The crystal structure of dipotassium tetranitroethide.
Crystal structure of dipotassium tetranitroethide determined by single crystal X ray diffraction
Dyke, M.↗
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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.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The crystal structure of strontium bromide monohydrate.
Crystal structure of strontium bromide monohydrate by X-ray single crystal diffraction techniques
STRONTIUM BROMIDE↗
Ab Initio Crystal Structure Prediction of the Energetic Materials LLM-105, RDX, and HMX
Not Available
36 MATERIALS SCIENCE↗
Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Accurate Crystal Structure Prediction of New 2D Hybrid Organic–Inorganic Perovskites
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Theoretical studies on the relationship between the thermionic work functions of refractory-metal intermetallic compounds and their electronic and crystal structures Final summary report
The Group VIA-Re binary systems are characterized by the presence of several intermediate phases. The u phase is present in all of the systems, but the a-Mn phases occur in only the Mo-Re and W-Re systems. The occurrence of these intermediate phases appears to be governed largely by electronic factors and is predictable on the basis of electron/atom ratio. The thermionic work functions of the intermediate phase materials were experimentally determined. function and the screening of the outermost electrons in the Group VIA metals was found. A correlation between the work As might be expected for purely metallic substances, the work functions were relatively high, in the range 4. 5 to 5. 0 eV, and in each case were bracketed by the work functions of the pure constituents. A discontinuous change in the average work function with composition is proposed, based on a thermodynamical treatment of the electron vapor.
REFRACTORY METAL↗
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.
36 MATERIALS SCIENCE↗
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.
42 ENGINEERING↗
Data-centric framework for crystal structure identification in atomistic simulations using machine learning
Atomic-level modeling performed at large scales enables the investigation of mesoscale materials properties with atom-by-atom resolution. The spatial complexity of such cross-scale simulations renders them unsuitable for simple human visual inspection. Instead, specialized structure characterization techniques are required to aid interpretation. These have historically been challenging to construct, requiring significant intuition and effort. Here we propose an alternative framework for a fundamental structural characterization task: classifying atoms according to the crystal structure to which they belong. Our approach is data-centric and favors the employment of Machine Learning over heuristic rules of classification. A group of data-science tools and simple local descriptors of atomic structure are employed together with an efficient synthetic training set. We also introduce the first standard and publicly available benchmark data set for evaluation of algorithms for crystal-structure classification. Further, it is demonstrated that our data-centric framework outperforms all of the most popular heuristic methods—especially at high temperatures when lattices are the most distorted—while introducing a systematic route for generalization to new crystal structures. Moreover, through the use of outlier detection algorithms our approach is capable of discerning between amorphous atomic motifs (i.e., noncrystalline phases) and unknown crystal structures, making it uniquely suited for exploratory materials synthesis simulations.
36 MATERIALS SCIENCE↗
Crystal Structure Prediction of Binary Alloys via Deep Potential
Predicting crystal structure has been a challenging problem in physics and materials science for a long time. A reliable energy calculation engine combined with an efficient global search algorithm, such as particle swarm optimization algorithm or genetic algorithm, is needed to conduct crystal structure prediction. In recent years, machine learning-based interatomic potential energy surface models have been proposed, potentially allowing us to perform crystal structure prediction for systems with the accuracy of density functional theory (DFT) and the speed of empirical force fields. In this paper, we employ a previously developed Deep Potential model to predict the intermetallic compound of the aluminum–magnesium system, and find six meta-stable phases with negative or nearly zero formation energy. In particular, Mg 12 Al 8 shows excellent ductility and Mg 5 Al 27 has a high Young's modulus. Based on our benchmark results, we propose a relatively robust structure screening criterion that selects potentially stable structures from the Deep Potential-based convex hull and performs DFT refinement. By using this criterion, the computational cost needed to construct the convex hull with ab initio accuracy can be dramatically reduced.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The crystal structure of lead chloride
Single crystal and x-ray diffraction methods for studing crystal structure of lead chloride
LEAD CHLORIDE↗
Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies
We report the novel crystal structure and characterization of symmetrical, homodimeric humanized heavy-chain-only antibodies or dimers (HC2s). HC2s were found to be significantly coexpressed and secreted along with mAbs from transient CHO HC/LC cotransfection, resulting in an unacceptable mAb developability attribute. Expression of full-length HC2s in the absence of LC followed by purification resulted in HC2s with high purity and thermal stability similar to conventional mAbs. The V H and C H 1 portion of the heavy chain (or Fd) was also efficiently expressed and yielded a stable, covalent, and reducible dimer (Fd2). Mutagenesis of all heavy chain cysteines involved in disulfide bond formation revealed that Fd2 intermolecular disulfide formation was similar to Fabs and elucidated requirements for Fd2 folding and expression. For one HC2, we solved the crystal structure of the Fd2 domain to 2.9 Å, revealing a highly symmetrical homodimer that is structurally similar to Fabs and is mediated by conserved (C H 1) and variable (V H ) contacts with all CDRs positioned outward for target binding. Interfacial dimer contacts revealed by the crystal structure were mutated for two HC2s and were found to dramatically affect HC2 formation while maintaining mAb bioactivity, offering a potential means to modulate novel HC2 formation through engineering. These findings indicate that human heavy-chain dimers can be secreted efficiently in the absence of light chains, may show good physicochemical properties and stability, are structurally similar to Fabs, offer insights into their mechanism of formation, and may be amenable as a novel therapeutic modality.
