Structure determination, thermal stability and dissolution rate of δ-indomethacin

Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction

3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.

Molecular replacement for small-molecule crystal structure determination from X-ray and electron diffraction data with reduced resolution

The resolution of 3D electron diffraction (ED) data of small-molecule crystals is often relatively poor, due to either electron-beam radiation damage during data collection or poor crystallinity of the material. Direct methods, used as standard for crystal structure determination, are not applicable when the data resolution falls below the commonly accepted limit of 1.2 Å. Therefore an evaluation was carried out of the performance of molecular replacement (MR) procedures, regularly used for protein structure determination, for structure analysis of small-molecule crystal structures from 3D ED data. In the course of this study, two crystal structures of Bi-3812, a highly potent inhibitor of the oncogenic transcription factor BCL6, were determined: the structure of α-Bi-3812 was determined from single-crystal X-ray data, the structure of β-Bi-3812 from 3D ED data, using direct methods in both cases. These data were subsequently used for MR with different data types, varying the data resolution limit (1, 1.5 and 2 Å) and by using search models consisting of connected or disconnected fragments of BI-3812. MR was successful with 3D ED data at 2 Å resolution using a search model that represented 74% of the complete molecule.

Study on polycyclic macromolecular drug solid stability: A case exploration of methylcobalamin

As one of derivatives of Vitamin B12, methylcobalamin (MeCbl) is an indispensable "Life Element" and plays an essential role in maintaining human normal physiology function and clinical medicine application. Because of the intricate molecular structure, strong hygroscopicity and optical instability, maintaining its solid stability is a great challenge in pharmaceutical preparation. Based on the structure features of MeCbl hydrates, this study explored the drug solid stability by designing solid-solid phase transformation (SSPT) experiments. Three hydrate powders of MeCbl that had special structure with isolated site and channel water molecules were discovered. It was found that drying condition and surrounding humidity were controlling factors influencing the final solid form. The inter-conversion relations relevant to heating-induced and humidity-induced structure changes were established among the three hydrate powders. Powder X-ray diffraction, thermogravimetric analysis, differential scanning calorimetry, high performance liquid chromatography and dynamic vapor sorption were used to characterize the differences and related properties of stably prepared MeCbl hydrate powders. The particle size of product could be regulated and controlled by optimizing operating conditions of crystallization process, where ultrasound-assisted and seeding-introduced were applied as promising strategies to enhance solution crystallization process. This study opens up the possibility for the stable preparation and large-scale production of polycyclic macromolecular bulk drugs like methylcobalamin.

Different Dissolution Molecular Pathways of Azilsartan Crystals with Different Forms Revealed by In Situ Atomic Force Microscopy

Here, using in situ atomic force microscopy (AFM), the dissolution behaviors and dissolution molecular pathways of two azilsartan crystals, the isopropanol solvate (AZ-IPA), and form I (AZ-I), in pure water and 6-30% poly(ethylene glycol) (PEG) aqueous solutions are revealed. The dissolution behaviors of step retreat and etch pit formation are observed on the (100) faces of the two crystals, with a single step corresponding to one molecular monolayer in crystal structures. Etching rates of pits increase with PEG concentration. Furthermore, our results show that AZ-IPA dissolves by the direct detachment of molecules from the step front to solution. Such a mechanism remains even when the PEG concentration changes. However, AZ-I dissolves primarily by the surface diffusion mechanism involving molecular detachment from the step front at first and then diffusion over the terraces before desorption into solution. PEG promotes the dissolution of AZ-I crystals by favoring the molecular detachment from the step front.

Saddles as rotational locks within shape-assisted self-assembled nanosheets

Two-dimensional (2D) materials are a key target for many applications in the modern day. Self-assembly is one approach that can bring us closer to this goal, which usually relies upon strong, directional interactions instead of covalent bonds. Control over less directional forces is more challenging and usually does not result in as well-defined materials. Explicitly incorporating topography into the design as a guiding effect to enhance the interacting forces can help to form highly ordered structures. Herein, we show the process of shape-assisted self-assembly to be consistent across a range of derivatives that highlights the restriction of rotational motion and is verified using a diverse combination of solid state analyses. A molecular curvature governed angle distribution nurtures monomers into loose columns that then arrange to form 2D structures with long-range order observed in both crystalline and soft materials. These features strengthen the idea that shape becomes an important design principle leading towards precise molecular self-assembly and the inception of new materials.

MicroED in drug discovery

The cryo-electron microscopy (cryo-EM) method microcrystal electron diffraction (MicroED) was initially described in 2013 and has recently gained attention as an emerging technique for research in drug discovery. As compared to other methods in structural biology, MicroED provides many advantages deriving from the use of nanocrystalline material for the investigations. Here, we review the recent advancements in the field of MicroED and show important examples of small molecule, peptide and protein structures that has contributed to the current development of this method as an important tool for drug discovery.

