Ab Initio Structure Determination Research Articles

The crystal structure of olanzapine form III.

The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the ab initio structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.

3D atomic structure from a single X-ray free electron laser pulse

X-ray Free Electron Lasers (XFEL) are cutting-edge pulsed x-ray sources, whose extraordinary pulse parameters promise to unlock unique applications. Several new methods have been developed at XFELs; however, no methods are known, which allow ab initio atomic level structure determination using only a single XFEL pulse. Here, we present experimental results, demonstrating the determination of the 3D atomic structure from data obtained during a single 25 fs XFEL pulse. Parallel measurement of hundreds of Bragg reflections was done by collecting Kossel line patterns of GaAs and GaP. To the best of our knowledge with these measurements, we reached the ultimate temporal limit of the x-ray structure solution possible today. These measurements open the way for obtaining crystalline structures during non-repeatable fast processes, such as structural transformations. For example, the atomic structure of matter at extremely non-ambient conditions or transient structures formed in irreversible physical, chemical, or biological processes may be captured in a single shot measurement during the transformation. It would also facilitate time resolved pump-probe structural studies making them significantly shorter than traditional serial crystallography.

STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials.

Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.

Li2GeS3: New Structural Type of Lithium Solid Electrolyte for All-Solid-State Batteries

Sulfide inorganic materials exhibit favorable qualities such as high ionic conductivity and mechanical softness, making them promising candidates for solid electrolytes in Li-ion all-solid-state batteries. Sulfide solid electrolytes exist in various structural types, including β-Li3PS4, Li10GeP2S12, argyrodite, Li4PS4I, Li7P3S11, and Li1.82SiP0.036S3. While these materials exhibit high ionic conductivities of up to ~10− 2 S cm− 1 at room temperature and possess mechanical softness, they also have limitations, such as a narrow electrochemical stability window and air instability, which can hinder their scalability. The electrochemical and air stabilities of a solid electrolyte (Li–M–S, where M = non-Li metal ions) are largely governed by its stability of crystal structure consisting of MSn polyhedra and Li ions. A material with a different crystal structure would show its distinct properties. However, despite extensive research, no single structure known to date has proven superior in all aspects of performance. Given the importance of crystal structure in developing high-performance solid electrolytes, exploring and identifying novel ion-conducting materials with unique crystal structures is imperative. Additionally, once a new structural type of material is discovered, its performance can be adjusted, enhanced, or optimized through various techniques, such as chemical substitution, morphology and particle size control, and surface coating. In this work, we discovered a new crystal structural type of Li-ion conductor Li2GeS3. It was first known in 2000 by Kanno et al., with only orthorhombic unit cell dimension reported. However, our study using ab initio structure determination techniques from powder X-ray diffraction data, similar to our previous works, unveiled its structure possessing a hexagonal P61 symmetry with lattice parameters of a = 6.80098(4) Å and c = 17.92827(11) Å, revealing a new type of crystal structure. Its structure is comprised of a distorted hexagonal close-packed arrangement of sulfur anions with three asymmetric metal atoms: Ge and Li2 are in tetrahedral cavities surrounded by sulfur atoms; Li1 is in the trigonal bipyramidal cavity. The material displayed an ionic conductivity of 1.63 × 10− 8 S cm− 1 at 303 K and 2.45 × 10− 7 S cm− 1 at 383 K. Bond valence energy landscape calculations revealed three-dimensional lithium diffusion pathways within the structure. These results suggest that Li2GeS3 is expected to be a host structure from which improved ionic conductors can be derived through appropriate chemical substitution.

Li2GeS3: Lithium Ionic Conductor with an Unprecedented Structural Type.

