Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation

Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.

Kinetic and Thermodynamic Interplay of Polymer-Mediated Liquid-Liquid Phase Separation for Poorly Water-Soluble Drugs

Understanding the interplay between kinetics and thermodynamics of polymer-mediated liquid-liquid phase separation is crucial for designing and implementing an amorphous solid dispersion formulation strategy for poorly water-soluble drugs. This work investigates the phase behaviors of a poorly water-soluble model drug, celecoxib (CXB), in a supersaturated aqueous solution with and without polymeric additives (PVP, PVPVA, HPMCAS, and HPMCP). Drug-polymer-water ternary phase diagrams were also constructed to estimate the thermodynamic behaviors of the mixtures at room temperature. The liquid-liquid phase separation onset point for CXB was detected using an inline UV/vis spectrometer equipped with a fiber optic probe. Varying CXB concentrations were achieved using an accurate syringe pump throughout this study. The appearance of the transient nanodroplets was verified by cryo-EM and total internal reflection fluoresence microscopic techniques. The impacts of various factors, such as polymer composition, drug stock solution pumping rates, and the types of drug-polymer interactions, are tested against the onset points of the CXB liquid-liquid phase separation (LLPS). It was found that the types of drug-polymer interactions, i.e., hydrogen bonding and hydrophobic interactions, are vital to the position and shapes of LLPS in the supersaturation drug solution. A relation between the behaviors of LLPS and its location in the CXB-polymer-water ternary phase diagram was drawn from the findings.

The effect of ligands on the size distribution of copper nanoclusters: Insights from molecular dynamics simulations

Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesis involves a complex system of solvents, ligands, and copper precursors with intertwining effects on the size of the nanoclusters. We combine molecular dynamics simulations and density functional theory calculations to provide insights into the nucleation mechanism in the presence of a triphenyl phosphite ligand. We identify the crucial role of the strength of the metal-phosphine interaction in inhibiting the cluster's growth. We demonstrate computationally several practical routes to fine-tune the interaction strength by modifying the side groups of the additive. Our work provides molecular insights into the complex nucleation process of protected copper nanocrystals, which can assist in controlling their size distribution and, eventually, their morphology.

Structural Rearrangement Followed by Entrapment of Subnanometer Building Blocks of Iron Oxyhydroxide in Aqueous Iron Chloride Solutions

Iron oxyhydroxide, a natural nanophase of iron found in the environment, plays a crucial role in regulating surface and groundwater composition. Recent research proposes that within the nonclassical prenucleation cluster growth model, subnanometer-sized clusters (olation clusters/Fe13 δ-Keggin oxolation clusters) might act as the prenucleation clusters (PNCs) of ferrihydrite or iron oxyhydroxide solid phase. However, these clusters are difficult to characterize as they are only observable momentarily in low-pH, high-Fe concentration solutions before agglomerating into extended solids, keeping the controversy over the true nature of the PNCs alive. In this study, we introduce large quantities of zinc acetate salt (ZA) into iron chloride solutions at the olation-oxolation boundary (3.6 mM Fe3+ at pH ∼2.6). Remarkably, this manipulation is found to alter the structural arrangement of these subnanometer clusters before blocking them in isolation for hours, even at pH 6, where extended iron oxyhydroxide phases typically precipitate. On the other hand, controlled addition of ZA allows partial unblocking, leading to anisotropic agglomeration into cylindrical rod-like structures. Experimental techniques such as synchrotron-based small-angle X-ray scattering, X-ray absorption spectroscopy, high-resolution transmission electron microscopy (TEM), and cryo-TEM, along with density functional theory (DFT) calculations, reveal the nature of the structural rearrangement and the crucial role of Zn2+ ions in cluster stabilization.

