Computational and materials structural science

This Editorial discusses recent development in computational and materials structural science as exemplified by recent articles published in IUCrJ.

Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays

A practical approach for obtaining S-SAD data from native protein microcrystals with low-wavelength synchrotron radiation [Guo et al. (2019), IUCrJ, 6, 532–542] is presented in this issue of IUCrJ.

Plasticity enhancement in pharmaceutical drugs by water of crystallization: unusual slip planes

Khandavilli et al. [(2019), IUCrJ, 6, 630–634] show the superior plasticity in hydrates of the pharmaceutical drugs, pregabalin and gabapetin, compared with their anhydrous forms. The water in the structure is believed to act as a lubricating agent in the packing of hydrates, thus facilitating slippage of molecules in the plastic bending of the crystals under external mechanical stress.

X-ray magnetic diffraction under high pressure

Resonant and non-resonant X-ray magnetic diffraction under high pressure (above 40 GPa) is comprehensively discussed and reviewed.

Medical contrast media as possible tools for SAXS contrast variation

Medical contrast media are presented as possible tools to probe the internal structure of soft-matter and biological systems by small-angle X-ray scattering solvent contrast variation.

Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

A pipeline tool called Namdinator is presented that enables the user to run a molecular dynamics flexible fitting (MDFF) simulation in a fully automated manner, online or locally. This provides a fast and easy way to create suitable initial models for both cryo-EM and crystallography, and help fix errors in the final steps of model building.

Synchrotron microcrystal native-SAD phasing at a low energy

Low-energy native-SAD phasing from microcrystals of less than 10 micrometres in size is demonstrated at a synchrotron microdiffraction beamline.

Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins

A method is described that enables both time- and sample-efficient X-ray crystallographic data collection from radiation-sensitive protein microcrystals and direct comparison of the resulting dose-resolved serial synchrotron and damage-free X-ray free-electron laser structures. It is demonstrated that real-space extrapolation from a synchrotron dose series reproduces key features of the damage-free structure obtained using an X-ray free-electron laser.

Preparation and physical properties of a Cr₃Al film with a DO₃ structure

A Heusler Cr₃Al thin film with a perfect DO₃ structure is successfully prepared for the first time and its physical properties are investigated.

X-ray diffraction data as a source of the vibrational free-energy contribution in polymorphic systems

Combinations of ab initio calculations and modelling against X-ray diffraction data are used to derive the free energy of polymorphic crystals. The results are discussed in relation to the relative stability and phase transitions of the enantiotropically related polymorphs.

The structural characterization of a glu­cosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation

Glucosylglycerate accumulates to high levels in nitrogen-starved mycobacteria. Here, a thorough structural and biochemical characterization unveils the molecular determinants of the substrate specificity and catalytic mechanism of a mycobacterial glucosylglycerate hydrolase, a highly conserved enzyme involved in the fast recovery of rapidly growing mycobacteria from nitrogen starvation.

Solving self-absorption in fluorescence

Equations and methodology for correcting the dominant systematic in fluorescence measurements are provided. They are particularly appropriate for X-ray absorption spectroscopy in fluorescence and for multi-pixel detection.

Theoretical study of charge-transport and optical properties of organic crystals: 4,5,9,10-pyrenedi­imides

The shapes of the HOMOs/LUMOs and the relative positions of adjacent molecules decide the size of the intermolecular electronic couplings.

Prediction of fully compensated ferrimagnetic spin-gapless semiconducting FeMnGa/Al/In half Heusler alloys

First-principles calculations suggest that C1_b-ordered FeMnZ (Z = Al, Ga, In and Al_0.5Ga_0.5) alloys are half-metallic fully compensated ferrimagnets with a spin-gapless semiconducting nature. In such materials, full spin polarization, spin-gapless properties and absence of external stray fields, thus exhibiting minimal energy losses, are expected.

Room-temperature photo-induced martensitic transformation in a protein crystal

Martensitic transformation in crystals of reversibly switchable fluorescent protein Tetdron can be photo-induced by illumination with 400 nm light at room temperature. The phase transition results in tetramerization of the protein in crystallo coupled with chromophore deprotonation as demonstrated by X-ray photocrystallography and spectroscopic measurements.

