The elementary reactions for incorporation into crystals.

The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.

Particle dispersion through porous media with heterogeneous attractions.

Porous media used in many practical applications contain natural spatial variations in composition and surface charge that lead to heterogeneous physicochemical attractions between the media and transported particles. We performed Stokesian dynamics (SD) simulations to examine the effects of heterogeneous attractions on quiescent diffusion and hydrodynamic dispersion of particles within geometrically ordered arrays of nanoposts. We find that transport under quiescent conditions occurs by two mechanisms, diffusion through the void space and intermittent hopping between the attractive wells of different nanoposts. As the attraction heterogeneity increases, the latter mechanism becomes dominant, resulting in an increase in the particle trajectory tortuosity, deviations from Gaussian behavior in the particle displacement distributions, and a decrease in the long-time particle diffusivity. Similarly, under flow conditions corresponding to low Péclet number (Pe), increased attraction heterogeneity leads to transient localization near the nanoposts, resulting in a broadening of the particle distribution and enhanced longitudinal dispersion in the direction of flow. At high Pe where advection strongly dominates, however, the longitudinal dispersion coefficient is insensitive to attraction heterogeneity and exhibits Taylor-Aris dispersion behavior. Our findings provide insight into how heterogeneous interactions may influence particle transport in complex 3-D porous media.

In Situ Imaging of Faujasite Surface Growth Reveals Unique Pathways of Zeolite Crystallization.

Zeolite crystallization occurs by complex processes involving a variety of possible mechanisms. The sol gel media used to prepare zeolites leads to heterogeneous mixtures of solution and solid states with diverse solute species. At later stages of zeolite synthesis when growth occurs predominantly from solution, classical two-dimensional nucleation and spreading of layers on crystal surfaces via the addition of soluble species is the dominant pathway. At earlier stages, these processes occur in parallel with nonclassical pathways involving crystallization by particle attachment (CPA). The relative roles of solution- and solid-state species in zeolite crystallization have been a subject of debate. Here, we investigate the growth mechanism of a commercially relevant zeolite, faujasite (FAU). In situ atomic force microscopy (AFM) measurements reveal that supernatant solutions extracted from a conventional FAU synthesis at various times do not result in growth, indicating that FAU growth predominantly occurs from the solid state through a disorder-to-order transition of amorphous precursors. Elemental analysis shows that supernatant solutions are significantly more siliceous than both the original growth mixture and the FAU zeolite product; however, in situ AFM studies using a dilute clear solution with a lower Si/Al ratio revealed three-dimensional growth of surfaces that is distinct from layer-by-layer and CPA pathways. This unique mechanism of growth differs from those observed in studies of other zeolites. Given that relatively few zeolite frameworks have been the subject of mechanistic investigation by in situ techniques, these observations of FAU crystallization raise the question whether its growth pathway is characteristic of other zeolite structures.

pH response of sequence-controlled polyampholyte brushes.

We use molecular simulation to investigate the pH response of sequence-controlled polyampholyte brushes (PABs) with polymer chains consisting of alternating blocks of weakly acidic and basic monomers. Changes in the ionization state, height, lateral structure, and chain conformations of PABs with pH are found to differ qualitatively from those observed for polyelectrolyte brushes. Grafting density has a relatively modest effect on PAB properties. By contrast, monomer sequence strongly affects the pH response, with the extent of the response increasing with the block size. This trend is attributed to strong electrostatic attractions between oppositely charged blocks, which lead to an increase in chain backfolding as block size increases. This behavior is consistent with that observed for polyampholytes with similar monomer sequences in solution in previous studies. Our study shows that monomer sequence can be used to tune the pH response of weak PABs to generate stimuli-responsive surfaces.

Spatiotemporal Coke Coupling Enhances para-Xylene Selectivity in Highly Stable MCM-22 Catalysts.

