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The seventh blind test of crystal structure prediction: structure generation methods
A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.
Crystal structure and orientation of organic semiconductor thin films by microcrystal electron diffraction and grazing-incidence wide-angle X-ray scattering
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Crystal structure and luminescence properties of lead-free metal halides (C 6 H 5 CH 2 NH 3 ) 3 MBr 6 (M = Bi and Sb)
Organic–inorganic hybrid metal halides have received extensive attention owing to their versatile structures and optoelectronic properties. Herein, we report two lead-free metal halides, (PMA) 3 BiBr 6 and (PMA) 3 SbBr 6 [PMA + : (C 6 H 5 CH 2 NH 3 ) + , as the abbreviation of phenylmethylammonium], which possess iso-structural zero-dimensional structures and crystallize in the monoclinic space group P2 1 /c. (PMA) 3 BiBr 6 and (PMA) 3 SbBr 6 exhibit optical band gaps of ~3.50 and 3.40 eV, respectively, and density functional theory calculations reveal their indirect bandgap behaviors. Upon 350 and 425 nm excitation, (PMA) 3 BiBr 6 and (PMA) 3 SbBr 6 exhibit broadband emission peaking at 510 nm and 625 nm with wide full-widths at half-maximum of ~153 and 175 nm, respectively. The emission mechanism of the metal halides is attributed to self-trapped exciton emission. The relationship between the crystal structure and luminescence intensity is also discussed. Lastly, both metal halides have high decomposition temperatures and are stable for long-term storage under ambient conditions, demonstrating their potential for optoelectronic applications.
Structural characteristics of lipocalin allergens: Crystal structure of the immunogenic dog allergen Can f 6
Lipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central β-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.
Comparing crystal structures with symmetry and geometry
Abstract Measuring the similarity between two arbitrary crystal structures is a common challenge in crystallography and materials science. Although there are an infinite number of ways to mathematically relate two crystal structures, only a few are physically meaningful. Here we introduce both a geometry-based and a symmetry-adapted similarity metric to compare crystal structures. Using crystal symmetry and combinatorial optimization we describe an algorithm to arrive at the structural relationship that minimizes these similarity metrics across all possible maps between any pair of crystal structures. The approach makes it possible to (i) identify pairs of crystal structures that are identical, (ii) quantitatively measure the similarity between crystal structures, and (iii) find and rank structural transformation pathways between any pair of crystal structures. We discuss the advantages of using the symmetry-adapted cost metric over the geometric cost. Finally, we show that all known structural transformation pathways between common crystal structures are recovered with the mapping algorithm. The methodology presented in this study will be of value to efforts that seek to catalogue crystal structures, identify structural transformation pathways or prune large first-principles datasets used to parameterize on-lattice Hamiltonians.
Crystal structure of aqua(citric acid)(hydrogen citrato)calcium monohydrate, [Ca(HC[subscript 6]H[subscript 5]O[subscript 7])(H[subscript 3]C[subscript 6]H[subscript 5]O[subscript 7])(H[subscript 2]O)]·H[subscript 2], from synchrotron X-ray powder data, and DFT-optimized crystal structure of existing calcium hydrogen citrate trihydrate, [Ca(HC[subscript 6]H[subscript 5]O[subscript 7])(H[subscript 2]O)[subscript 3]]
Abstract not provided
Crystal structure engineering in multimetallic high-index facet nanocatalysts
Significance Crystal structure engineering in nanoparticles represents an important strategy in catalyst design, as catalytic performance is highly dependent on atomic arrangement. However, realizing crystal structure engineering in high-index facet nanocatalysts has been a synthetic challenge for decades. Here, we first employed density functional theory calculations to determine whether surface modifications can stabilize high-index facets during crystal structure transformations and then synthesized a library of multimetallic high-index facet tetrahexahedral (THH) nanoparticles with controllable crystal structures. Importantly, the crystal structural transition between the intermetallic and chemically disordered states is reversable, and the THH morphology of nanocatalysts is maintained during this transformation. This approach broadens the synthetic scope of nanocatalysts available for use in diverse chemical processes.
CSD 2078665: Experimental Crystal Structure Determination
An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
CSD 2312746: Experimental Crystal Structure Determination
An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
CSD 2374310: Experimental Crystal Structure Determination
An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Assigning Optical Absorption Transitions with Light-Induced Crystal Structures: Case Study of a Single-Crystal Nanooptomechanical Transducer
UV/vis absorption spectroscopy affords indirect structural information about the photochemistry and photophysics of molecules by inferring types of electronic transitions from spectral features. Direct structural information would become available, though, if light-induced crystal structures could be mapped against changes in optical absorption spectra as a photochemical process evolves. We present a series of light-induced crystal structures that track real-time changes in solid-state optical absorption spectra of a crystalline nanooptomechanical transducer, while the transduction process unfolds within its crystal lattice at 100 K. Results afford a combined structural and spectral mapping of its solid-state optical absorption, from which the operational mechanism of nanooptomechanical transduction is revealed. Metal-to-ligand and metal-centered charge-transfer bands are assigned to optical absorption peaks directly from their 3-D light-induced crystal structures. This approach could be used to characterize many solid-state optoelectronic materials.
Ab Initio Crystal Structure Prediction of the Energetic Materials LLM-105, RDX, and HMX
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Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization
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Accurate Crystal Structure Prediction of New 2D Hybrid Organic–Inorganic Perovskites
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Synthesis and Crystal Structures of Alkali (Na, Rb, Cs) Iron Phosphate Crystals
Three alkali-containing diphosphate crystals of A FeP 2 O 7 (A = Na, Rb, Cs) were synthesized through melt-crystallization. The crystal structures were determined using single-crystal X-ray diffraction (XRD) data. The synthesized diphosphates crystallized within the P 2 1 /c space group, and the structural parameters were compared to literature data of other A FeP 2 O 7 crystals within the P 2 1 /c space group.
How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals?
Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used dispersion-corrected density functional theory (DFT-D) to assess the capabilities of an evolutionary algorithm (EA) for the crystal structure prediction (CSP) of well-known but challenging high-energy molecular crystals (HMX, RDX, CL-20, and FOX-7). While providing the EA with the experimental conformation of the molecule quickly re-discovers the experimental packing, it is more realistic to start instead from a naïve, flat, or neutral initial conformation, which reflects the limited experimental knowledge we generally have in the computational design of molecular crystals. By doing so, and using fully flexible molecules in fully variable unit cells, we show that the experimental structures can be predicted in fewer than 20 generations. Nonetheless, one must be aware that some molecular crystals have naturally hindered evolutions, requiring as many attempts as there are space groups of interest to predict their structures, and some may require the accuracy of all-electron calculations to discriminate between closely ranked structures. To save resources in this computationally demanding process, we showed that a hybrid xTB/DFT-D approach could be considered in a subsequent study to push the limits of CSP beyond 200+ atoms and for cocrystals.