Plasticity in zwitterionic drugs: the bending properties of Pregabalin and Gabapentin and their hydrates

The hydrate forms of the zwitterionic drugs Pregabalin and Gabapentin show plastic bending in a single crystal, whereas the anhydrous equivalents are brittle. A close structural analysis attempts to justify such behaviour.

Fluctuation X-ray scattering from nanorods in solution reveals weak temperature-dependent orientational ordering

Angular cross-correlation analysis of X-ray scattering from solutions of nanoparticles demonstrates high sensitivity to orientational particle inhomogeneities.

Conservation of the structure and function of bacterial tryptophan synthases

The tryptophan synthases from three human pathogens show remarkable structural conservation, but at the same time display local differences in both their catalytic and allosteric sites that may be responsible for the observed differences in catalysis and inhibitor binding. This functional dissimilarity may be exploited in the design of species-specific enzyme inhibitors.

Specific radiation damage is a lesser concern at room temperature

Both global and specific radiation damage have been investigated using three different proteins at cryogenic and room temperature. The large decoupling between global and specific radiation damage at cryogenic temperature appears to be practically abolished at room temperature, which has positive implications for time-resolved protein crystallography.

Competitive formation between 2D and 3D metal-organic frameworks: insights into the selective formation and lamination of a 2D MOF

A method for the selective synthesis of a 2D layered MOF in the presence of the competitive formation of a 3D cubic MOF was developed. In addition, the laminated 2D MOF layers are directly synthesized via a modified bottom-up lamination method involving both chemical (surfactants) and physical (ultrasonication) stimuli.

Screening topological materials with a CsCl-type structure in crystallographic databases

A large number of topological materials with a CsCl-type structure in crystallographic databases are explored and their crystal and electronic structures are studied.

Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging

Exploration of a `time on shelf' protein structure containing the radiopharmaceutical synthon fac-[Re(CO)₃(H₂O)₃]⁺ as an in vivo reaction vessel to form tetranuclear rhenium clusters appropriate for theranostic applications is reported.

Radiation damage in small-molecule crystallography: fact not fiction

Radiation damage to small-molecule compounds during synchrotron-diffraction data collection, under a range of conditions, is reported, characterized and analysed.

On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

Direct protein crystallization on fixed-target sample holders allows highly efficient serial crystallography experiments and ligand-binding studies.

Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder

Ependymin-related proteins fold into a dimer using a subunit formed by stacking antiparallel β-sheets and contain a hydrophobic pocket that is found in the similar folds of bacterial VioE and LolA/LolB. As in VioE and LolA/LolB, this hydrophobic pocket may be used to bind hydrophobic molecules.

Symmetry-mode analysis for intuitive observation of structure–property relationships in the lead-free antiferroelectric (1−x)AgNbO₃–xLiTaO₃

Symmetry-mode analysis has been used to construct the direct linkage between structure and properties for (anti)ferroelectric materials.

Supramolecular synthon hierarchy in sulfonamide cocrystals with syn-amides and N-oxides

Crystal engineering of the sulfonamide group with competing coformer molecules (lactam, syn-amide and N-oxide) using MEP calculations suggests that the SO₂NH₂ group will bond to the lactam and syn-amide preferentially compared with N-oxide and carb­oxy­lic acid, but complexation studies showed superior bonding with N-oxide. These results provide a ranking of hydrogen-bonding synthons for crystal engineering with the sulfonamide group.

Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography

Damage-free structures of the resting state of one of the most studied copper nitrite reductases were obtained independently by X-ray free-electron laser (XFEL) and neutron crystallography, representing the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography.

Cryo-EM structure of Neurospora crassa respiratory complex IV

The cryo-EM structure of Neurospora crassa respiratory complex IV was determined to 5.5 Å resolution and is compared with related structures from Saccharomyces cerevisiae and Bos taurus.

Room-temperature photo-induced martensitic transformation in a protein crystal. Corrigendum

Corrigendum to the article by Dajnowicz et al. [IUCrJ (2019). 6, 619–629].