Enhanced Nesquehonite Formation and Stability in the Presence of Dissolved Silica

One possible carbon dioxide sequestration strategy is via the carbonation of dissolved Mg2+ obtained through olivine ((Mg,Fe)2SiO4) dissolution. However, silica is also produced during the breakdown of olivine. This component may have a detrimental effect on the yield of Mg-carbonate as Mg2+ incorporation into complex Mg silicate phases would limit CO2 uptake by this system. Yet this potential competition is currently not considered. Here, we use crystal growth experiments at temperatures applicable for potential coastal applications to test the effect of silica on the formation of the hydrated Mg-carbonate phase nesquehonite (MgCO3·3H2O). Solution chemistry analysis coupled with phase identification demonstrates that the presence of silica in the solution can actually assist the formation of nesquehonite and increase its yield by as much as 60 times. Our findings suggest that the presence of silica changes interfacial stabilities, lowering the energetic barrier for nesquehonite nucleation. In addition, in situ attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) transformation experiments demonstrated that nesquehonite precipitating in a solution containing a high concentration of dissolved silica exhibits enhanced stability against its transformation into hydromagnesite. These findings will help to better constrain what we expect for applications of olivine during carbon remediation strategies as well as assist yields for industrial applications that use Mg-based cement as building materials to facilitate a CO2-neutral or negative footprint.

"Sounding" out crystal nuclei-A mathematical-physical and experimental investigation

We outline techniques for the control and measurement of the nucleation of crystalline materials. Small angle x-ray scattering/wide angle x-ray scattering x-ray diffraction measurements are presented that demonstrate the impact of low power, continuous, non-cavitational ultrasound on the nucleation and crystallization of a wax-n-eicosane dissolved in a heptane/toluene solvent. A mathematical-physical approach based on the rectification of heat and mass transport by such a low power oscillating pressure field is outlined, and it is suggested that this approach be combined with dissipative particle dynamics computational modeling to develop a predictive method capable of modeling the impact of low power oscillating pressure fields (acoustics and ultrasonics) on a wide range of nucleating systems. Combining the ultrasound pitch and catch speed of sound measurements with low power harmonically oscillating pressure fields to monitor and control nucleation presents the prospect of entirely new industrially significant methods of process control in crystallization. It also offers new insights into nucleation processes in general. However, for the acoustic control technique to be widely applied , further theoretical and modeling work will be necessary since, at present, we are unable to predict the precise effect of low power ultrasound in any given situation.

Sulfate mineral scaling: From fundamental mechanisms to control strategies

Sulfate scaling, as insoluble inorganic sulfate deposits, can cause serious operational problems in various industries, such as blockage of membrane pores and subsurface media and impairment of equipment functionality. There is limited article to bridge sulfate formation mechanisms with field scaling control practice. This article reviews the molecular-level interfacial reactions and thermodynamic basis controlling homogeneous and heterogeneous sulfate mineral nucleation and growth through classical and non-classical pathways. Common sulfate scaling control strategies were also reviewed, including pretreatment, chemical inhibition and surface modification. Furthermore, efforts were made to link the fundamental theories with industrial scale control practices. Effects of common inhibitors on different steps of sulfate formation pathways (i.e., ion pair and cluster formation, nucleation, and growth) were thoroughly discussed. Surface modifications to industrial facilities and membrane units were clarified as controlling either the deposition of homogeneous precipitates or the heterogeneous nucleation. Future research directions in terms of optimizing sulfate chemical inhibitor design and improving surface modifications are also discussed. This article aims to keep the readers abreast of the latest development in mechanistic understanding and control strategies of sulfate scale formation and to bridge knowledge developed in interfacial chemistry with engineering practice.

Extracellular DNA: A Missing Link in the Pathogenesis of Ectopic Mineralization

Although deoxyribonucleic acid (DNA) is the genetic coding for the very essence of life, these macromolecules or components thereof are not necessarily lost after a cell dies. There appears to be a link between extracellular DNA and biomineralization. Here the authors demonstrate that extracellular DNA functions as an initiator of collagen intrafibrillar mineralization. This is confirmed with in vitro and in vivo biological mineralization models. Because of their polyanionic property, extracellular DNA molecules are capable of stabilizing supersaturated calcium phosphate solution and mineralizing 2D and 3D collagen matrices completely as early as 24 h. The effectiveness of extracellular DNA in biomineralization of collagen is attributed to the relatively stable formation of amorphous liquid droplets triggered by attraction of DNA to the collagen fibrils via hydrogen bonding. These findings suggest that extracellular DNA is biomimetically significant for fabricating inorganic-organic hybrid materials for tissue engineering. DNA-induced collagen intrafibrillar mineralization provides a clue to the pathogenesis of ectopic mineralization in different body tissues. The use of DNase for targeting extracellular DNA at destined tissue sites provides a potential solution for treatment of diseases associated with ectopic mineralization.

