Tautomerism unveils a self-inhibition mechanism of crystallization

The Hematin-dihydroartemisinin Adduct Mobilizes a Potent Mechanism to Suppress β-hematin Crystallization

Malaria remains a significant public health challenge in equatorial regions of the world largely owing to the parasite's emerging resistance to the recently introduced drugs of the artemisinin (ART) family. In the human body most ART-derivative drugs are metabolized to dihydroartemisinin (DHA), which, in the parasite, after activation by heme, can form a hematin-dihydroartemisinin adduct (H-DHA). Here we test whether and how H-DHA inhibits hematin crystallization, the main constituent of the heme detoxification pathway of malaria parasites. We find that H-DHA is a poor inhibitor of classical crystal growth- it weakly blocks the growth sites on crystal surfaces-and, counterproductively, a promotor of β-hematin nucleation, driven by a boost in the formation of precursors. We establish that at elevated hematin concentrations H-DHA activates two non-classical pathways that transform it into a potent β-hematin growth inhibitor. First, β-hematin crystallites, whose nucleation is promoted by H-DHA, incorporate into large β-hematin crystals and suppress their growth, likely by straining the crystal lattice. A second consequence of H-DHA is the generation of macrosteps on β-hematin crystal surfaces that hinder growth. Importantly, the induced growth suppression is irreversible and persists even in the absence of H-DHA. Our findings suggest that a partial resistance mechanism to artemisinin-class drugs in trophozoite-stage parasites may be due to the reduced concentrations of hematin and H-DHA, which deactivate the dual non-classical mode of action of the adduct in the delayed-clearance parasite strains.

Conformational Self-Poisoning in Crystal Growth

With the ever-increasing complexity of new drug compounds, their crystallization is becoming more challenging than ever. Controlling the crystallization of present and future drugs will remain a chimera unless we gain an improved understanding of the effects of molecular flexibility on crystal nucleation and growth at the molecular level. As a contribution to this understanding, we report here the growth kinetics of a series of diacids with chain lengths from 4 to 10 carbon atoms. These compounds are ideal for such a study since (a) they all crystallize as linear conformers, (b) their crystal structures are very similar across the series, and (c) their molecular flexibility increases with increasing chain length. Upon analysis of their crystal growth behavior, we stumbled upon a surprising finding: the growth of these crystals along the length increases linearly for the series up to the diacid containing seven carbon atoms, beyond which the rates drop dramatically. Such a dramatic decrease in growth rates at longer chain lengths cannot be explained by the crystal structure differences of the diacids. To gain further insights, we explored the conformational landscapes of two diacids in solution using well-tempered metadynamics simulations. With increasing chain length, the conformational landscape becomes more complex, with folded conformations becoming more important for long chain acids. Our simulations show that some of the minor conformers present in the solution act as potent crystal growth inhibitors (a phenomenon we refer to as conformational self-poisoning). To the best of our knowledge, this work represents the first report of conformational self-poisoning in crystal growth, with experimental evidence supported by a molecular-level mechanism. While this effect is bad news for crystallization scientists, who must work with complex flexible compounds, for these diacids, we show that selected solvents are able to disfavor the problematic conformers in the solution, turning off the self-poisoning effect.

Supersaturation-Controlled Single-Crystal Growth of Covalent Organic Frameworks with Binary Solvents

The ability to rapidly produce large single crystals is crucial for advancing the applications of covalent organic frameworks (COFs). Although the modulation strategy provides a straightforward method for growing high-quality single crystals, the slow crystallization process of COFs often limits their practical use. In this study, we combined the principles of crystallization thermodynamics and kinetics with the modulation strategy to develop a binary solvent-supersaturation method, enabling the growth of single-crystal COFs in a significantly shorter time. By systematically investigating the crystal-growth kinetics across different solvent ratios, we established a diffusion-reaction growth model, highlighting the essential role of supersaturation in controlling COF crystal growth. Especially, under this crystallization guidance, elegant single crystals of COFs built with heteroatom or other functionality can also facilely obtained, which spontaneously validate the universality of the protocol. Importantly, the resulting single-crystal COFs, characterized by high structural symmetry, exhibited notable second harmonic generation (SHG) activity, which could open new avenues for future research in this field.

Unusual Tautomerism of Methyl Allophanate: Selective Crystallization of the Minor Component via Hydrogen-Bond Network

The unexpected tautomerism of methyl allophanates has been observed in the solid state. X-ray analysis, IR/UV spectroscopic data, and density functional theory (DFT) calculations showed that the molecule adopts an imidic form in the crystal, whereas the amide form, which is more stable in aqueous solution, is expected. The imidic form in the solid state is stabilized by a robust hydrogen-bond network, which facilitates the selective isolation of minor imidic species.

