Functional aggregation of cell-free proteins enables fungal ice nucleation

Biological ice nucleation plays a key role in the survival of cold-adapted organisms. Several species of bacteria, fungi, and insects produce ice nucleators (INs) that enable ice formation at temperatures above -10 °C. Bacteria and fungi produce particularly potent INs that can promote water crystallization above -5 °C. Bacterial INs consist of extended protein units that aggregate to achieve superior functionality. Despite decades of research, the nature and identity of fungal INs remain elusive. Here, we combine ice nucleation measurements, physicochemical characterization, numerical modeling, and nucleation theory to shed light on the size and nature of the INs from the fungus Fusarium acuminatum. We find ice-binding and ice-shaping activity of Fusarium IN, suggesting a potential connection between ice growth promotion and inhibition. We demonstrate that fungal INs are composed of small 5.3 kDa protein subunits that assemble into ice-nucleating complexes that can contain more than 100 subunits. Fusarium INs retain high ice-nucleation activity even when only the ~12 kDa fraction of size-excluded proteins are initially present, suggesting robust pathways for their functional aggregation in cell-free aqueous environments. We conclude that the use of small proteins to build large assemblies is a common strategy among organisms to create potent biological INs.

Nanobubble Stability and Formation on Solid-Liquid Interfaces in Open Environments

Are surface nanobubbles transient or thermodynamically stable structures? This question remained controversial until recently, when the stability of gas nanobubbles at solid-liquid interfaces was demonstrated from thermodynamic arguments in closed systems, establishing that bubbles with radii of hundreds of nanometers can be stable at modest supersaturations if the gas amount is finite. Here we develop a grand-canonical description of bubble formation that predicts that nanobubbles can nucleate and remain thermodynamically stable in open boundaries at high supersaturations when pinned to hydrophobic supports as small as a few nanometers. While larger bubbles can also be stable at lower supersaturations, the corresponding barriers are orders of magnitude above kT, meaning that their formation cannot proceed via heterogeneous nucleation on a uniform solid interface but must follow some alternative path. Moreover, we conclude that a source of growth-limiting mechanism, such as pinning or gas availability, is necessary for the thermodynamic stabilization of surface bubbles.

Kinetics and Mechanisms of Pressure-Induced Ice Amorphization and Polyamorphic Transitions in a Machine-Learned Coarse-Grained Water Model

Water glasses have attracted considerable attention due to their potential connection to a liquid-liquid transition in supercooled water. Here we use molecular simulations to investigate the formation and phase behavior of water glasses using the machine-learned bond-order parameter (ML-BOP) water model. We produce glasses through hyperquenching of water, pressure-induced amorphization (PIA) of ice, and pressure-induced polyamorphic transformations. We find that PIA of polycrystalline ice occurs at a lower pressure than that of monocrystalline ice and through a different mechanism. The temperature dependence of the amorphization pressure of polycrystalline ice for ML-BOP agrees with that in experiments. We also find that ML-BOP accurately reproduces the density, coordination number, and structural features of low-density (LDA), high-density (HDA), and very high-density (VHDA) amorphous water glasses. ML-BOP accurately reproduces the experimental radial distribution function of LDA but overpredicts the minimum between the first two shells in high-density glasses. We examine the kinetics and mechanism of the transformation between low-density and high-density glasses and find that the sharp nature of these transitions in ML-BOP is similar to that in experiments and all-atom water models with a liquid-liquid transition. Transitions between ML-BOP glasses occur through a spinodal-like mechanism, similar to ice crystallization from LDA. Both glass-to-glass and glass-to-ice transformations have Avrami-Kolmogorov kinetics with exponent n = 1.5 ± 0.2 in experiments and simulations. Importantly, ML-BOP reproduces the competition between crystallization and HDA→LDA transition above the glass transition temperature T_g, and separation of their time scales below T_g, observed also in experiments. These findings demonstrate the ability of ML-BOP to accurately reproduce water properties across various regimes, making it a promising model for addressing the competition between polyamorphic transitions and crystallization in water and solutions.

