 2022
(Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - February 22, 2024 Category: Chemistry Authors: International Union of Crystallography Tags: International Union of Crystallography IUCr Executive Committee Source Type: research
Universal parameters of bulk-solvent masks
The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemi...
Source: Acta Crystallographica Section A - February 9, 2024 Category: Chemistry Authors: Urzhumtsev, A. Adams, P. Afonine, P. Tags: bulk-solvent modelling flat models solvent masks grid steps mask parameters research papers Source Type: research
Advanced implication theory. Symmetry tables
The MIF (multiple implication function) group symmetry was assigned to all 230 space groups. Knowledge of MIF symmetry allows the calculation of an asymmetric unit. A more accurate procedure for calculating MIFs has been developed. Extensive tables of MIF symmetry and asymmetric units were computer generated. The development of implication theory for crystal structure determination seems to have reached completion. (Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - February 8, 2024 Category: Chemistry Authors: Pavelcik, F. Tags: MIF symmetry tables multiple implication function symmetry minimum function MIF asymmetric unit implication theory research papers Source Type: research
Understanding extended homometry based on complementary crystallographic orbit sets
Extended homometry is a phenomenon in which distinct structures have the same X-ray diffraction (XRD) intensities, which may lead to incorrect results of structural analysis based on XRD methods. It is proposed and proved herein that half of a crystallographic orbit has the same powder X-ray diffraction intensity as its complementary set; three more theorems are deduced. These results are conducive to understanding the formation of extended homometric structures. Also analyzed are some reported or potential homometric or weakly homometric structures in the Inorganic Crystal Structure Database to confirm the theorems. This ...
Source: Acta Crystallographica Section A - February 8, 2024 Category: Chemistry Authors: Zhang, Z. Shen, Y. Sun, J. Tags: homometry crystallographic orbits tautoeikonic structures research papers Source Type: research
Machine learning in crystallography and structural science
(Source: Acta Crystallographica Section A)
Source: Acta Crystallographica Section A - January 26, 2024 Category: Chemistry Authors: Billinge, S.J.L. Proffen, Th. Tags: machine learning artificial intelligence deep learning neural networks IUCr Journals editorial Source Type: research
Modelling dynamical 3D electron diffraction intensities. II. The role of inelastic scattering
The strong interaction of high-energy electrons with a crystal results in both dynamical elastic scattering and inelastic events, particularly phonon and plasmon excitation, which have relatively large cross sections. For accurate crystal structure refinement it is therefore important to uncover the impact of inelastic scattering on the Bragg beam intensities. Here a combined Bloch wave – Monte Carlo method is used to simulate phonon and plasmon scattering in crystals. The simulated thermal and plasmon diffuse scattering are consistent with experimental results. The simulations also confirm the empirical observation of a...
Source: Acta Crystallographica Section A - January 25, 2024 Category: Chemistry Authors: Mendis, B. Tags: inelastic diffuse scattering phonons plasmons Bloch waves research papers Source Type: research
Modelling dynamical 3D electron diffraction intensities. I. A scattering cluster algorithm
Three-dimensional electron diffraction (3D-ED) is a powerful technique for crystallographic characterization of nanometre-sized crystals that are too small for X-ray diffraction. For accurate crystal structure refinement, however, it is important that the Bragg diffracted intensities are treated dynamically. Bloch wave simulations are often used in 3D-ED, but can be computationally expensive for large unit cell crystals due to the large number of diffracted beams. Proposed here is an alternative method, the `scattering cluster algorithm' (SCA), that replaces the eigen-decomposition operation in Bloch waves with a simpler m...
Source: Acta Crystallographica Section A - January 25, 2024 Category: Chemistry Authors: Mendis, B. Tags: dynamical electron diffraction Bloch waves structure matrix multislice research papers Source Type: research
Parameterized absorptive electron scattering factors
In electron diffraction, thermal atomic motion produces incoherent scattering over a relatively wide angular range, which appears as a diffuse background that is usually subtracted from measurements of Bragg spot intensities in structure solution methods. The transfer of electron flux from Bragg spots to diffuse scatter is modelled using complex scattering factors f + if ′ in the Bloch wave methodology. In a two-beam Einstein model the imaginary `absorptive' scattering factor f ′ can be obtained by the evaluation of an integral containing f over all possible scattering angles. While more sophisticated models of diffuse...
Source: Acta Crystallographica Section A - January 25, 2024 Category: Chemistry Authors: Thomas, M. Cleverley, A. Beanland, R. Tags: electron diffraction absorption 3D-ED three-dimensional electron diffraction thermal diffuse scattering research papers Source Type: research
Double-slit asymmetrical dynamical diffraction of X-rays in ideal crystals
The theoretical investigation of double-slit asymmetrical dynamical diffraction of X-rays in perfect crystals establishes that Young's interference fringes on the exit surface are formed. The position of the fringes in the cross section of the beam depends on deviation from the Bragg exact orientation and asymmetry angle. An equation for the period of the fringes is presented, according to which the period is polarization sensitive. The period increases with increasing the absolute value of the asymmetry angle. In its turn, the size of the interference region also increases with increasing the absolute value of the asymmet...
Source: Acta Crystallographica Section A - January 23, 2024 Category: Chemistry Authors: Balyan, M. Tags: double-slit dynamical diffraction Young's fringes X-ray diffraction interferometer asymmetrical diffraction research papers Source Type: research