Identifying zeolite catalysts that can simultaneously optimize p-xylene selectivity and feed utilization is critical to toluene alkylation with methanol (TAM). Here, we show that zeolite MCM-22 (MWW) has an exceptional catalyst lifetime in the TAM reaction at high operating pressure, conversion, and selectivity. We systematically probe the catalytic behavior of active sites in distinct topological features of MCM-22, revealing that high p-xylene yield and catalyst stability are predominantly attributed to sinusoidal channels and supercages, respectively. Using a combination of catalyst design and testing, density functional theory, and molecular dynamics simulations, we propose a spatiotemporal coke coupling phenomenon to explain a multistage p-xylene selectivity profile wherein the formation of light coke in supercages initiates the deactivation of unselective external surface sites. Our findings indicate that the specific nature of coke is critical to catalyst performance. Moreover, they provide unprecedented insight into the synchronous roles of distinct topological features giving rise to the exceptional stability and selectivity of MCM-22 in the TAM reaction.

Precrystallization solute assemblies and crystal symmetry.

Solution crystallization is a part of the synthesis of materials ranging from geological and biological minerals to pharmaceuticals, fine chemicals, and advanced electronic components. Attempts to predict the structure, growth rates and properties of emerging crystals have been frustrated, in part, by the poor understanding of the correlations between the oligomeric state of the solute, the growth unit, and the crystal symmetry. To explore how a solute monomer or oligomer is selected as the unit that incorporates into kinks and how crystal symmetry impacts this selection, we combine scanning probe microscopy, optical spectroscopy, and all-atom molecular simulations using as examples two organic materials, olanzapine (OZPN) and etioporphyrin I (EtpI). The dominance of dimeric structures in OZPN crystals has spurred speculation that the dimers preform in the solution, where they capture the majority of the solute, and then assemble into crystals. By contrast, EtpI in crystals aligns in parallel stacks of flat EtpI monomers unrelated by point symmetry. Raman and absorption spectroscopies show that solute monomers are the majority solute species in solutions of both compounds. Surprisingly, the kinetics of incorporation of OZPN into kinks is bimolecular, indicating that the growth unit is a solute dimer, a minority solution component. The disconnection between the dominant solute species, the growth unit, and the crystal symmetry is even stronger with EtpI, for which the (010) face grows by incorporating monomers, whereas the growth unit of the (001) face is a dimer. Collectively, the crystallization kinetics results with OZPN and EtpI establish that the structures of the dominant solute species and of the incorporating solute complex do not correlate with the symmetry of the crystal lattice. In a broader context, these findings illuminate the immense complexity of crystallization scenarios that need to be explored on the road to the understanding and control of crystallization.

Signatures of sluggish dynamics and local structural ordering during ice nucleation.

We investigate the microscopic pathway of spontaneous crystallization in the ST2 model of water under deeply supercooled conditions via unbiased classical molecular dynamics simulations. After quenching below the liquid-liquid critical point, the ST2 model spontaneously separates into low-density liquid (LDL) and high-density liquid phases, respectively. The LDL phase, which is characterized by lower molecular mobility and enhanced structural order, fosters the formation of a sub-critical ice nucleus that, after a stabilization time, develops into the critical nucleus and grows. Polymorphic selection coincides with the development of the sub-critical nucleus and favors the formation of cubic (Ic) over hexagonal (Ih) ice. We rationalize polymorphic selection in terms of geometric arguments based on differences in the symmetry of second neighbor shells of ice Ic and Ih, which are posited to favor formation of the former. The rapidly growing critical nucleus absorbs both Ic and Ih crystallites dispersed in the liquid phase, a crystal with stacking faults. Our results are consistent with, and expand upon, recent observations of non-classical nucleation pathways in several systems.

Finned zeolite catalysts.

There is growing evidence for the advantages of synthesizing nanosized zeolites with markedly reduced internal diffusion limitations for enhanced performances in catalysis and adsorption. Producing zeolite crystals with sizes less than 100 nm, however, is non-trivial, often requires the use of complex organics and typically results in a small product yield. Here we present an alternative, facile approach to enhance the mass-transport properties of zeolites by the epitaxial growth of fin-like protrusions on seed crystals. We validate this generalizable methodology on two common zeolites and confirm that fins are in crystallographic registry with the underlying seeds, and that secondary growth does not impede access to the micropores. Molecular modelling and time-resolved titration experiments of finned zeolites probe internal diffusion and reveal substantial improvements in mass transport, consistent with catalytic tests of a model reaction, which show that these structures behave as pseudo-nanocrystals with sizes commensurate to that of the fin. This approach could be extended to the rational synthesis of other zeolite and aluminosilicate materials.

Factors controlling the molecular modification of one-dimensional zeolites.