Direct observation of crystal nucleation and growth in a quasi-two-dimensional nonvibrating granular system

We study a quasi-two-dimensional macroscopic system of magnetic spherical particles settled on a shallow concave dish under a temporally oscillating magnetic field. The system reaches a stationary state where the energy losses from collisions and friction with the concave dish surface are compensated by the continuous energy input coming from the oscillating magnetic field. Random particle motions show some similarities with the motions of atoms and molecules in a glass or a crystal-forming fluid. Because of the curvature of the surface, particles experience an additional force toward the center of the concave dish. When decreasing the magnetic field, the effective temperature is decreased and diffusive particle motion slows. For slow cooling rates we observe crystallization, where the particles organize into a hexagonal lattice. We study the birth of the crystalline nucleus and the subsequent growth of the crystal. Our observations support nonclassical theories of crystal formation. Initially a dense amorphous aggregate of particles forms, and then in a second stage this aggregate rearranges internally to form the crystalline nucleus. As the aggregate grows, the crystal grows in its interior. After a certain size, all the aggregated particles are part of the crystal and after that crystal growth follows the classical theory for crystal growth.

Self-assembling, structure and nonlinear optical properties of fluorescent organic nanoparticles in water

Owing to their intense emission, low toxicity and solubility in aqueous medium, fluorescent organic nanoparticles (FONs) have emerged as promising alternatives to inorganic ones for the realization of exogenous probes for bioimaging applications. However, the intimate structure of FONs in solution, as well as the role played by intermolecular interactions on their optical properties, remains challenging to study. Following a recent Second-Harmonic Scattering (SHS) investigation led by two of us [Daniel et al., ACS Photonics, 2015, 2, 1209], we report herein a computational study of the structural organization and second-order nonlinear optical (NLO) properties of FONs based on dipolar chromophores incorporating a hydrophobic triphenylamine electron-donating unit and a slightly hydrophilic aldehyde electron-withdrawing unit at their extremities. Molecular dynamics simulations of the FON formation in water are associated with quantum chemical calculations, to provide insight into the molecular aggregation process, the molecular orientation of the dipolar dyes within the nanoparticles, and the dynamical behavior of their NLO properties. Moreover, the impact of intermolecular interactions on the NLO responses of the FONs is investigated by employing the tight-binding version of the recently developed simplified time-dependent density functional theory (sTD-DFT) approach, allowing the all-atom quantum mechanics treatment of nanoparticles.

Formation and Evolution of Nanoscale Calcium Phosphate Precursors under Biomimetic Conditions

Simulated body fluids (SBFs) that mimic human blood plasma are widely used media for in vitro studies in an extensive array of research fields, from biomineralization to surface and corrosion sciences. We show that these solutions undergo dynamic nanoscopic conformational rearrangements on the timescale of minutes to hours, even though they are commonly considered stable or metastable. In particular, we find and characterize nanoscale inhomogeneities made of calcium phosphate (CaP) aggregates that emerge from homogeneous SBFs within a few hours and evolve into prenucleation species (PNS) that act as precursors in CaP crystallization processes. These ionic clusters consist of ∼2 nm large spherical building units that can aggregate into suprastructures with sizes of over 200 nm. We show that the residence times of phosphate ions in the PNS depend critically on the total PNS surface. These findings are particularly relevant for understanding nonclassical crystallization phenomena, in which PNS are assumed to act as building blocks for the final crystal structure.

Variation in Properties of Pre-Nucleation Calcium Carbonate Clusters Induced by Aggregation: A Molecular Dynamics Study

Numerous studies have speculated calcium carbonate (CaCO3) nucleation induced by pre-nucleation clusters (PNCs) aggregation. However, it is challenging for experiments to directly obtain the relationship between PNCs aggregation and nucleation. Herein, we employ molecular dynamics simulations to explore the variation during PNCs aggregation, which can describe the beginning stage of CaCO3 nucleation induced by PNCs aggregation in supersaturated solutions. The results reveal that the formation of CaCO3 nucleus consists of PNCs spontaneous growth, PNCs solubility equilibrium, and aggregation of PNCs inducing nucleation. The PNCs aggregation, accompanied by the variation in the configuration and stability of CaCO3 aggregate, breaks the solubility equilibrium of PNCs and creates conditions for the formation of the more stable nucleus. Besides, the CaCO3 nucleus with the higher coordination number and the lower hydration number form when decreasing the CaCO3 concentration or increasing the temperature. This work not only sheds light on the formation of the CaCO3 nucleus but also contributes to the explanation for CaCO3 polymorphism.