Vitamin B2 Operates by Dual Thermodynamic and Kinetic Mechanisms to Selectively Tailor Urate Crystallization

Here we demonstrate how a biologically relevant molecule, riboflavin (vitamin B2), operates by a dual mode of action to effectively control crystallization of ammonium urate (NH4HU), which is associated with cetacean kidney stones. In situ microfluidics and atomic force microscopy experiments confirm a strong interaction between riboflavin and NH4HU crystal surfaces that substantially inhibits layer nucleation and spreading by kinetic mechanisms of step pinning and kink blocking. Riboflavin does not alter the distribution of tautomeric urate isomers, but its adsorption on NH4HU crystal surfaces does interfere with the effects of minor urate tautomer by limiting its ability to induce NH4HU crystal defects while also suppressing NH4HU nucleation and inhibiting crystal growth by 80% at an uncharacteristically low modifier concentration. Time-resolved spectroscopy measurements, ab initio calculations, and molecular dynamics simulations confirm that each riboflavin molecule forms a complex with six or more urate molecules to lower supersaturation, thereby reducing the rate of NH4HU crystallization by a thermodynamically driven mechanism. The degree of complexation observed for riboflavin far exceeds that of common chelating agents, and results in crystal dissolution when the free urate concentration falls below NH4HU solubility. The synergism that is created by riboflavin's dual kinetic and thermodynamic mechanisms is rarely achieved by more conventional crystal growth inhibitors. These insights offer new approaches that could be influential for the design of molecular modifiers in crystal engineering applications, the development of therapeutics for pathological conditions, and establishing broader understanding of the roles played by foreign agents in natural and biological crystallization.

Unraveling the complexity of amorphous solid as direct ingredient for conventional oral solid dosage form: The story of Elagolix Sodium

Conventional solid oral dosage form development is not typically challenged by reliance on an amorphous drug substance as a direct ingredient in the drug product, as this may result in product development hurdles arising from process design and scale-up, control of physical quality attributes, drug product processability and stability. Here, we present the Chemistry, Manufacturing and Controls development journey behind the successful commercialization of an amorphous drug substance, Elagolix Sodium, a first-in-class, orally active gonadotropin-releasing hormone antagonist. The reason behind the lack of crystalline state was assessed via Molecular Dynamics (MD) at the molecular and inter-molecular level, revealing barriers for nucleation due to prevalence of intra-molecular hydrogen bond, repulsive interactions between active pharmaceutical ingredient (API) molecules and strong solvation effects. To provide a foundational basis for the design of the API manufacturing process, we modeled the solvent-induced plasticization behavior experimentally and computationally via MD for insights into molecular mobility. In addition, we applied material science tetrahedron concepts to link API porosity to drug product tablet compressibility. Finally, we designed the API isolation process, incorporating computational fluid dynamics modeling in the design of an impinging jet mixer for precipitation and solvent-dependent glass transition relationships in the cake wash, blow-down and drying process, to enable the consistent manufacture of a porous, non-sintered amorphous API powder that is suitable for robust drug product manufacturing.

Rationalizing the Influence of Small-Molecule Dopants on Guanine Crystal Morphology

Many spectacular optical phenomena in animals are produced by reflective assemblies of guanine crystals. The crystals comprise planar H-bonded layers of π-stacked molecules with a high in-plane refractive index. By preferentially expressing the highly reflective π-stacked (100) crystal face and controlling its cross-sectional shape, organisms generate a diverse array of photonic superstructures. How is this precise control over crystal morphology achieved? Recently, it was found that biogenic guanine crystals are composites, containing high quantities of hypoxanthine and xanthine in a molecular alloy. Here, we crystallized guanine in the presence of these dopants and used computations to rationalize their influence on the crystal morphology and energy. Exceptional quantities of hypoxanthine are incorporated into kinetically favored solid solutions, indicating that fast crystallization kinetics underlies the heterogeneous compositions of biogenic guanine crystals. We find that weakening of H-bonding interactions by additive incorporation elongates guanine crystals along the stacking direction-the opposite morphology of biogenic crystals. However, by modulation of the strength of competing in-plane H-bonding interactions, additive incorporation strongly influences the cross-sectional shape of the crystals. Our results suggest that small-molecule H-bond disrupting additives may be simultaneously employed with π-stack blocking additives to generate reflective platelet crystal morphologies exhibited by organisms.