Interactions between organic molecules and inorganic materials are ubiquitous in many applications and often play significant roles in directing pathways of crystallization. It is frequently debated whether kinetics or thermodynamics plays a more prominent role in the ability of molecular modifiers to impact crystal nucleation and growth processes. In the case of nanoporous zeolites, approaches in rational design often capitalize on the ability of organics, used as either modifiers or structure-directing agents, to markedly impact the physicochemical properties of zeolites. It has been demonstrated for multiple topologies that modifier-zeolite interactions can alter crystal size and morphology, yet few studies have distinguished the roles of thermodynamics and kinetics. We use a combination of calorimetry and molecular modeling to estimate the binding energies of organics on zeolite surfaces and correlate these results with synthetic trends in crystal morphology. Our findings reveal unexpectedly small energies of interaction for a range of modifiers with two zeolite structures, indicating the effect of organics on zeolite crystal surface free energy is minor and kinetic factors most likely govern growth modification.

Advances in Computational Studies of the Liquid-Liquid Transition in Water and Water-Like Models.

There has been uninterrupted interest in supercooled water ever since the pioneering experiments of Speedy and Angell revealed sharp increases in this substance's response functions upon supercooling. One intriguing hypothesis that was formulated to explain this behavior involves the existence of a metastable liquid-liquid transition (LLT) at deeply supercooled conditions. The preponderance of experimental evidence is consistent with this hypothesis, although no definitive proof exists to date. Computational studies have played an important role in this area, because ice nucleation can in principle be controlled in silico. It has been claimed, controversially, that the LLT is a misinterpreted liquid-solid transition in all models of water. Recent studies disprove this viewpoint by providing unambiguous counter-examples of distinct liquid-liquid and liquid-crystal transitions in tetrahedral models. In one, state-of-the-art sampling methods were used to compute the free energy surface of a molecular model of water and revealed the existence of two liquid phases in metastable equilibrium with each other and a stable crystal phase, at the same, deeply supercooled thermodynamic conditions. Further studies showed that, by tuning the potential parameters of a model tetrahedral system, it is possible to make the LLT evolve continuously from metastability to being thermodynamically stable with respect to crystallization. Most recently, it has been shown that the simulation code used to challenge the hypothesis of an LLT contains conceptual errors that invalidate the results on which the challenge was based, definitively resolving the controversy. The debate has vastly expanded the range of fundamental questions being pursued about phase transitions in metastable systems and ushered the use of increasingly sophisticated computational methods to explore the possible existence of LLTs in model systems.

Reply to the 'Comment on "Pressure enhancement in carbon nanopores: a major confinement effect"' by D. van Dijk, Phys. Chem. Chem. Phys., 2020, 22, DOI: 10.1039/C9CP02890K.

In his 'Comment' van Dijk points out that the local pressure at a point r in an inhomogeneous thermodynamic system, like other thermodynamic properties, is not uniquely defined; one must make an operational definition that involves deciding how to assign the intermolecular forces between pairs of molecules to the point r. This non-uniqueness difficulty is well known, and was discussed in our paper. It was discussed in detail in the 1950 paper of Irving and Kirkwood, and in many books and papers since then. We reply to these comments, and note that an average of the local pressure over a region of space may yield a well-defined pressure. We also discuss other possible ways to quantify the adsorption compression effect near an attractive wall. van Dijk also suggests that the non-uniqueness difficulty can be avoided by using the pressure of the uniform bulk fluid in equilibrium with the pore. While this pressure is well-defined, it only reflects the intermolecular forces in the bulk phase, and gives no information about the behavior in the pore.

Metastable liquid-liquid transition in a molecular model of water.

Liquid water's isothermal compressibility and isobaric heat capacity, and the magnitude of its thermal expansion coefficient, increase sharply on cooling below the equilibrium freezing point. Many experimental, theoretical and computational studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions. Some experimental evidence is consistent with this hypothesis, but no definitive proof of a liquid-liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently. Computer simulations are therefore crucial for exploring water's structure and behaviour in this regime, and have shown that some water models exhibit liquid-liquid transitions and others do not. However, recent work has argued that the liquid-liquid transition has been mistakenly interpreted, and is in fact a liquid-crystal transition in all atomistic models of water. Here we show, by studying the liquid-liquid transition in the ST2 model of water with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition. We follow the rearrangement of water's coordination shell and topological ring structure along a thermodynamically reversible path from the low-density liquid to cubic ice. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid-liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it.