Selective Synthesis of α-, β-, and γ-Ag2WO4 Polymorphs: Promising Platforms for Photocatalytic and Antibacterial Materials

Silver tungstate (Ag₂WO₄) shows structural polymorphism with different crystalline phases, namely, orthorhombic, hexagonal, and cubic structures that are commonly known as α, β, and γ, respectively. In this work, these Ag₂WO₄ polymorphs were selectively and successfully synthesized through a simple precipitation route at ambient temperature. The polymorph-controlled synthesis was conducted by means of the volumetric ratios of the silver nitrate/tungstate sodium dehydrate precursors in solution. The structural and electronic properties of the as-synthesized Ag₂WO₄ polymorphs were investigated by using a combination of X-ray diffraction and Rietveld refinements, X-ray absorption spectroscopy, X-ray absorption near-edge structure spectroscopy, field-emission scanning electron microscopy images, and photoluminescence. To complement and rationalize the experimental results, first-principles calculations, at the density functional theory level, were carried out, leading to an unprecedented glimpse into the atomic-level properties of the morphology and the exposed surfaces of Ag₂WO₄ polymorphs. Following the analysis of the local coordination of Ag and W cations (clusters) at each exposed surface of the three polymorphs, the structure-property relationship between the morphology and the photocatalytic and antibacterial activities against amiloride degradation under ultraviolet light irradiation and methicillin-resistant Staphylococcus aureus, respectively, was investigated. A possible mechanism of the photocatalytic and antibacterial activity as well the formation process and growth of the polymorphs is also explored and proposed.

Involvement of prenucleation clusters in calcium phosphate mineralization of collagen

Involvement of thermodynamically-stable prenucleation clusters (PNCs) in the biomineralization of collagen has been speculated since their existence was reported in mineralization systems. It has been hypothesized that intrafibrillar mineralization proceeds via nucleation of inhibitor-stabilized intermediates produced by liquid-liquid separation (aka. polymer-induced liquid precursors; PILPs). Here, the contribution of PNCs and PILPs to calcium phosphate intrafibrillar mineralization of collagen was examined in a model with a semipermeable membrane that excludes nucleation inhibitor-stabilized PILPs from reaching the collagen fibrils, using cryogenic electron microscopy of reconstituted fibrils and conventional transmission electron microscopy of collagen sponges. Molecular dynamics simulation with the Interface force field (IFF) was used to confirm the existence of PILPs with amorphous calcium phosphate and elucidate details of the dynamics. Furthermore, intrafibrillar mineralization of single collagen fibrils was experimentally observed with unstabilized PNCs when anionic/cationic polyelectrolytes were used to establish Donnan equilibrium across the semipermeable membrane. Molecular dynamics simulation verified PNC formation within the collagen intrafibrillar gap zones at the atomic scale and explained the role of external PILPs. The PILPs decrease the interfibrillar water content and increase the interfibrillar ionic concentration. Nevertheless, intrafibrillar mineralization of collagen sponges with PNCs alone was inefficacious, being constrained by competition from extrafibrillar mineral precipitation. STATEMENT OF SIGNIFICANCE: Compared with conventional PILP-based intrafibrillar mineralization, mineralization of collagen fibrils using unstabilized PNCs is constrained by competition from extrafibrillar mineral deposition. The narrow window of opportunity for PNCs to produce intrafibrillar mineralization provides a plausible explanation for the feasibility of nucleation inhibitor-free intrafibrillar apatite assembly during reconstitution of type I collagen.

Homogeneous nucleation of sheared liquids: advances and insights from simulations and theory

One of the most ubiquitous and technologically important phenomena in nature is the nucleation of homogeneous flowing systems. The microscopic effects of shear on a nucleating system are still imperfectly understood, although in recent years a consistent picture has emerged. The opposing effects of shear can be split into two major contributions for simple atomic and molecular liquids: increase of the energetic cost of nucleation, and enhancement of the kinetics. In this perspective, we describe the latest computational and theoretical techniques which have been developed over the past two decades. We collate and unify the overarching influences of shear, temperature, and supersaturation on the process of homogeneous nucleation. Experimental techniques and capabilities are discussed, against the backdrop of results from simulations and theory. Although we primarily focus on simple systems, we also touch upon the sheared nucleation of more complex systems, including glasses and polymer melts. We speculate on the promising directions and possible advances that could come to fruition in the future.