4,4'-(Anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) Lead Iodide C30H22N2Pb2I6: A Highly Luminescent, Chemically and Thermally Stable One-Dimensional Hybrid Iodoplumbate

A new one-dimensional hybrid iodoplumbate, namely, 4,4'-(anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) lead iodide C₃₀H₂₂N₂Pb₂I₆ (AEPyPbI), is reported here for the first time with its complete characterization. The material exhibits remarkable thermal stability (up to 300 °C), and it is unreactive under ambient conditions toward water and atmospheric oxygen, due to the quaternary nature of the nitrogen atoms present in the organic cation. The cation exhibits strong visible fluorescence under ultraviolet (UV) irradiation, and when its iodide is combined with PbI₂, it forms AEPyPb₂I₆, an efficient light-emitting material, with a photoluminescence emission intensity comparable to that of high-quality InP epilayers. The structure determination was obtained using three-dimensional electron diffraction, and the material was extensively studied by using a wide range of techniques, such as X-ray powder diffraction, diffuse reflectance UV-visible spectroscopy, thermogravimetry-differential thermal analysis, elemental analysis, Raman and infrared spectroscopies, and photoluminescence spectroscopy. The emissive properties of the material were correlated with its electronic structure by using state-of-the-art theoretical calculations. The complex, highly conjugated electronic structure of the cation interacts strongly with that of the Pb-I network, giving rise to the peculiar optoelectronic properties of AEPyPb₂I₆. The material, considering its relatively easy synthesis and stability, shows promise for light-emitting and photovoltaic devices. The use of highly conjugated quaternary ammonium cations may be useful for the development of new hybrid iodoplumbates and perovskites with optoelectronic properties tailored for specific applications.

Direct structure determination of vemurafenib polymorphism from compact spherulites using 3D electron diffraction

The spherulitic morphology is considered to be the most common morphology of crystalline materials and is particularly apparent in melt-crystallized products. Yet, historically, the polycrystalline nature of spherulites has hindered successful crystal structure determination. Here, we report the direct structure determination of a clinical drug, vemurafenib (VMN), in compact spherulite form using 3D electron diffraction (3D ED). VMN has four known polymorphs. We first solved the crystal structures of α-, β-, and γ-VMN from compact spherulites using 3D ED, and the resulting structures were highly consistent with those obtained by single-crystal X-ray diffraction. We then determined the crystal structure of δ-VMN-the least stable polymorph which cannot be cultivated as a single crystal-directly from the compact spherulite sample. We unexpectedly discovered a new polymorph during our studies, denoted as ε-VMN. Single crystals of ε-VMN are extremely thin and not suitable for study by X-ray diffraction. Again, we determined the structure of ε-VMN in a compact spherulite form. This successful structure elucidation of all five VMN polymorphs demonstrates the possibility of directly determining structures from melt-grown compact spherulite samples. Thereby, this discovery will improve the efficiency and broaden the scope of polymorphism research, especially within the field of melt crystallization.

True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications

The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet-triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.

A High Energy X-ray Diffraction Study of Amorphous Indomethacin

Amorphous pharmaceuticals often possess a wide range of molecular conformations and bonding arrangements. The x-ray pair distribution function (PDF) method is a powerful technique for the characterization of variations in both intra-molecular and inter-molecular packing arrangements. Here, the x-ray PDF of amorphous Indomethacin is shown to be particularly sensitive to the preferred orientations of the chlorobenzyl ring found in isomers in the crystalline state. In some cases, the chlorobenzyl ring has no preferred torsional angle in the amorphous form, while in others evidence of distinct isomer orientations are observed. Amorphous samples with no preferred torsion angles of the chlorobenzyl ring are found to favor enhanced inter-molecular hydrogen bonding, and this is reflected in the intensity of the first sharp diffraction peak. These significant variations in structure rule out amorphous Indomethacin as a possible standard for x-ray PDF measurements. At high humidity, time resolved PDF's for >40 h reveal water molecules forming hydrogen bonds with Indomethacin molecules. A simple linear hydrogen bond model indicates that water molecules in the wet amorphous form have similar hydrogen bond strengths to those found between Indomethacin dimers or chains in the dry amorphous form.

Two New Organic Co-Crystals Based on Acetamidophenol Molecules

Herein we present two new organic co-crystals obtained through a simple solution growth process based on an acetamidophenol molecule, either paracetamol or metacetamol, and on 7,7,8,8-tetracyanoquinodimethane (TCNQ). These co-crystals are part of a family of potential organic charge transfer complexes, where the acetamidophenol molecule behaves as an electron donor and TCNQ behaves as an electron acceptor. Due to the sub-micron size of the crystalline domains, 3D electron diffraction was employed for the structure characterization of both systems. Paracetamol-TCNQ structure was solved by standard direct methods, while the analysis of metacetamol-TCNQ was complicated by the low resolution of the available diffraction data and by the low symmetry of the system. The structure determination of metacetamol-TCNQ was eventually achieved after merging two data sets and combining direct methods with simulated annealing. Our study reveals that both paracetamol-TCNQ and metacetamol-TCNQ systems crystallize in a 1:1 stoichiometry, assembling in a mixed-stack configuration and adopting a non-centrosymmetric P1 symmetry. It appears that paracetamol and metacetamol do not form a strong structural scaffold based on hydrogen bonding, as previously observed for orthocetamol-TCNQ and orthocetamol-TCNB (1,2,4,5-tetracyanobenzene) co-crystals.

Indomethacin Polymorph δ Revealed to be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47-Year-Old Misunderstanding

Indomethacin is a clinically classical non‐steroidal anti‐inflammatory drug that has been marketed since 1965. The third polymorph, Form δ, was discovered by both melt and solution crystallization in 1974. δ‐indomethacin cannot be cultivated as large single crystals suitable for X‐ray crystallography and, therefore, its crystal structure has not yet been determined. Here, we report the structure elucidation of δ‐indomethacin by 3D electron diffraction and reveal the truth that melt‐crystallized and solution‐crystallized δ‐indomethacin are in fact two polymorphs with different crystal structures. We propose to keep the solution‐crystallized polymorph as Form δ and name the melt‐crystallized polymorph as Form θ. Intriguingly, both structures display plastic flexibility based on a slippage mechanism, making indomethacin the first drug to have two plastic polymorphs. This discovery and correction of a 47‐year‐old misunderstanding signify that 3D electron diffraction has become a powerful tool for polymorphic structural studies.