Structure Determination Methods Research Articles

Analysis of COF-300 synthesis: probing degradation processes and 3D electron diffraction structure.

Although COF-300 is often used as an example to study the synthesis and structure of (3D) covalent organic frameworks (COFs), knowledge of the underlying synthetic processes is still fragmented. Here, an optimized synthetic procedure based on a combination of linker protection and modulation was applied. Using this approach, the influence of time and temperature on the synthesis of COF-300 was studied. Synthesis times that were too short produced materials with limited crystallinity and porosity, lacking the typical pore flexibility associated with COF-300. On the other hand, synthesis times that weretoo long could be characterized by loss of crystallinity and pore order by degradation of the tetrakis(4-aminophenyl)methane (TAM) linker used. The presence of the degradation product was confirmed by visual inspection, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). As TAM is by far the most popular linker for the synthesis of 3D COFs, this degradation process might be one of the reasons why the development of 3D COFs is still lagging compared with 2D COFs. However, COF crystals obtained via an optimized procedure could be structurally probed using 3D electron diffraction (3DED). The 3DED analysis resulted in a full structure determination of COF-300 at atomic resolution with satisfying data parameters. Comparison of our 3DED-derived structural model with previously reported single-crystal X-ray diffraction data for this material, as well as parameters derived from the Cambridge Structural Database, demonstrates the high accuracy of the 3DED method for structure determination. This validation might accelerate the exploitation of 3DED as a structure determination technique for COFs and other porous materials.

Benchmarking Guanidinium Organosulfonate Hydrogen-Bonded Frameworks for Structure Determination of Encapsulated Guests.

Single crystal X-ray diffraction (SCXRD) is arguably the most definitive method for molecular structure determination, but it is often challenged by compounds that are liquids or oils at room temperature or do not form crystals adequate for analysis. Our laboratory previously reported a simple, cost-effective, single-step crystallization method based on guanidinium organosulfonate (GS) hydrogen bonded frameworks for structure determination of a wide range of encapsulated guest molecules, including assignment of the absolute configuration of chiral centers. Herein, we expand on those results and report a head-to-head comparison of the GS method with adamantoid "molecular chaperones", which have been reported to be useful hosts for structure determination. Inclusion compounds limited to only two GS hosts are characterized by low R1 values and Flack parameters, infrequent disorder of the host and guest, and manageable disorder when it does exist. The structures of some target molecules that were not included or resolved using the adamantoid chaperones were successfully included and resolved by the GS hosts, and vice versa. Of the 32 guests attempted by the GS method, 31 inclusion compounds afforded successful guest structure solutions, a 97% success rate. The GS hosts and adamantoid chaperones are complementary with respect to guest inclusion, arguing that both should be employed in the arsenal of methods for structure determination. Furthermore, the low cost of organosulfonate host components promises an accessible route to molecular structure determination for a wide range of users.

Comparing Microcrystal Electron Diffraction (MicroED) and X-ray crystallography as methods for structure determination of Oseltamivir phosphate

Oseltamivir phosphate is a pharmaceutical used in the treatment of influenza viruses. Panče Naumov et al. took two years of dedicated single crystal cultivation and successfully obtained low-quality single crystals through a diffusion method. Cultivation of Oseltamivir phosphate single crystals was proved to be difficult and can extend over several months or more. We employed microcrystalline electron diffraction (MicroED) for direct powder measurements, eliminating the need for lengthy single-crystal cultivation, and the time to obtain the molecular structure of Oseltamivir phosphate was shortened from several months to five hours. Comparative analyses of single crystal (Crystal 1) and MicroED (Crystal 2) results revealed equivalent crystal structures, with minimal differences in hydrogen bond distances, identical powder X-ray diffraction patterns, and negligible variations in Hirshfeld surface analysis. The differential scanning calorimetry (DSC) analysis showcased a higher melting point of Oseltamivir phosphate (206.0 °C) than Oseltamivir (110.7 °C), indicating that Oseltamivir phosphate had high temperature stability, and may result in the selection of Oseltamivir phosphate as a formulation form. The study establishes and verifies a congruence between MicroED detection and traditional single-crystal detection methods and may be applied in the elucidation of compound structures and the surveillance of drug polymorphism.