A conceptual change in crystallisation mechanisms of oxide materials from solutions in closed systems

Atomic and molecular level interactions in solutions dictate the structural and functional attributes of crystals. These features clearly dictate the properties of materials and their applicability in technologies. However, the microscopic phenomena of particle formation-nucleation and growth-in real systems are still not fully understood. Specifically, crystallisation occurring in closed systems are largely unproven. Combining coherent experimental data, we here demonstrate a fundamental nucleation-growth mechanism that occurs in a model zinc oxide system when particles are formed under continuous, rapid heating under closed reaction conditions. Defying all previous reports, we show that the nucleation commences only when the heating is terminated. A prenucleation clusters pathway is observed for nucleation, followed by crystallite assembly-growth. We show that the nucleation-growth processes result from temporal and dynamic activity of constituent ions and gaseous molecules in solution and by the irreversible expulsion of the dissolved gaseous molecules. We suggest that this nucleation process is generic to most closed systems that go through precipitation, and, therefore, important for the crystallisation of a variety of metal oxides, composites and minerals. We anticipate that the work may be a platform for future experimental and theoretical investigation promoting deeper understanding of the nucleation-growth phenomena of a variety of practical systems.

Molecular evolution pathways during nucleation of small organic molecules: solute-rich pre-nucleation species enable control over the nucleation process

Increasing evidence has shown that nucleation pathways involving disordered pre-nucleation species exist in the nucleation process of many types of solid state products, especially inorganic solid state products. Studying the thermodynamic and kinetic properties of these pre-nucleation species is crucial to understand and control the nucleation process of solid state products. In this work, the evolution pathway of molecular or supramolecular structures during the nucleation process was investigated by using 2-cyano-4'-methylbiphenyl (OTBN) as a model compound. In the resultant solutions, similar pre-nucleation clusters were analyzed and characterized by dynamic light scattering (DLS), small-angle X-ray scattering (SAXS) and nanoparticle tracking analysis (NTA). It was found that the clusters were disordered and liquid-like and did not represent any of the known OTBN condensed phases. They were of interest since they may be the key sites for the formation of new crystal nuclei of OTBN. It was demonstrated that the change in the solvation effect would drive the pre-nucleation clusters to exhibit very different structures. How the clusters vary with concentration and temperature, and how they differ before and after nucleation have been systematically studied. In addition, the molecular dynamics of the evolution of clusters, the effect of initial mixing process on clusters and the nucleation dynamics were also investigated. The results suggested that the pre-nucleation clusters played a key role in the process of crystallization of organic small molecules, indicating that the dynamics of nucleation could be regulated by changing the structure and size of the pre-nulceation clusters.

Assessing the Onset of Calcium Phosphate Nucleation by Hyperpolarized Real-Time NMR

We report an experimental approach for high-resolution real-time monitoring of transiently formed species occurring during the onset of precipitation of ionic solids from solution. This is made possible by real-time nuclear magnetic resonance (NMR) monitoring using dissolution dynamic nuclear polarization (D-DNP) to amplify signals of functional intermediates and is supported by turbidimetry, cryogenic electron microscopy, and solid-state NMR measurements. D-DNP can provide drastic signal improvements in NMR signal amplitudes, permitting dramatic reductions in acquisition times and thereby enabling us to probe fast interaction kinetics such as those underlying formation of prenucleation species (PNS) that precede solid–liquid phase separation. This experimental strategy allows for investigation of the formation of calcium phosphate (CaP)-based minerals by ³¹P NMR—a process of substantial industrial, geological, and biological interest. Thus far, many aspects of the mechanisms of CaP nucleation remain unclear due to the absence of experimental methods capable of accessing such processes on sufficiently short time scales. The approach reported here aims to address this by an improved characterization of the initial steps of CaP precipitation, permitting detection of PNS by NMR and determination of their formation rates, exchange dynamics, and sizes. Using D-DNP monitoring, we find that under our conditions (i) in the first 2 s after preparation of oversaturated calcium phosphate solutions, PNS with a hydrodynamic radius of R_h ≈ 1 nm is formed and (ii) following this rapid initial formation, the entire crystallization processes proceed on considerably longer time scales, requiring >20 s to form the final crystal phase.