Lithium-ion batteries (LIBs) are widely used in electric vehicles, mobile electronic devices, and large-scale stationary energy storage systems. However, their liquid electrolytes present significant safety concerns due to their inherent flammability. To address this, the focus has shifted toward all-solid-state batteries (ASSBs) utilizing inorganic solid electrolytes that promise enhanced safety. In this work, we report the discovery of a new crystal structural type of Li-ion conductor, Li2GeS3, with a unique structure, synthesized by a solid-state reaction from Li2S and GeS2. It was first reported in 2000 with an orthorhombic unit cell, but its detailed crystal structure remains veiled. We have unveiled its structure for the first time, employing an ab initio structure determination technique from powder X-ray and time-of-flight neutron diffraction data. The compound has an unprecedented crystal structural type with a hexagonal P61 symmetry and a unit cell of a = 6.79364(4) Å and c = 17.90724(14) Å. Its structure is comprised of a distorted hexagonal close-packed arrangement of sulfur anions with three asymmetric metal atoms: Li1, Li2, and Ge are in tetrahedral cavities surrounded by sulfur atoms. The ionic conductivity of Li2GeS3 was measured to be 1.63 × 10-8 S cm-1 at 303 K and 2.45 × 10-7 S cm-1 at 383 K. Bond valence energy landscape calculations revealed three-dimensional lithium diffusion pathways within the structure. This novel crystal structure in Li2GeS3 holds the potential for developing high-performance ionic conductors through suitable chemical substitution and offers valuable insights into designing new ionic conductors for ASSBs.

Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.

Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. However, the inherent dynamics and structural variability of biological complexes coupled with the large number of experimental images generated by a cryo-EM experiment make data processing nontrivial. In particular, ab initio reconstruction and atomic model building remain major bottlenecks that demand substantial computational resources and manual intervention. Approaches utilizing recent innovations in artificial intelligence (AI) technology, particularly deep learning, have the potential to overcome the limitations that cannot be adequately addressed by traditional image processing approaches. Here, we review newly proposed AI-based methods for ab initio volume generation, heterogeneous 3D reconstruction, and atomic model building. We highlight the advancements made by the implementation of AI methods, as well as discuss remaining limitations and areas for future development.

Atomic-level structural responsiveness to environmental conditions from 3D electron diffraction

Electron microscopy has been widely used in the structural analysis of proteins, pharmaceutical products, and various functional materials in the past decades. However, one fact is often overlooked that the crystal structure might be sensitive to external environments and response manners, which will bring uncertainty to the structure determination and structure-property correlation. Here, we report the atomic-level ab initio structure determinations of microcrystals by combining 3D electron diffraction (3D ED) and environmental transmission electron microscope (TEM). Environmental conditions, including cryo, heating, gas and liquid, have been successfully achieved using in situ holders to reveal the simuli-responsive structures of crystals. Remarkable structural changes have been directly resolved by 3D ED in one flexible metal-organic framework, MIL-53, owing to the response of framework to pressures, temperatures, guest molecules, etc.

Atomic-resolution structures from polycrystalline covalent organic frameworks with enhanced cryo-cRED

The pursuit of atomic precision structure of porous covalent organic frameworks (COFs) is the key to understanding the relationship between structures and properties, and further developing new materials with superior performance. Yet, a challenge of how to determine their atomic structures has always existed since the first COFs reported seventeen years ago. Here, we present a universal method for ab initio structure determination of polycrystalline three-dimensional (3D) COFs at atomic level using enhanced cryo-continuous rotation electron diffraction (cryo-cRED), which combines hierarchical cluster analysis with cryo-EM technique. The high-quality datasets possess not only up to 0.79-angstrom resolution but more than 90% completeness, leading to unambiguous solution and precise refinement with anisotropic temperature factors. With such a powerful method, the dynamic structures with flexible linkers, degree of interpenetration, position of functional groups, and arrangement of ordered guest molecules are successfully revealed with atomic precision in five 3D COFs, which are almost impossible to be obtained without atomic resolution structure solution. This study demonstrates a practicable strategy for determining the structures of polycrystalline COFs and other beam-sensitive materials and to help in the future discovery of novel materials on the other.