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.

Topological Analysis and Structural Determination of 3D Covalent Organic Frameworks.

3D covalent organic frameworks (3D COFs) constitute a new type of crystalline materials that consist of a range of porous structures with numerous applications in the fields of adsorption, separation, and catalysis. However, because of the complexity of the three-periodic net structure, it is desirable to develop a thorough structural comprehension, along with a means to precisely determine the actual structure. Indeed, such advancements would considerably contribute to the rational design and application of 3D COFs. In this review, the reported topologies of 3D COFs are introduced and categorized according to the configurations of their building blocks, and a comprehensive overview of diffraction-based structural determination methods is provided. The current challenges and future prospects for these materials will also be discussed.

Three Methods for Structure Determination from Powder Diffraction Data

Three Methods for Structure Determination from Powder Diffraction Data

X-Ray Crystallography for Macromolecular Complexes.

X-ray crystallography has for most of the last century been the standard technique to determine the high-resolution structure of biological macromolecules, including multi-subunit protein-protein and protein-nucleic acids as large as the ribosome and viruses. As such, the successful application of X-ray crystallography to many biological problems revolutionized biology and biomedicine by solving the structures of small molecules and vitamins, peptides and proteins, DNA and RNA molecules, and many complexes-affording a detailed knowledge of the structures that clarified biological and chemical mechanisms, conformational changes, interactions, catalysis and the biological processes underlying DNA replication, translation, and protein synthesis. Now reaching well into the first quarter of the twenty-first century, X-ray crystallography shares the structural biology stage with cryo-electron microscopy and other innovative structure determination methods, as relevant and central to our understanding of biological function and structure as ever. In this chapter, we provide an overview of modern X-ray crystallography and how it interfaces with other mainstream structural biology techniques, with an emphasis on macromolecular complexes.

Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability.

The biological activities and pharmacological properties of peptides and peptide mimetics are determined by their conformational states. Therefore, a detailed understanding of the conformational landscape is crucial for rational drug design. Nuclear magnetic resonance (NMR) is the only method for structure determination in solution. However, it remains challenging to determine the structures of peptides using NMR because of very weak nuclear Overhauser effects (NOEs), the semiquantitative nature of the rotating frame Overhauser effect (ROE), and the low number of NOEs/ROEs in N-methylated peptides. In this study, we introduce a new approach to investigating the structures of modified macrocyclic peptides. We utilize exact NOEs (eNOEs) in viscous solvent mixtures to replicate various cellular environments. eNOEs provide detailed structural information for highly dynamic modified peptides. Structures of high precision were obtained for cyclosporin A, with a backbone atom rmsd of 0.10 Å. Distinct conformational states in different environments were identified for omphalotin A (OmphA), a fungal nematotoxic and multiple backbone N-methylated macrocyclic peptides. A model for cell-permeation is presented for OmphA, based on its structures in polar, apolar, and mixed polarity solvents. During the transition from a polar to an apolar environment, OmphA undergoes a rearrangement of its H-bonding network, accompanied by a cis to trans isomerization of the ω torsion angle within a type VIa β-turn. We hypothesize that the kinetics of these conformational transitions play a crucial role in determining the membrane-permeation capabilities of OmphA.