Strategy to control magnetic coercivity by elucidating crystallization pathway-dependent microstructural evolution of magnetite mesocrystals

Mesocrystals are assemblies of smaller crystallites and have attracted attention because of their nonclassical crystallization pathway and emerging collective functionalities. Understanding the mesocrystal crystallization mechanism in chemical routes is essential for precise control of size and microstructure, which influence the function of mesocrystals. However, microstructure evolution from the nucleus stage through various crystallization pathways remains unclear. We propose a unified model on the basis of the observation of two crystallization pathways, with different ferric (oxyhydr)oxide polymorphs appearing as intermediates, producing microstructures of magnetite mesocrystal via different mechanisms. An understanding of the crystallization mechanism enables independent chemical control of the mesocrystal diameter and crystallite size, as manifested by a series of magnetic coercivity measurements. We successfully implement an experimental model system that exhibits a universal crystallite size effect on the magnetic coercivity of mesocrystals. These findings provide a general approach to controlling the microstructure through crystallization pathway selection, thus providing a strategy for controlling magnetic coercivity in magnetite systems.

Transient metastable intermediates play an important role in the crystallization process. Here, the authors unveil the microstructural changes in magnetite mesocrystals that depend on the intermediate polymorphism and the universal crystallite size effect on the magnetic coercivity of mesocrystals.

Shaping Magnetite with Poly-l-arginine and pH: From Small Single Crystals to Large Mesocrystals

Control over particle size, size distribution, and colloidal stability are central aims in producing functional nanomaterials. Recently, biomimetic approaches have been successfully used to enhance control over properties in the synthesis of those materials. Magnetotactic bacteria produce protein-stabilized magnetite away from its thermodynamic equilibrium structure. Mimicking the bacteria's proteins using poly-l-arginine we show that by simply increasing the pH, the dimensions of magnetite increase and a single- to mesocrystal transformation is induced. Using synchrotron X-ray diffraction and transmission electron microscopy, we show that magnetite nanoparticles with narrow size distributions and average diameters of 10 ± 2 nm for pH 9, 20 ± 2 nm for pH 10, and up to 40 ± 4 nm for pH 11 can be synthesized. We thus selectively produce superparamagnetic and stable single-domain particles merely by controlling the pH. Remarkably, while an increase in pH brings about a thermodynamically driven decrease in size for magnetite without additives, this dependency on pH is inverted when poly-l-arginine is present.

Entropic colloidal crystallization pathways via fluid-fluid transitions and multidimensional prenucleation motifs

Complex crystallization pathways are common in protein crystallization, tetrahedrally coordinated systems, and biomineralization, where single or multiple precursors temporarily appear before the formation of the crystal. The emergence of precursors is often explained by a unique property of the system, such as short-range attraction, directional bonding, or ion association. But, structural characteristics of the prenucleation phases found in multistep crystallization remain unclear, and models are needed for testing and expanding the understanding of fluid-to-solid ordering pathways. Here, we report 3 instances of 2-step crystallization of hard-particle fluids. Crystallization in these systems proceeds via a high-density precursor fluid phase with prenucleation motifs in the form of clusters, fibers and layers, and networks, respectively. The density and diffusivity change across the fluid-fluid phase transition increases with motif dimension. We observe crystal nucleation to be catalyzed by the interface between the 2 fluid phases. The crystals that form are complex, including, notably, a crystal with 432 particles in the cubic unit cell. Our results establish the existence of complex crystallization pathways in entropic systems and reveal prenucleation motifs of various dimensions.