Crystallization of Mordenite Platelets using Cooperative Organic Structure-Directing Agents.

Organic structure-directing agents (OSDAs) are exploited in the crystallization of microporous materials to tailor the physicochemical properties of the resulting zeolite for applications ranging from separations to catalysis. The rational design of these OSDAs often entails the identification of molecules with a geometry that is commensurate with the channels and cages of the target zeolite structure. Syntheses tend to employ only a single OSDA, but there are a few examples where two or more organics operate synergistically to yield a desired product. Using a combination of state-of-the-art characterization techniques and molecular modeling, we show that the coupling of N,N,N-trimethyl-1,1-adamantammonium and 1,2-hexanediol, each yielding distinct zeolites when used alone, results in the cooperative direction of a third structure, HOU-4, with the mordenite framework type (MOR). Rietveld refinement using synchrotron X-ray diffraction data reveals the spatial arrangement of the organics in the HOU-4 crystals, with amines located in the large channels and alcohols oriented in the side pockets lining the one-dimensional pores. These results are in excellent agreement with molecular dynamics calculations, which predict similar spatial distributions of organics with an energetically favorable packing density that agrees with experimental measurements of OSDA loading, as well as with solid-state two-dimensional 27Al{29Si}, 27Al{1H}, and 13C{1H} NMR correlation spectra, which establish the proximities and interactions of occluded OSDAs. A combination of high-resolution transmission electron microscopy and atomic force microscopy is used to quantify the size of the HOU-4 crystals, which exhibit a platelike morphology, and to index the crystal facets. Our findings reveal that the combined OSDAs work in tandem to produce ultrathin, nonfaulted HOU-4 crystals that exhibit improved catalytic activity for cumene cracking in comparison to mordenite crystals prepared via conventional syntheses. This novel demonstration of cooperativity highlights the potential possibilities for expanding the use of dual structure-directing agents in zeolite synthesis.

Influence of polymer flexibility on nanoparticle dynamics in semidilute solutions.

The hierarchical structure and dynamics of polymer solutions control the transport of nanoparticles (NPs) through them. Here, we perform multi-particle collision dynamics simulations of solutions of semiflexible polymer chains with tunable persistence length lp to investigate the effect of chain stiffness on NP transport. The NPs exhibit two distinct dynamical regimes - subdiffusion on short time scales and diffusion on long time scales. The long-time NP diffusivities are compared with predictions from the Stokes-Einstein relation (SER), mode-coupling theory (MCT), and a recent polymer coupling theory (PCT). Increasing deviations from the SER as the polymer chains become more rigid (i.e. as lp increases) indicate that the NP motions become decoupled from the bulk viscosity of the polymer solution. Likewise, polymer stiffness leads to deviations from PCT, which was developed for fully flexible chains. Independent of lp, however, the long-time diffusion behavior is well-described by MCT, particularly at high polymer concentration. We also observed that the short-time subdiffusive dynamics are strongly dependent on polymer flexibility. As lp is increased, the NP dynamics become more subdiffusive and decouple from the dynamics of the polymer chain center-of-mass. We posit that these effects are due to differences in the segmental mobility of the semiflexible chains.

Tracer transport in attractive and repulsive supercooled liquids and glasses.

The transport of small penetrants through disordered materials with glassy dynamics is encountered in applications ranging from drug delivery to chemical separations. Nonetheless, understanding the influence of the matrix structure and fluctuations on penetrant motions remains a persistent challenge. Here, we use event-driven molecular dynamics to investigate the transport of small, hard-sphere tracers embedded in matrices of square-well particles. Short-range attractions between matrix particles give rise to reentrant dynamics in the supercooled regime, in which the liquid's relaxation time increases dramatically upon heating or cooling. Heating results in a "repulsive" supercooled liquid where relaxations are frustrated by steric interactions between particles, whereas cooling produces an "attractive" liquid in which relaxations are hindered by long-lived interparticle bonds. Further cooling or heating, or compression, of the supercooled liquids results in the formation of distinct glasses. Our study reveals that tracer transport in these supercooled liquids and glasses is influenced by the matrix structure and dynamics. The relative importance of each factor varies between matrices and is examined in detail by analyzing particle mean-square displacements, caging behavior, and trajectories sampled from the isoconfigurational ensemble. We identify features of tracer dynamics that reveal the spatial and temporal heterogeneity of the matrices and show that matrix arrest is insufficient to localize tracers.