A dual growth mode unique for organic crystals relies on mesoscopic liquid precursors

Organic solvents host the synthesis of high-value crystals used as pharmaceuticals and optical devices, among other applications. A knowledge gap persists on how replacing the hydrogen bonds and polar attraction that dominate aqueous environments with the weaker van der Waals forces affects the growth mechanism, including its defining feature, whether crystals grow classically or nonclassically. Here we demonstrate a rare dual growth mode of etioporphyrin I crystals, enabled by liquid precursors that associate with crystal surfaces to generate stacks of layers, which then grow laterally by incorporating solute molecules. Our findings reveal the precursors as mesoscopic solute-rich clusters, a unique phase favored by weak bonds such as those between organic solutes. The lateral spreading of the precursor-initiated stacks of layers crucially relies on abundant solute supply directly from the solution, bypassing diffusion along the crystal surface; the direct incorporation pathway may, again, be unique to organic solvents. Clusters that evolve to amorphous particles do not seamlessly integrate into crystal lattices. Crystals growing fast and mostly nonclassically at high supersaturations are not excessively strained. Our findings demonstrate that the weak interactions typical of organic systems promote nonclassical growth modes by supporting liquid precursors and enabling the spreading of multilayer stacks.

Formation, Selective Encapsulation, and Tautomerization Control of Isoindolone Utilizing Guanidinium Sulfonate Frameworks

Herein we report the use of tetrakis (guanidinium) pyrenetetrasulfonate (G4PYR) and bis (guanidinium) 1,5-napthalene disulfonate (G2NDS) to catalyze the cyclization of 2-cyanobenzamide (1) to isoindolone (2). Moreover, we demonstrate the remarkable selectivity of these guanidinium organosulfonate hosts in encapsulating 2 over 1. By thoroughly investigating the intramolecular cyclization reaction, we determined that guanidinium and the organosulfonate moiety acts as the catalyst in this process. Additionally, 2 is selectively encapsulated, even in mixtures of other structurally similar heterocycles like indole. Furthermore, the tautomeric state of 2 (amino isoindolone (2-A) and imino isoindolinone forms (2-I)) can be controlled by utilizing different guanidinium organosulfonate frameworks.

Anomalous Correlation between Thermal Conductivity and Elastic Modulus in Two-Dimensional Hybrid Metal Halide Perovskites

Device-level implementation of soft materials for energy conversion and thermal management demands a comprehensive understanding of their thermal conductivity and elastic modulus to mitigate thermo-mechanical challenges and ensure long-term stability. Thermal conductivity and elastic modulus are usually positively correlated in soft materials, such as amorphous macromolecules, which poses a challenge to discover materials that are either soft and thermally conductive or hard and thermally insulative. Here, we show anomalous correlations of thermal conductivity and elastic modulus in two-dimensional (2D) hybrid organic-inorganic perovskites (HOIP) by engineering the molecular interactions between organic cations. By replacing conventional alkyl-alkyl and aryl-aryl type organic interactions with mixed alkyl-aryl interactions, we observe an enhancement in elastic modulus with a reduction in thermal conductivity. This anomalous dependence provides a route to engineer thermal conductivity and elastic modulus independently and a guideline to search for better thermal management materials. Further, introducing chirality into the organic cation induces a molecular packing that leads to the same thermal conductivity and elastic modulus regardless of the composition across all half-chiral 2D HOIPs. This finding provides substantial leeway for further investigations in chiral 2D HOIPs to tune optoelectronic properties without compromising thermal and mechanical stability.

Tartronic Acid as a Potential Inhibitor of Pathological Calcium Oxalate Crystallization

Kidney stones are a pervasive disease with notoriously high recurrence rates that require more effective treatment strategies. Herein, tartronic acid is introduced as an efficient inhibitor of calcium oxalate monohydrate (COM) crystallization, which is the most prevalent constituent of human kidney stones. A combination of in situ experimental techniques and simulations are employed to compare the inhibitory effects of tartronic acid with those of its molecular analogs. Tartronic acid exhibits an affinity for binding to rapidly growing apical surfaces of COM crystals, thus setting it apart from other inhibitors such as citric acid, the current preventative treatment for kidney stones. Bulk crystallization and in situ atomic force microscopy (AFM) measurements confirm the mechanism by which tartronic acid interacts with COM crystal surfaces and inhibits growth. These findings are consistent with in vivo studies that reveal the efficacy of tartronic acid is similar to that of citric acid in mouse models of hyperoxaluria regarding their inhibitory effect on stone formation and alleviating stone-related physical harm. In summary, these findings highlight the potential of tartronic acid as a promising alternative to citric acid for the management of calcium oxalate nephropathies, offering a new option for clinical intervention in cases of kidney stones.