Oriented attachment kinetics for rod-like particles at a flat surface: Buffon's needle at the nanoscale

The adsorption of large rod-like molecules or crystallites on a flat crystal face, similar to Buffon's needle, requires the rods to "land," with their binding sites in precise orientational alignment with matching sites on the surface. An example is provided by long, helical antifreeze proteins (AFPs), which bind at specific facets and orientations on the ice surface. The alignment constraint for adsorption, in combination with the loss in orientational freedom as the molecule diffuses toward the surface, results in an entropic barrier that hinders the adsorption. Prior kinetic models do not factor in the complete geometry of the molecule, nor explicitly enforce orientational constraints for adsorption. Here, we develop a diffusion-controlled adsorption theory for AFP molecules binding at specific orientations to flat ice surfaces. We formulate the diffusion equation with relevant boundary conditions and present analytical solutions to the attachment rate constant. The resulting rate constant is a function of the length and aspect ratio of the AFP, the distance threshold associated with binding, and solvent conditions such as temperature and viscosity. These results and methods of calculation may also be useful for predicting the kinetics of crystal growth through oriented attachment.

Stability and Metastability of Liquid Water in a Machine-Learned Coarse-Grained Model with Short-Range Interactions

Coarse-grained water models are ∼100 times more efficient than all-atom models, enabling simulations of supercooled water and crystallization. The machine-learned monatomic model ML-BOP reproduces the experimental equation of state (EOS) and ice-liquid thermodynamics at 0.1 MPa on par with the all-atom TIP4P/2005 and TIP4P/Ice models. These all-atom models were parametrized using high-pressure experimental data and are either accurate for water's EOS (TIP4P/2005) or ice-liquid equilibrium (TIP4P/Ice). ML-BOP was parametrized from temperature-dependent ice and liquid experimental densities and melting data at 0.1 MPa; its only pressure training is from compression of TIP4P/2005 ice at 0 K. Here we investigate whether ML-BOP replicates the experimental EOS and ice-water thermodynamics along all pressures of ice I. We find that ML-BOP reproduces the temperature, enthalpy, entropy, and volume of melting of hexagonal ice up to 400 MPa and the EOS of water along the melting line with an accuracy that rivals that of both TIP4P/2005 and TIP4P/Ice. We interpret that the accuracy of ML-BOP originates from its ability to capture the shift between compact and open local structures to changes in pressure and temperature. ML-BOP reproduces the sharpening of the tetrahedral peak of the pair distribution function of water upon supercooling, and its pressure dependence. We characterize the region of metastability of liquid ML-BOP with respect to crystallization and cavitation. The accessibility of ice crystallization to simulations of ML-BOP, together with its accurate representation of the thermodynamics of water, makes it promising for investigating the interplay between anomalies, glass transition, and crystallization under conditions challenging to access through experiments.

AlphaFold2 models indicate that protein sequence determines both structure and dynamics

AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.

Is It Possible to Follow the Structural Evolution of Water in "No-Man's Land" Using a Pulsed-Heating Procedure?

The anomalous increase in compressibility and heat capacity of supercooled water has been attributed to its structural transformation of into a four-coordinated liquid. Experiments revealed that κ_T and C_p peak at T_W^thermo ≈ 229 K [Kim et al. Science 2017, 358, 1589; Pathak et al. Proc. Natl. Acad. Sci. 2021, 118, e2018379118]. Recently, a pulsed heating procedure (PHP) was employed to interrogate the structure of water, reporting a steep increase in tetrahedrality around T_W^PHP = 210 ± 3 K [Kringle et al. Science 2020, 369, 1490]. This discrepancy questions whether water structure and thermodynamics are decoupled, or if the shift in T_W is an artifact of PHP. Here we implement PHP in molecular simulations. We find that the stationary states captured at the bottom of the pulse are not representative of the thermalized liquid or its inherent structure. Our analysis reveals a temperature-dependent distortion that shifts T_W^PHP to ∼20 K below T_W^thermo. We conclude that 2 orders of magnitude faster rates are required to sample water's inherent structure with PHP.

Polymorph Selection in Zeolite Synthesis Occurs after Nucleation

Zeolites are porous crystals with extensive polymorphism. The hydrothermal synthesis of zeolites is a multistage process involving amorphous precursors that evolve continuously in solubility and local order toward those of the crystal. These results pose several questions: Why does a first-order transition appear as a continuous transformation? At which stage is the polymorph selected? How large are the barriers and critical sizes for zeolite nucleation? Here we address these questions using nucleation theory with experimental data. We find that the nucleation barriers and critical zeolite nuclei are extremely small at temperatures of hydrothermal synthesis, resulting in spinodal-like crystallization that produces a mosaic of tiny zeolitic crystallites that compete to grow inside each glassy precursor nanoparticle. The subnanometer size of the critical nuclei reveals that the selection between zeolite polymorphs occurs after the nucleation stage, during the growth and coarsening of the crystals around the excluded volume of the structure-directing agents.