Thermodynamic analysis of the stability of planar interfaces between coexisting phases and its application to supercooled water.

Two-phase simulations are commonly used to evaluate coexistence conditions, interfacial tensions, and other thermodynamic properties associated with first-order phase transitions. Calculation of these properties is often simplified when the interfaces between the two phases are flat or planar. Here, we derive a general thermodynamic criterion for selecting simulation cell dimensions to stabilize planar interfaces in phase-separated fluid-fluid systems with respect to homogeneous, single-phase states. The resulting expression is validated by analyzing the effects of simulation cell dimensions on the formation of planar liquid-vapor interfaces in the Lennard-Jones fluid and in the TIP4P/2005 model of water. We also perform large scale molecular dynamics simulations to study metastable liquid-liquid phase separation in the ST2 and TIP4P/2005 models of water under deeply supercooled conditions. Our simulations confirm the stability of a liquid-liquid interface in ST2, and they demonstrate that the corresponding interface for TIP4P/2005 can be stabilized by judiciously choosing the simulation cell aspect ratio in a manner consistent with the thermodynamic criterion. We posit that this sensitivity to the simulation cell aspect ratio may explain discrepancies between previous studies examining liquid-liquid separation in models of supercooled water.

Computational investigation of cold denaturation in the Trp-cage miniprotein.

The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.

Fluctuations near the liquid-liquid transition in a model of silica.

We perform large-scale molecular dynamics (MD) simulations of systems with up to 216 000 atoms to study the low-temperature behavior of the mWAC model of silica. Recent studies show that mWAC exhibits a liquid-liquid phase transition (LLPT), similar to the one hypothesized to occur in deeply supercooled water. Characterization of mWAC's small-angle scattering behavior reveals an anomalous increase in fluctuations in density and local tetrahedral order in the liquid upon cooling. Moreover, the static correlation length computed from the anomalous scattering component exhibits power-law growth as temperature decreases and appears to diverge near 3300 K. These observations are consistent with previous studies indicating the existence of a liquid-liquid critical point near this temperature. Finally, we use MD to thermally quench systems ranging from 4500 to 432 000 atoms in size into the predicted region of liquid-liquid coexistence. Spontaneous liquid-liquid separation is observed in each system following the quench, demonstrating that this behavior is not strongly influenced by finite-size effects. These findings parallel those recently reported for the ST2 model of water near its LLPT, suggesting common signatures that may be useful for identifying similar transitions in other systems.

Molecular modeling and structural characterization of a high glycine-tyrosine hair keratin associated protein.

High glycine-tyrosine (HGT) proteins are an important constituent of the keratin associated proteins (KAPs) present in human hair. The glassy state physics of hair fibres are thought to be largely regulated by KAPs, which exist in an amorphous state and are readily affected by environmental conditions. However, there are no studies characterizing the individual KAPs. In this paper, we present the first step to fill this gap by computational modeling and experimental studies on a HGT protein, KAP8.1. In particular, we have modeled the three-dimensional structure of this 63-residue protein using homology information from an anti-freeze protein in snow flea. The model for KAP8.1 is characterized by four strands of poly-proline II (or PPII) type helical secondary structures, held together by two cysteine disulphide bridges. Computer simulations confirm the stability of the modelled structure and show that the protein largely samples the PPII and ß-sheet conformations during the molecular dynamics simulations. Spectroscopic studies including Raman, IR and vibrational circular dichroism have also been performed on synthesized KAP8.1. The experimental studies suggest that KAP8.1 is characterised by ß-sheet and PPII structures, largely consistent with the simulation studies. The model built in this work is a good starting point for further simulations to study in greater depth the glassy state physics of hair, including its water sorption isotherms, glass transition, and the effect of HGT proteins on KAP matrix plasticization. These results are a significant step towards our goal of understanding how the properties of hair can be affected and manipulated under different environmental conditions of temperature, humidity, ageing and small molecule additives.