How to get maximum structure information from anisotropic displacement parameters obtained by three-dimensional electron diffraction: an experimental study on metal-organic frameworks.

Three-dimensional electron diffraction (3D ED) has been used for ab initio structure determination of various types of nanocrystals, such as metal-organic frameworks (MOFs), zeolites, metal oxides and organic crystals. These crystals are often obtained as polycrystalline powders, which are too small for single-crystal X-ray diffraction (SCXRD). While it is now possible to obtain accurate atomic positions of nanocrystals by adopting kinematical refinement against 3D ED data, most new structures are refined with isotropic displacement parameters (U eq), which limits the detection of possible structure disorders and atomic motions. Anisotropic displacement parameters (ADPs, Uij ) obtained by anisotropic structure refinement, on the other hand, provide information about the average displacements of atoms from their mean positions in a crystal, which can provide insights with respect to displacive disorder and flexibility. Although ADPs have been obtained from some 3D ED studies of MOFs, they are seldom mentioned or discussed in detail. We report here a detailed study and interpretation of structure models refined anisotropically against 3D ED data. Three MOF samples with different structural complexity and symmetry, namely ZIF-EC1, MIL-140C and Ga(OH)(1,4-ndc) (1,4-ndcH2 is naphthalene-1,4-dicarboxylic acid), were chosen for the studies. We compare the ADPs refined against individual data sets and how they are affected by different data-merging strategies. Based on our results and analysis, we propose strategies for obtaining accurate structure models with interpretable ADPs based on kinematical refinement against 3D ED data. The ADPs of the obtained structure models provide clear and unambiguous information about linker motions in the MOFs.

Polymorphism and sodium-ion conductivity of NaTa2PO8 synthesized via the Li+/Na+ ion-exchange reaction of LiTa2PO8

Ion exchange reaction is a promising method to explore metastable compounds that could not be synthesized by conventional high-temperature solid-phase reactions. Herein, a new sodium tantalum phosphate, NaTa2PO8 was synthesized via the Li+/Na+ ion-exchange reaction of the parent compound, LiTa2PO8 in molten NaNO3 medium. NaTa2PO8 underwent an irreversible phase transition from the low- (LT-NaTa2PO8) to the high-temperature polymorph (HT-NaTa2PO8) at approximately 1000 °C. The crystal structures were solved using an ab initio structural determination method based on synchrotron X-ray powder diffraction data. The LT-NaTa2PO8 presented an orthorhombic structure, closely related to that of the parent LiTa2PO8 structure. In contrast, the HT-NaTa2PO8 was found to adopt a monoclinic structure, belonging to a family of monophosphate tungsten bronzes with pentagonal tunnels. The ionic conductivities of LT-NaTa2PO8 (σ = 5 × 10−5 S/cm at 309 °C) and HT-NaTa2PO8 (σ = 2 × 10−7 S/cm at 300 °C) exhibited Arrhenius behavior with activation energies of 0.49 and 0.79 eV, respectively. Bond valence energy landscape (BVEL) calculations indicated that a three-dimensional (3D) conduction pathway is formed in LT-NaTa2PO8 structure, while the conduction pathway in HT-NaTa2PO8 shows a two-dimensional (2D) character.

Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross-correlation functions.

A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit-cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL-GO (`FIt with DEviating Lattice parameters - Global Optimization'). FIDEL-GO uses a similarity measure based on cross-correlation functions, which allows the comparison of simulated and experimental powder data even if the unit-cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit-cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi-step procedure with built-in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user-controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11-difluoro-, 2,9-dichloro- and 2,9-dichloro-6,13-dihydro-quinacridone, which were solved from powder patterns with 14-20 peaks only, and of the coordination polymer dichloro-bis(pyridine-N)copper(II).

Crystal Structures of Two Titanium Phosphate-Based Proton Conductors: Ab Initio Structure Solution and Materials Properties.