Characterizing key features in the formation of ice and gas hydrate systems

Crystallization in liquids is critical to a range of important processes occurring in physics, chemistry and life sciences. In this article, we review our efforts towards understanding the crystallization mechanisms, where we focus on theoretical modelling and molecular simulations applied to ice and gas hydrate systems. We discuss the order parameters used to characterize molecular ordering processes and how different order parameters offer different perspectives of the underlying mechanisms of crystallization. With extensive simulations of water and gas hydrate systems, we have revealed unexpected defective structures and demonstrated their important roles in crystallization processes. Nucleation of gas hydrates can in most cases be characterized to take place in a two-step mechanism where the nucleation occurs via intermediate metastable precursors, which gradually reorganizes to a stable crystalline phase. We have examined the potential energy landscapes explored by systems during nucleation, and have shown that these landscapes are rugged and funnel-shaped. These insights provide a new framework for understanding nucleation phenomena that has not been addressed in classical nucleation theory. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'.

Thermodynamically driven assemblies and liquid-liquid phase separations in biology

The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical origin of such organization is not fully understood, and even though it is clear that cells and organisms cannot maintain their integrity without consuming energy, there is growing evidence that individual assembly processes can be thermodynamically driven and occur spontaneously due to changes in thermodynamic variables such as intermolecular interactions and concentration. Understanding the phase separation in vivo requires a multidisciplinary approach, integrating the theory and physics of phase separation with experimental and computational techniques. This paper aims at providing a brief overview of the physics of phase separation and its biological implications, with a particular focus on the assembly of membraneless organelles. We discuss the underlying physical principles of phase separation from its thermodynamics to its kinetics. We also overview the wide range of methods utilized for experimental verification and characterization of phase separation of membraneless organelles, as well as the utility of molecular simulations rooted in thermodynamics and statistical physics in understanding the governing principles of thermodynamically driven biological self-assembly processes.

Development of a novel CaCO3 PILP based cementation method for quartz sand

Development and investigation of a cementation method for soil grade quartz sand by utilizing aqueous Polymer Induced Liquid Precursor (PILP) solutions.

Rationalising crystal nucleation of organic molecules in solution using artificial neural networks

Artificial neural network modelling is used to analyse and predict primary nucleation based on various physicochemical solute and solvent parameters.

Modeling Dissolution-Precipitation Kinetics of Alkali-Activated Metakaolin

The numerical model HydratiCA was used to simulate the reaction kinetics of alkali-activated metakaolin, a material belonging to a class of sustainable binders alternative to Portland cement. The full chemistry of the system, including solid phases and aqueous species, is taken into account in these simulations. Specifically, metakaolin dissolution, reaction product nucleation and growth, and ion speciation, and diffusion in solution are simulated. The sodium aluminosilicate (N-A-S-H), formed by the reaction of metakaolin in alkaline solution, is implemented in the model as a combination of co-precipitating pseudo-zeolitic phases, with variable stoichiometry. The results show how variations of the reaction pathways, occurring when alkaline activators of different composition and concentration are used, can be associated with different macroscopic behaviors in terms of mechanical performance and durability. Reconciling these macroscopic properties with the basic chemical processes will be a fundamental technological challenge for the deployment of sustainable technologies in the construction industry.

Crystallization of Organic Molecules: Nonclassical Mechanism Revealed by Direct Imaging

Organic crystals are of primary importance in pharmaceuticals, functional materials, and biological systems; however, organic crystallization mechanisms are not well-understood. It has been recognized that "nonclassical" organic crystallization from solution involving transient amorphous precursors is ubiquitous. Understanding how these precursors evolve into crystals is a key challenge. Here, we uncover the crystallization mechanisms of two simple aromatic compounds (perylene diimides), employing direct structural imaging by cryogenic electron microscopy. We reveal the continuous evolution of density, morphology, and order during the crystallization of very different amorphous precursors (well-defined aggregates and diffuse dense liquid phase). Crystallization starts from initial densification of the precursors. Subsequent evolution of crystalline order is gradual, involving further densification concurrent with optimization of molecular ordering and morphology. These findings may have implications for the rational design of organic crystals.