60 APPLIED LIFE SCIENCES↗
The XtalOpt Evolutionary Algorithm for Crystal Structure Prediction
Significant progress has been made in the field of a priori crystal structure prediction, with a number of recent remarkable success stories. Herein, we briefly outline the methods that have been developed for finding the global minimum structure and interesting local minima without the need for experimental information. Focus is placed on describing the XTALOPT evolutionary algorithm (EA) developed in our group towards this end. XTALOPT is published under well-known open-source licenses, and the EA searches can be analyzed via the AVOGADRO chemical editor and visualizer. We describe new algorithmic developments that have made it possible to predict the structures of ever-more complex crystalline lattices. Benchmark tests, which clearly illustrate how the new developments improve the success rate and accelerate the discovery of the global minimum structure, are carried out. Lastly, we describe how XTALOPT has been employed to predict novel ternary hydrides that have the propensity for high-temperature superconductivity under pressure.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Applying Configurational Complexity to the 2D Ruddlesden–Popper Crystal Structure
The layered Ruddlesden–Popper crystal structure can host a broad range of functionally important behaviors. In this work, we establish extraordinary configurational disorder in a layered Ruddlesden–Popper (RP) structure using entropy stabilization assisted synthesis. A protype A 2 CuO 4 RP cuprate oxide with five cations on the A-site sublattice is designed and fabricated into epitaxial single crystal films using pulsed laser deposition. When grown on a near lattice matched substrate, the (La 0.2 Pr 0.2 Nd 0.2 Sm 0.2 Eu 0.2 ) 2 CuO 4 film features a T'-type RP structure with uniform A-site cation mixing and square-planar CuO4 units. These observations are made with a range of combined characterizations using X-ray diffraction, atomic-resolution scanning transmission electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray absorption spectroscopy measurements. It is further found that heteroepitaxial strain plays an important role in crystal phase formation during synthesis. Compressive strain over ~1.5% results in the formation of a non-RP cubic phase consistent with a Cu X 2O 4 spinel structure. The ability to manipulate configurational complexity and move between 2D layered RP and 3D cubic crystal structures in cuprate and related materials promises to enable flexible design strategies for a range of functionalities, such as magnetoresistance, unconventional superconductivity, ferroelectricity, catalysis, and ion transport.
36 MATERIALS SCIENCE↗
Crystal structure analysis of intermetallic compounds
Study concerns crystal structures and lattice parameters for a number of new intermetallic compounds. Crystal structure data have been collected on equiatomic compounds, formed between an element of the Sc, Ti, V, or Cr group and an element of the Co or Ni group. The data, obtained by conventional methods, are presented in an easily usable tabular form.
Conner, R. A., Jr.↗
Quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) of zwitterionic organic HCl salts
In this work, we benchmark quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) for determining the crystal structures of two zwitterionic organic HCl salts, L-ornithine HCl ( Orn ) and L-histidine HCl·H 2 O ( Hist ). These salts present an interesting challenge for QNMRX-CSP, as gas-phase geometry optimizations used to generate starting structures for the organic zwitterionic fragments fail to capture their correct solid-state geometries. To overcome this limitation, geometry optimizations using the COSMO water-solvation model are employed to generate initial structural models. Using this approach, QNMRX-CSP yields structural models of the two zwitterionic organic HCl salts that closely match experimentally determined crystal structures. In addition, the application of QNMRX-CSP to Hist represents a further step toward the de novo structural determination of solvated organic HCl salts, as Hist is the first benchmark system of this type to include a water molecule as a component of its crystal structure. This work is significant for its potential application to the structural determination of active pharmaceutical ingredients, which often feature complex organic components and solvated solid forms.
Fleischer, Carl H. [Florida State Univ., Tallahass↗
Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a distinctive mode of engaging poly(ADP-ribose)
PARP13/ZAP (zinc-finger antiviral protein) acts against multiple viruses by promoting degradation of viral mRNA. PARP13 has four N-terminal zinc (Zn) fingers that bind CG-rich nucleotide sequences, a C-terminal ADP ribosyltransferase fold, and a central region with a fifth Zn finger and tandem WWE domains. The central PARP13 region, ZnF5-WWE1-WWE2, is implicated in binding poly(ADP-ribose); however, there are limited insights into its structure and function. We present crystal structures of ZnF5-WWE1-WWE2 from mouse PARP13 in complex with ADP-ribose and in complex with ATP. The crystal structures and binding studies demonstrate that WWE2 interacts with ADP-ribose and ATP, whereas WWE1 does not have a functional binding site. Binding studies with poly(ADP-ribose) ligands indicate that WWE2 serves as an anchor for preferential binding to the terminal end of poly(ADP-ribose) chains. The composite ZnF5-WWE1-WWE2 structure forms an extended surface to engage ADP-ribose chains, representing a distinctive mode of recognition that provides a framework for investigating the impact of poly(ADP-ribose) on PARP13 function.
59 BASIC BIOLOGICAL SCIENCES↗