Best method to determine DNA G-quadruplex folding: The 1H–13C HSQC NMR experiment

NMR spectroscopy is the major method for G-quadruplex structure determination under physiologically relevant solution conditions. Unlike duplex B-DNA, in which all nucleotides adopt an anti glycosidic conformation, the core tetrad-guanines in a G-quadruplex can adopt anti or syn glycosidic conformation depending on the folding structure. An experimental method that can clearly and unambiguously determine syn and anti tetrad-Gs in a G-quadruplex is highly desirable and necessary. In the present study, we exploit the advantages of the 1H–13C HSQC experiment to determine tetrad-G’s glycosidic conformation and thus folding topology of G-quadruplexes. We use several examples to demonstrate the clear and straightforward determination of the guanine glycosidic conformations and G-quadruplex folding structures. Moreover, 1H–13C HSQC data can readily identify adenine H2 resonances as well as determine unusual syn conformation in loop and flanking sequences, a challenging task by standard 2D NOESY.

The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.

The Nucleic Acid Knowledgebase (nakb.org) is a new data resource, updated weekly, for experimentally determined 3D structures containing DNA and/or RNA nucleic acid polymers and their biological assemblies. NAKB indexes nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMRand EM), including all held by the Protein Data Bank (PDB). As the planned successor to the Nucleic Acid Database (NDB), NAKB's design preserves all functionality of the NDB and provides novel nucleic acid-centric content, including structural and functional annotations, as well as annotations from and links to external resources. A variety of custom interactive tools have been developed to enable rapid exploration and drill-down of NAKB's content.

Machine learning and DFT-based combined framework for predicting transmission spectra of quantum-confined bio-molecular nanotube.

The Adenine-based nanotube is theoretically designed, and its transmission spectra are investigated. The quantum-confined Adenine nanotube shows electronic transmission of the carrier at minimum stress. In this paper, the prediction of transmission spectra of the quantum-confined bio-molecular nanotube is investigated and deeply studied. Molecular level structure prediction and their electronic characterization can be possible with ab initio accuracy using a machine learning algorithmic approach. At the molecular level, it is difficult to predict quantum transmission spectra as these results are always hampered by the carrier backscattering effect. However, mostly these predictive models are available for intrinsic semi-conducting materials and other inorganic structures. Machine learning algorithms are designed to predict the electronic properties of the nano-scale structure. This task is even more difficult when quantum-confined molecular arrangements are considered, whose transmission spectra are sensitive to the confinements applied. This paper presents an effective machine learning algorithms framework for predicting transmission spectra of quantum-confined nanotubes from their geometries. In this paper, we consider regression machine learning algorithms to find maximum accuracy with varying configurations and geometries to excerpt their atoms' local environment information. The Hamiltonian components are then used to enable the utilization of the information to predict the electronic structure at any arbitrary sampling point or k-point. The theoretical basics introduced in this process help to capture and incorporate minor changes in quantum confinements into transmission spectra and provide the framework algorithm with more accuracy. This paper shows the ability to predict the accurate algorithmic models of the Adenine nanotube. In this framework, we have considered a tiny data set to achieve a rapid and reliable method for electronic structure determination and also propose the best algorithm for predictive model analysis.

Lattice Shrinkage of 2D-COFs under Electron Beam Irradiation

Over the past two decades, covalent organic frameworks (COFs) have become the most widely studied porous crystalline materials. Their specific physical and chemical properties are determined by the arrangement of atoms (crystal structure). Therefore, the determination of their structure is arguably the most important characterization step for COFs. Although single-crystal X-ray diffraction is the most widely used method for structure determination, confirmation of the structure of COFs is limited to lattice fringes in transmission electron microscopy (TEM) because of their small crystal size (nanocrystals) or poor crystal quality. At present, many two-dimensional COFs (2D-COFs) have clear powder X-ray diffraction (PXRD) patterns, but specific lattice fringes are not available for all 2D-COFs. This severely hinders the development of the COF field. Here, we discovered the lattice shrinkage behavior of COFs under electron beam irradiation by comparing the lattice fringes of 2D-COFs under different conditions. By comparing the lattice fringes of a 1,3,5-tris-(4-aminophenyl)triazine-1,3,5-tris-(4-formylphenyl)triazine covalent organic framework (TAPT-TFPT COF) at room temperature and under liquid nitrogen freezing conditions, we found that the lattice fringes are in good agreement with the PXRD and the theoretical values of the COF (2.213 nm) under freezing conditions. However, the lattice fringe spacing is only 1.656 nm at room temperature. The discovery not only provides new insights into the TEM characterization of COFs, but also further expands the range of crystalline COF materials.