Enhanced bioactivity and osteoinductivity of carboxymethyl chitosan/nanohydroxyapatite/graphene oxide nanocomposites

Tissue engineering approaches combine a bioscaffold with stem cells to provide biological substitutes that can repair bone defects and eventually improve tissue functions. The prospective bioscaffold should have good osteoinductivity. Surface chemical and roughness modifications are regarded as valuable strategies for developing bioscaffolds because of their positive effects on enhancing osteogenic differentiation. However, the synergistic combination of the two strategies is currently poorly studied. In this work, a nanoengineered scaffold with surface chemistry (oxygen-containing groups) and roughness (R_q = 74.1 nm) modifications was fabricated by doping nanohydroxyapatite (nHA), chemically crosslinked graphene oxide (GO) and carboxymethyl chitosan (CMC). The biocompatibility and osteoinductivity of the nanoengineered CMC/nHA/GO scaffold was evaluated in vitro and in vivo, and the osteogenic differentiation mechanism of the nanoengineered scaffold was preliminarily investigated. Our data demonstrated that the enhanced osteoinductivity of CMC/nHA/GO may profit from the surface chemistry and roughness, which benefit the β1 integrin interactions with the extracellular matrix and activate the FAK–ERK signaling pathway to upregulate the expression of osteogenic special proteins. This study indicates that the nanocomposite scaffold with surface chemistry and roughness modifications could serve as a novel and promising bone substitute for tissue engineering.

The CMC/nHA/GO scaffold with the surface chemistry and roughness dual effects and the release of phosphate and calcium ions synergistically assist the mineralization and facilitate the bone regeneration.

Phase transition dynamics of single optically trapped aqueous potassium carbonate particles

This study reveals that complex multiple processes occur during efflorescence and deliquescence in unsupported, submicron sized particles.

Polymorphic phase transitions: Macroscopic theory and molecular simulation

Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic transitions in an accessible way, rather than claiming completeness. With exciting prospects in both simulation methods development and enhancements in computer hardware, we are on the verge of accessing an unprecedented capability for designing and developing dosage forms and drug delivery systems in silico, including tackling challenges in polymorph control on a rational basis.

Kinetics and polymorphs of yeast prion Sup35NM amyloidogenesis

Amyloidogenic proteins often form many types of aggregates, which are a critical determinant of cytotoxicity and tissue specificity. However, the molecular mechanisms underlying the generation of distinct amyloids and their influence on cells remain largely unknown. We herein investigated the polymorphic amyloid formation of the yeast prion protein, Sup35NM, an intrinsically disordered N-terminal fragment of Sup35, under various conditions and its potential relationship to cytotoxicity. Sup35NM aggregated to amyloid fibrils with distinct kinetics, structures, morphologies, tinctorial properties, and conformational stabilities depending on the concentration of NaCl, pH, and temperature, indicating the polymorphic amyloidogenesis of Sup35NM. Detailed kinetic analyses of Sup35NM amyloid formation revealed a strong inverse correlation between the lag time and elongation rate without a correlation between kinetic and structural parameters. These results suggest that kinetic polymorphisms due to distinct nucleation and elongation rates result in structural polymorphs of amyloid fibrils, and also that conditions that enhance or inhibit the nucleation of Sup35NM promote or delay fibril growth. The deleterious effects of polymorphic Sup35NM amyloid fibrils on membrane integrity and cell vitality were minimal. We hypothesize that the innocuous polymorphic nature of Sup35NM amyloid fibrils may be beneficial for gaining time for prion infection prior to cell death.

Induction time of a polymorphic transformation

We analyze the processes governing the lifetimes of transient metastable polymorphs, within the context of classical nucleation theory.

Facile Fabrication of Sandwich Structured WO3 Nanoplate Arrays for Efficient Photoelectrochemical Water Splitting

Herein, sandwich structured tungsten trioxide (WO3) nanoplate arrays were first synthesized for photoelectrochemical (PEC) water splitting via a facile hydrothermal method followed by an annealing treatment. It was demonstrated that the annealing temperature played an important role in determining the morphology and crystal phase of the WO3 film. Only when the hydrothermally prepared precursor was annealed at 500 °C could the sandwich structured WO3 nanoplates be achieved, probably due to the crystalline phase transition and increased thermal stress during the annealing process. The sandwich structured WO3 photoanode exhibited a photocurrent density of 1.88 mA cm(-2) and an incident photon-to-current conversion efficiency (IPCE) as high as 65% at 400 nm in neutral Na2SO4 solution under AM 1.5G illumination. To our knowledge, this value is one of the best PEC performances for WO3 photoanodes. Meanwhile, simultaneous hydrogen and oxygen evolution was demonstrated for the PEC water splitting. It was concluded that the high PEC performance should be attributed to the large electrochemically active surface area and active monoclinic phase. The present study can provide guidance to develop highly efficient nanostructured photoelectrodes with the favorable morphology.

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.