Transition-metal phosphates show a wide range of chemical compositions, variations of the valence states, and crystal structures. They are commercially used as solid-state catalysts, cathode materials in rechargeable batteries, or potential candidates for proton-exchange membranes in fuel cells. Here, we report on the successful ab initio structure determination of two novel titanium pyrophosphates, Ti(III)p and Ti(IV)p, from powder X-ray diffraction (PXRD) data. The low-symmetry space groups P21/c for Ti(III)p and P1̅ for Ti(IV)p required the combination of spectroscopic and diffraction techniques for structure determination. In Ti(III)p, trivalent titanium ions occupy the center of TiO6 polyhedra, coordinated by five pyrophosphate groups, one of them as a bidentate ligand. This secondary coordination causes the formation of one-dimensional six-membered ring channels with a diameter dmax of 3.93(2) Å, which is stabilized by NH4+ ions. Annealing Ti(III)p in inert atmospheres results in the formation of a new compound, denoted as Ti(IV)p. The structure of this compound shows a similar three-dimensional framework consisting of [PO4]3– tetrahedra and TiIV+O6 octahedra and an empty one-dimensional channel with a diameter dmax of 5.07(1) Å. The in situ PXRD of the transformation of Ti(III)p to Ti(IV)p reveals a two-step mechanism, i.e., the decomposition of NH4+ ions in a first step and subsequent structure relaxation. The specific proton conductivity and activation energy of the proton migration of Ti(III)p, governed by the Grotthus mechanism, belong to the highest and lowest, respectively, ever reported for this class of materials, which reveals its potential application in electrochemical devices like fuel cells and water electrolyzers in the intermediate temperature range.

Ab initio structure determination of two new titanium phosphates synthesized via molten salt synthesis

<i>Ab initio</i> structure determination of two new titanium phosphates synthesized <i>via</i> molten salt synthesis

Retraction Notice: Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data

This paper deals with the ab initio structure determination of La1.26 N0.24 Na2.5 O2.54 Zr0.25 triclinic structure having triclinic crystal system via powder X-ray data using the Rietveld refinement method, and with physical properties characterization of a related solid solution at the room temperature structure of three compounds belonging to the Aurivillius family La1.26 N0.24 Na2.5 O2.54 Zr0.25 has been analyzed. La1.26 N0.24 Na2.5 O2.54 Zr0.25 crystallizes in a triclinic crystal system with P-1 space group. The starting material was Na2CO3,Zr(NO3)4 La2O3 for the Zr,La and Na analogues was derived from ab initio methods and refined using the Rietveld refinement method using JANA software package and visualization by Diamond computer program. The cations Na and La are disordered over the Zr sites while the La cation is found exclusively in the layers. The cell parameters are a=4.1040 A b=9.9102 A c=17.6117 A α=98.4299° β=93.4378° γ=92.2041°.The morphology and electrical properties are carried out of cited oxide.

Retraction Notice: Synthesis and ab initio Determination of Bi1.25 V0.123 Ca 0.245 N1.24 O8 cubic structure via powder X-ray diffraction data

