### Journal: Acta crystallographica. Section A, Foundations and advances

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##### Quasicrystals: What do we know? What do we want to know? What can we know?

- OPEN
- Acta crystallographica. Section A, Foundations and advances
- Published almost 3 years ago
- Discuss

More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.

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##### Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. II. The Fourier transform method

- Acta crystallographica. Section A, Foundations and advances
- Published over 1 year ago
- Discuss

The Fourier transform method for analytical determination of the two-center Coulomb integrals needed for evaluation of the electrostatic interaction energies between pseudoatom-based charge distributions is presented, and its Fortran-based implementation using the 128-bit floating-point arithmetic in the XDPROP module of the XD software is described. In combination with mathematical libraries included in the Lahey/Fujitsu LF64 Linux compiler, the new implementation outperforms the previously reported Löwdin α-function technique [Nguyen et al. (2018). Acta Cryst. A74, 524-536] in terms of precision of the determined individual Coulomb integrals regardless of whether the latter uses the 64-, 80- or 128-bit precision floating-point format, all the while being only marginally slower. When the Löwdin α-function or Fourier transform method is combined with a multipole moment approximation for large interatomic separations (such a hybrid scheme is called the analytical exact potential and multipole moment method, aEP/MM) the resulting electrostatic interaction energies are evaluated with a precision of ≤5 × 10-5 kJ mol-1 for the current set of benchmark systems composed of H, C, N and O atoms and ranging in size from water-water to dodecapeptide-dodecapeptide dimers. Using a 2012 4.0 GHz AMD FX-8350 computer processor, the two recommended aEP/MM implementations, the 80-bit precision Löwdin α-function and 128-bit precision Fourier transform methods, evaluate the total electrostatic interaction energy between two 225-atom monomers of the benchmark dodecapeptide molecule in 6.0 and 7.9 s, respectively, versus 3.1 s for the previously reported 64-bit Löwdin α-function approach.

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##### Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

- OPEN
- Acta crystallographica. Section A, Foundations and advances
- Published over 4 years ago
- Discuss

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e(-) Å(-2) s(-1)) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).

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##### Viruses and fullerenes - symmetry as a common thread?

- Acta crystallographica. Section A, Foundations and advances
- Published over 6 years ago
- Discuss

The principle of affine symmetry is applied here to the nested fullerene cages (carbon onions) that arise in the context of carbon chemistry. Previous work on affine extensions of the icosahedral group has revealed a new organizational principle in virus structure and assembly. This group-theoretic framework is adapted here to the physical requirements dictated by carbon chemistry, and it is shown that mathematical models for carbon onions can be derived within this affine symmetry approach. This suggests the applicability of affine symmetry in a wider context in nature, as well as offering a novel perspective on the geometric principles underpinning carbon chemistry.

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##### Aspherical scattering factors for SHELXL - model, implementation and application

- OPEN
- Acta crystallographica. Section A, Foundations and advances
- Published almost 2 years ago
- Discuss

A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.

#### 2

##### Miniaturized beamsplitters realized by X-ray waveguides

- Acta crystallographica. Section A, Foundations and advances
- Published about 4 years ago
- Discuss

This paper reports on the fabrication and characterization of X-ray waveguide beamsplitters. The waveguide channels were manufactured by electron-beam lithography, reactive ion etching and wafer bonding techniques, with an empty (air) channel forming the guiding layer and silicon the cladding material. A focused synchrotron beam is efficiently coupled into the input channel. The beam is guided and split into two channels with a controlled (and tunable) distance at the exit of the waveguide chip. After free-space propagation and diffraction broadening, the two beams interfere and form a double-slit interference pattern in the far-field. From the recorded far-field, the near-field was reconstructed by a phase retrieval algorithm (error reduction), which was found to be extremely reliable for the two-channel setting. By numerical propagation methods, the reconstructed field was then propagated along the optical axis, to investigate the formation of the interference pattern from the two overlapping beams. Interestingly, phase vortices were observed and analysed.

#### 2

##### Bragg-von Laue diffraction generalized to twisted X-rays

- Acta crystallographica. Section A, Foundations and advances
- Published over 4 years ago
- Discuss

A pervasive limitation of nearly all practical X-ray methods for the determination of the atomic scale structure of matter is the need to crystallize the molecule, compound or alloy in a sufficiently large (∼10 × 10 × 10 µm) periodic array. In this paper an X-ray method applicable to structure determination of some important noncrystalline structures is proposed. It is designed according to a strict mathematical analog of von Laue’s method, but replacing the translation group by another symmetry group, and simultaneously replacing plane waves by different exact closed-form solutions of Maxwell’s equations. Details are presented for helical structures like carbon nanotubes or filamentous viruses. In computer simulations the accuracy of the determination of structure is shown to be comparable to the periodic case.

#### 2

##### Complex modeling: a strategy and software program for combining multiple information sources to solve ill posed structure and nanostructure inverse problems

- Acta crystallographica. Section A, Foundations and advances
- Published almost 5 years ago
- Discuss

A strategy is described for regularizing ill posed structure and nanostructure scattering inverse problems (i.e. structure solution) from complex material structures. This paper describes both the philosophy and strategy of the approach, and a software implementation, DiffPy Complex Modeling Infrastructure (DiffPy-CMI).

#### 2

##### SHELXT - Integrated space-group and crystal-structure determination

- Acta crystallographica. Section A, Foundations and advances
- Published almost 6 years ago
- Discuss

The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

#### 1

##### pinkIndexer - a universal indexer for pink-beam X-ray and electron diffraction snapshots

- OPEN
- Acta crystallographica. Section A, Foundations and advances
- Published 7 months ago
- Discuss

A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.