Diffusion Attachment Model for Long Helical Antifreeze Proteins to Ice

Some of the most potent antifreeze proteins (AFPs) are approximately rigid helical structures that bind with one side in contact with the ice surface at specific orientations. These AFPs take random orientations in solution; however, most orientations become sterically inaccessible as the AFP approaches the ice surface. The effect of these inaccessible orientations on the rate of adsorption of AFP to ice has never been explored. Here, we present a diffusion-controlled theory of adsorption kinetics that accounts for these orientational restrictions to predict a rate constant for adsorption (k_on, in m/s) as a function of the length and width of the AFP molecules. We find that k_on decreases with length and diameter of the AFP and is almost proportional to the inverse of the area of the binding surface. We demonstrate that the restricted orientations create an entropic barrier to AFP adsorption, which we compute to be approximately 7 k_BT for most AFPs and up to 9 k_BT for Maxi, the largest known AFP. We compare the entropic resistance 1/k_on to resistances for diffusion through boundary layers and across typical distances in the extracellular matrix and find that these entropic and diffusion resistances could become comparable in the small confined spaces of biological environments.

Is Ice Nucleation by Organic Crystals Nonclassical? An Assessment of the Monolayer Hypothesis of Ice Nucleation

Potent ice nucleating organic crystals display an increase in nucleation efficiency with pressure and memory effect after pressurization that set them apart from inorganic nucleants. These characteristics were proposed to arise from an ordered water monolayer at the organic-water interface. It was interpreted that ordering of the monolayer is the limiting step for ice nucleation on organic crystals, rendering their mechanism of nucleation nonclassical. Despite the importance of organics in atmospheric ice nucleation, that explanation has never been investigated. Here we elucidate the structure of interfacial water and its role in ice nucleation at ambient pressure on phloroglucinol dihydrate, the paradigmatic example of outstanding ice nucleating organic crystal, using molecular simulations. The simulations confirm the existence of an interfacial monolayer that orders on cooling and becomes fully ordered upon ice formation. The monolayer does not resemble any ice face but seamlessly connects the distinct hydrogen-bonding orders of ice and the organic surface. Although large ordered patches develop in the monolayer before ice nucleates, we find that the critical step is the formation of the ice crystallite, indicating that the mechanism is classical. We predict that the fully ordered, crystalline monolayer nucleates ice above -2 °C and could be responsible for the exceptional ice nucleation by the organic crystal at high pressures. The lifetime of the fully ordered monolayer around 0 °C, however, is too short to account for the memory effect reported in the experiments. The latter could arise from an increase in the melting temperature of ice confined by strongly ice-binding surfaces.

Electrochemically Generated Nanobubbles: Invariance of the Current with Respect to Electrode Size and Potential

Gas-producing electrochemical reactions are key to energy conversion and generation technologies. Bubble formation dramatically decreases gas-production rates on nanoelectrodes, by confining the reaction to the electrode boundary. This results in the collapse of the current to a stationary value independent of the potential. Startlingly, these residual currents also appear to be insensitive to the nanoelectrode diameter in the 5 to 500 nm range. These results are counterintuitive, as it may be expected that the current be proportional to the circumference of the electrode, i.e., the length of the three-phase line where the reaction occurs. Here, we use molecular simulations and a kinetic model to elucidate the origin of current insensitivity with respect to the potential and establish its relationship to the size of nanoelectrodes. We provide critical insights for the design and operation of nanoscale electrochemical devices and demonstrate that nanoelectrode arrays maximize conversion rates compared to macroscopic electrodes with same total area.