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.

Application of the crystalline sponge method for structure determination of persistent organic pollutants of agrochemical degradation products

Application of the crystalline sponge method for structure determination of persistent organic pollutants of agrochemical degradation products

A method for structure determination of GPCRs in various states.

G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by various ligands has been one of the primary goals in the field. Here we developed an effective universal method for GPCR cryo-electron microscopy structure determination without the need to prepare GPCR-signaling protein complexes. Using this method, we successfully solved the structures of the β2-adrenergic receptor (β2AR) bound to antagonistic and agonistic ligands and the adhesion GPCR ADGRL3 in the apo state. For β2AR, an intermediate state stabilized by the partial agonist was captured. For ADGRL3, the structure revealed that inactive ADGRL3 adopts a compact fold and that large unusual conformational changes on both the extracellular and intracellular sides are required for activation of adhesion GPCRs. We anticipate that this method will open a new avenue for understanding GPCR structure‒function relationships and drug development.

RNA target highlights in CASP15: Evaluation of predicted models by structure providers.

The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA-only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x-ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA-protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models.

First-principles calculations to investigate structural, optical and electronic properties of ZrO2, Zr0.93Si0.07O2 and Zr0.86Si0.14O2 for dye-sensitised solar cells applications

ABSTRACT Initially, density approximations and generalised gradient approximations (GGA) functional of DFT were executed to determine the electronic structure where the non-local functionals of GGA obtained more close value of reference value, so that GGA method was used to calculate the band structures, DOS, PDOS and optical properties of ZrO2, Zr0.93Si0.07O2 and Zr0.86Si0.14O2 using the Perdew–Burke–Ernzerhof (PBE), Revised Perdew–Burke–Ernzerhof (RPBE), Perdew Wang (PW91), and Wu-Cohen. The transferability of electrons is completely related to PseudoPotential (PP), where four methods, such as OTFG ultra-soft, OTFG norm-conserving, ultra-soft, and norm-conserving, were used in this study. Finally, the norm-conserving PP has been selected as the most accurate method for determination of electronic structure. In addition, to assess the nature of orbital, the DOS and PDOS were additionally simulated and even the optical properties of crystals were calculated. Furthermore, the chemical reactivity, such as HOMO and LUMO, quantum properties, is justified where doping can have a vast effect as well as the open circuit voltage (Voc) is increased after doping. Finally, the toxicity data from in silico study refers to us that these are non-toxic or non-carcinogenic materials with not readily biodegradable status.

A robust absolute structure determination method by dynamical refinement against electron diffraction data

A robust absolute structure determination method by dynamical refinement against electron diffraction data

Determining the Projected Crystal Structure from Four-dimensional Scanning Transmission Electron Microscopy via the Scattering Matrix.

We present a gradient-descent-based approach to determining the projected electrostatic potential from four-dimensional scanning transmission electron microscopy measurements of a periodic, crystalline material even when dynamical scattering occurs. The method solves for the scattering matrix as an intermediate step, but overcomes the so-called truncation problem that limited previous scattering-matrix-based projected structure determination methods. Gradient descent is made efficient by using analytic expressions for the gradients. Through simulated case studies, we show that iteratively improving the scattering matrix determination can significantly improve the accuracy of the projected structure determination.

Single crystal X-ray analysis using the crystalline sponge method for direct structure determination of new and earlier synthetic cannabinoids including OXIZIDs, AKB48, and JWH-424 from a trace sample

Single crystal X-ray analysis using the crystalline sponge method for direct structure determination of new and earlier synthetic cannabinoids including OXIZIDs, AKB48, and JWH-424 from a trace sample