Modulation of the dissolution with ASP from a supersaturated solution on a bionic platform for gout pathology crystals

The core to the treatment of gout is the elimination of pathologic crystal, monosodium urate monohydrate (MSUM). The primary treatment available is to gradually dissolve the "culprit crystals" by lowering the blood uric acid concentration with medications, which often takes a long time and in severe cases must still be treated surgically. Herein, we developed a dynamic bionic platform based on a hydrogel composite membrane (HCM) to screen the direct facilitated solubilization of MSUM crystals by small organic molecules in bionic saturated, or even supersaturated, solutions. The customized and biologically safe (NAGA/PEGDA/NIPAM) HCM, which is consistent with the main amino acid composition of articular cartilage, well mimics the entire process of organic molecules leading to the dissolution of MSUM crystals in the joint system. With the verifications of this platform, it is shown that l-aspartic acid (ASP) significantly promotes the dissolution of MSUM crystals not only in saturated but also in supersaturated solutions. Furthermore, a novel mechanism called "crane effect" was used to explain this "dissolution effect" of ASP on MSUM, which stems from the ability of ASP to lock onto the surface of MSUM crystals through hydrogen bonding by virtue of its two carboxyl groups, and simultaneously its amino group lifts the uric acid molecules from the surface of MSUM crystals by virtue of interactions of hydrogen bonding. The results of bulk crystallization, scanning electron microscopy (SEM), powder X-diffraction (PXRD), and density-functional theory (DFT) studies are quantitatively consistent with this hypothetical "crane effect" mechanism. Hence, this HCM-based functional platform could provide entirely novel ideas and methods for drug design and screening for the treatment of pathological crystal diseases of gout.

Growth "self-inhibition" of irbesartan desmotrope: surface intra-annular tautomer inter-conversion is the culprit

The newly discovered growth self-inhibition phenomenon of tautomeric crystals is now generalized to the demostrope (form B) of irbesartan that displays intra-annular tautomerism in neutral aqueous solutions. The dynamic intra-annular tautomer inter-conversion on the surface is the key factor. Our findings provide implications for producing and engineering tautomeric materials.

Semiempirical Approach to the Fukui Function Analysis of Uric Acid under Different pH Conditions

Analytic Fukui functions calculated at a first-principles level are combined with experimental pKa values and the calculation of tautomerization energies to obtain the effective regioselectivity of uric acid toward electron-transfer reactions under different pH conditions. Second-order electron binding energies are also computed to determine which of the tautomers is more likely to participate in the electron transfer. A comparison of vertical and adiabatic proton detachment energies allows us to conclude that tautomerization is not mediating deprotonation and that two monoanionic species are of comparable relevance. The main difference between these monoanionic species is the ring that has been deprotonated. Both monoanionic species are produced from a single neutral tautomer and mainly produce a single dianionic tautomer. As a method for the analysis of systems affected by pH such as uric acid, we propose to plot condensed Fukui functions versus pH, allowing us to draw the effect of pH on the regioselectivity of electron transfer in a single image.

An Improved Model for Biogenic Ammonium Urate

The pathological crystallization of ammonium urate inside the urinary tract is a well-documented medical condition; however, structural studies of the biogenic material have proven challenging owing to its propensity to precipitate as a powder and to exhibit diffraction patterns with widely varying intensities. Using block Rietveld refinement methods of powder diffraction data, here we identify ammonium urate hydrate (AUH) as a likely component in natural uroliths. AUH has a planar 2-D hydrogen-bonded organic framework of urate ions separated by ammonium ions with water molecules residing in bisecting channels. AUH is stable up to 150 °C for short time periods but begins to decompose with prolonged heating times and/or at higher temperatures. Changes in the solid-state structure and composition of synthetic material over a temperature range from 25 to 300 °C are elucidated through thermogravimetric and spectroscopic data, combustion analysis, and time-resolved synchrotron powder X-ray diffraction studies. We contend that biogenic ammonium urate is more accurately modeled as a mixture of AUH and anhydrous ammonium urate, in ratios that can vary depending on the growth environment. The similar but not identical diffraction patterns of these two forms likely account for much of the variability seen in natural ammonium urate samples.

Probing the Boundary between Classical and Quantum Mechanics by Analyzing the Energy Dependence of Single-Electron Scattering Events at the Nanoscale

The relation between the energy-dependent particle and wave descriptions of electron-matter interactions on the nanoscale was analyzed by measuring the delocalization of an evanescent field from energy-filtered amplitude images of sample/vacuum interfaces with a special aberration-corrected electron microscope. The spatial field extension coincided with the energy-dependent self-coherence length of propagating wave packets that obeyed the time-dependent Schrödinger equation, and underwent a Goos-Hänchen shift. The findings support the view that wave packets are created by self-interferences during coherent-inelastic Coulomb interactions with a decoherence phase close to Δφ = 0.5 rad. Due to a strictly reciprocal dependence on energy, the wave packets shrink below atomic dimensions for electron energy losses beyond 1000 eV, and thus appear particle-like. Consequently, our observations inevitably include pulse-like wave propagations that stimulate structural dynamics in nanomaterials at any electron energy loss, which can be exploited to unravel time-dependent structure-function relationships on the nanoscale.