Following the nucleation pathway from disordered liquid to gyroid mesophase

Mesophases have order intermediate between liquids and crystals and arise in systems with frustration, such as surfactants, block copolymers, and Janus nanoparticles. The gyroid mesophase contains two interpenetrated, nonintersecting chiral networks that give it properties useful for photonics. It is challenging to nucleate a gyroid from the liquid. Elucidating the reaction coordinate for gyroid nucleation could assist in designing additives that facilitate the formation of the mesophase. However, the complexity of the gyroid structure and the extreme weakness of the first-order liquid to gyroid transition make this a challenging quest. Here, we investigate the pathway and transition states for the nucleation of a gyroid from the liquid in molecular simulations with a mesogenic binary mixture. We find that the gyroid nuclei at the transition states have a large degree of positional disorder and are not compact, consistent with the low surface free energy of the liquid-gyroid interface. A combination of bond-order parameters for the minor component is best to describe the passage from liquid to gyroid, among those we consider. The committor analyses, however, show that this best coordinate is not perfect and suggests that accounting for the relative ordering of the two interpenetrated networks in infant nuclei, as well as for signatures of ordering in the major component of the mesophase, would improve the accuracy of the reaction coordinate for gyroid formation and its use to evaluate nucleation barriers. To our knowledge, this study is the first to investigate the reaction coordinate and critical nuclei for the formation of any mesophase from an amorphous phase.

How Do Surfactants Control the Agglomeration of Clathrate Hydrates?

Clathrate hydrates can spontaneously form under typical conditions found in oil and gas pipelines. The agglomeration of clathrates into large solid masses plugs the pipelines, posing adverse safety, economic, and environmental threats. Surfactants are customarily used to prevent the aggregation of clathrate particles and their coalescence with water droplets. It is generally assumed that a large contact angle between the surfactant-covered clathrate and water is a key predictor of the antiagglomerant performance of the surfactant. Here we use molecular dynamic simulations to investigate the structure and dynamics of surfactant films at the clathrate-oil interface, and their impact on the contact angle and coalescence between water droplets and hydrate particles. In agreement with the experiments, the simulations predict that surfactant-covered clathrate-oil interfaces are oil wet but super-hydrophobic to water. Although the water contact angle determines the driving force for coalescence, we find that a large contact angle is not sufficient to predict good antiagglomerant performance of a surfactant. We conclude that the length of the surfactant molecules, the density of the interfacial film, and the strength of binding of its molecules to the clathrate surface are the main factors in preventing the coalescence and agglomeration of clathrate particles with water droplets in oil. Our analysis provides a molecular foundation to guide the molecular design of effective clathrate antiagglomerants.

Ice nucleation by particles containing long-chain fatty acids of relevance to freezing by sea spray aerosols

Heterogeneous ice nucleation in the atmosphere regulates cloud properties, such as phase (ice versus liquid) and lifetime. Aerosol particles of marine origin are relevant ice nucleating particle sources when marine aerosol layers are lifted over mountainous terrain and in higher latitude ocean boundary layers, distant from terrestrial aerosol sources. Among many particle compositions associated with ice nucleation by sea spray aerosols are highly saturated fatty acids. Previous studies have not demonstrated their ability to freeze dilute water droplets. This study investigates ice nucleation by monolayers at the surface of supercooled droplets and as crystalline particles at temperatures exceeding the threshold for homogeneous freezing. Results show the poor efficiency of long chain fatty acid (C16, C18) monolayers in templating freezing of pure water droplets and seawater subphase to temperatures of at least -30 °C, consistent with theory. This contrasts with freezing of fatty alcohols (C22 used here) at nearly 20 °C warmer. Evaporation of μL-sized droplets to promote structural compression of a C19 acid monolayer did not favor warmer ice formation of drops. Heterogeneous ice nucleation occurred for nL-sized droplets condensed on 5 to 100 μm crystalline particles of fatty acid (C12 to C20) at a range of temperatures below -28 °C. These experiments suggest that fatty acids nucleate ice at warmer than -36 °C only when the crystalline phase is present. Rough estimates of ice active site densities are consistent with those of marine aerosols, but require knowledge of the proportion of surface area comprised of fatty acids for application.