This paper deals with the ab initio structure determination of Bi1.25 V0.123 Ca 0.245 N1.24 O8 cubic structure from powder X-ray data using the Rietveld method, and with physical properties characterization of a related solid solution. Bi1.25 V0.123 Ca 0.245 N 1.24 O 8 obtained from the annealing of a quenched cubic high temperature of sample, is cubic crystal system and lattice a=14.1243 A; Z =4. The structure refinement converged to Rp=0.018, R wp=0.0212 GOF=0.0102. The structure is built from cationic slabs parallel to (100) faces of the cubic cell. Each cell corresponds to one slab containing a mixed Bi1.25 V0.123 Ca 0.245 cationic layer (Bi(1)) sandwiched between two equivalent bismuth layers (Bi(2)). The cohesion of the cations in the slabs results from the presence of the oxygen atoms and nitrogen atoms distributed over three sites. Six O(1) and two O(2) atoms form a slightly distorted cubical polyhedron around the mixed cationic site (Bi(1)). (Bi(2)) atoms are surrounded by seven oxygen nitrogen atoms in a very distorted polyhedron. The important delocalization of (Bi(2)) lone pairs toward the integers spaces leads to significant bonds with the adjacent slabs and to the cohesion of the structure. Bi1.25 V0.123 Ca 0.245 O8 is the low symmetry variety of a particular sample of a wide solid solution domain that, formulated Bi1.25 V0.123 Ca0.245 O8, has been investigated. The formation of this phase from the irreversible transformation of quenched on heating and the subsequent transitions and non-transition metal oxides mixed valence have been evidenced by thermo diffractometry, conductivity measurements versus temperature, dilatometer, and thermal analyses. The morphological study was carried out by SEM.

Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing.

A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called 'PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.

Three-Dimensional Electron Diffraction for Structural Analysis of Beam-Sensitive Metal-Organic Frameworks

Electrons interact strongly with matter, which makes it possible to obtain high-resolution electron diffraction data from nano- and submicron-sized crystals. Using electron beam as a radiation source in a transmission electron microscope (TEM), ab initio structure determination can be conducted from crystals that are 6–7 orders of magnitude smaller than using X-rays. The rapid development of three-dimensional electron diffraction (3DED) techniques has attracted increasing interests in the field of metal-organic frameworks (MOFs), where it is often difficult to obtain large and high-quality crystals for single-crystal X-ray diffraction. Nowadays, a 3DED dataset can be acquired in 15–250 s by applying continuous crystal rotation, and the required electron dose rate can be very low (&lt;0.1 e s−1 Å−2). In this review, we describe the evolution of 3DED data collection techniques and how the recent development of continuous rotation electron diffraction techniques improves data quality. We further describe the structure elucidation of MOFs using 3DED techniques, showing examples of using both low- and high-resolution 3DED data. With an improved data quality, 3DED can achieve a high accuracy, and reveal more structural details of MOFs. Because the physical and chemical properties of MOFs are closely associated with their crystal structures, we believe 3DED will only increase its importance in developing MOF materials.

Ab Initio Determination of Peptide Structures by MicroED.

Structural elucidation of small macromolecules such as peptides has recently been facilitated by a growing number of technological advances to existing crystallographic methods. The emergence of electron micro-diffraction (MicroED) of protein nanocrystals under cryogenic conditions has enabled the interrogation of crystalline peptide assemblies only hundreds of nanometers thick. Collection of atomic or near-atomic resolution data by these methods has permitted the ab initio determination of structures of various amyloid-forming peptides, including segments derived from prions and ice-nucleating proteins. This chapter focuses on the process of ab initio structural determination from nano-scale peptide assemblies and other similar molecules.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

This paper deals with the ab initio structure determination of La1.26 N0.24 Na2.5 O2.54 Zr0.25 triclinic structure having triclinic crystal system via powder X-ray data using the Rietveld refinement method, and with physical properties characterization of a related solid solution at the room temperature structure of three compounds belonging to the Aurivillius family La1.26 N0.24 Na2.5 O2.54 Zr0.25 has been analyzed. La1.26 N0.24 Na2.5 O2.54 Zr0.25 crystallizes in a triclinic crystal system with P-1 space group. The starting material was Na2CO3,Zr(NO3)4 La2O3 for the Zr,La and Na analogues was derived from ab initio methods and refined using the Rietveld refinement method using JANA software package and visualization by Diamond computer program. The cations Na and La are disordered over the Zr sites while the La cation is found exclusively in the layers. The cell parameters are a=4.1040 Å b=9.9102 Å c=17.6117 Å α=98.4299° β=93.4378° γ=92.2041°.The morphology and electrical properties are carried out of cited oxide.