Two-Step to One-Step Nucleation of a Zeolite through a Metastable Gyroid Mesophase

The importance of nonclassical nucleation pathways in the formation of complex crystals has become apparent in recent years. Nonclassical pathways were unraveled for, among others, the crystallization of proteins, colloids, and clathrates. In those cases, the formation of a metastable fluid with density close to the crystal decreases the crystallization barrier. Recent simulations indicate that mesophases can facilitate the nucleation of zeolites. Here, we use molecular simulations to investigate the role of a gyroid mesophase on the crystallization of a model zeolite from liquid. The nucleation pathway is always nonclassical. At warmer temperatures, the mechanism proceeds in two well-defined steps: nucleation of a metastable gyroid followed by its crystallization into a zeolite. At colder temperatures, the second barrier becomes negligible, and the crystallization occurs in one step. This second scenario is also nonclassical, as the critical nucleus for the crystallization has the structure of the gyroid and seamlessly transforms into a zeolite as it grows past its critical size. To our knowledge, this is the first report of a nonclassical mechanism of crystallization mediated by a mesophase.

Why Is It So Difficult to Identify the Onset of Ice Premelting?

Premelting of ice at temperatures below 0 °C is of fundamental importance for environmental processes. Various experimental techniques have been used to investigate the temperature at which liquid-like water first appears at the ice-vapor interface, reporting onset temperatures from -160 to -2 °C. The signals that identify liquid-like order at the ice-vapor interface in these studies, however, do not show a sharp initiation with temperature. That is at odds with the expected first-order nature of surface phase transitions, and consistent with recent large-scale molecular simulations that show the first premelted layer to be sparse and to develop continuously over a wide range of temperatures. Here we perform a thermodynamic analysis to elucidate the origin of the continuous formation of the first layer of liquid at the ice-vapor interface. We conclude that a negative value of the line tension of the ice-liquid-vapor three-phase contact line is responsible for the continuous character of the transition and the sparse nature of the liquid-like domains in the incomplete first layer.

Ice-Liquid Oscillations in Nanoconfined Water

Nanoscale confinement has a strong effect on the phase behavior of water. Studies in the last two decades have revealed a wealth of novel crystalline and quasicrystalline structures for water confined in nanoslits. Less is known, however, about the nature of ice-liquid coexistence in extremely nanoconfined systems. Here, we use molecular simulations to investigate the ice-liquid equilibrium for water confined between two nanoscopic disks. We find that the nature of ice-liquid phase coexistence in nanoconfined water is different from coexistence in both bulk water and extended nanoslits. In highly nanoconfined systems, liquid water and ice do not coexist in space because the two-phase states are unstable. The confined ice and liquid phases coexist in time, through oscillations between all-liquid and all-crystalline states. The avoidance of spatial coexistence of ice and liquid originates on the non-negligible cost of the interface between confined ice and liquid in a small system. It is the result of the small number of water molecules between the plates and has no analogue in bulk water.

The Clathrate-Water Interface Is Oleophilic

The slow nucleation of clathrate hydrates is a central challenge for their use in the storage and transportation of natural gas. Molecules that strongly adsorb to the clathrate-water interface decrease the crystal-water surface tension, lowering the barrier for clathrate nucleation. Surfactants are widely used to promote the nucleation and growth of clathrate hydrates. It has been proposed that these amphiphilic molecules bind to the clathrate surface via hydrogen bonding. However, recent studies reveal that PVCap, an amphiphilic polymer, binds to clathrates through hydrophobic moieties. Here we use molecular dynamic simulations and theory to investigate the mode and strength of binding of surfactants to the clathrate-water interface and their effect on the nucleation rate. We find that the surfactants bind to the clathrate-water interface exclusively through their hydrophobic tails. The binding is strong, driven by the entropy of dehydration of the alkyl chain, as it penetrates empty cavities at the hydrate surface. The hydrophobic attraction of alkyl groups to the clathrate surface also results in strong adsorption of alkanes. We identify two regimes for the binding of surfactants as a function of their density at the hydrate surface, which we interpret to correspond to the two steps of the Langmuir adsorption isotherm observed in experiments. Our results indicate that hydrophobic attraction to the clathrate-water interface is key for the design of soluble additives that promote the nucleation of hydrates. We use the calculated adsorption coefficients to estimate the concentration of sodium dodecyl sulfate (SDS) required to reach nucleation rates for methane hydrate consistent with those measured in experiments. To our knowledge, this study is the first to quantify the effect of surfactant concentration in the nucleation rate of clathrate hydrates.

Why Is Gyroid More Difficult to Nucleate from Disordered Liquids than Lamellar and Hexagonal Mesophases?

Block copolymers, surfactants, and biomolecules form lamellar, hexagonal, and gyroid mesophases. Across these systems, the nucleation of lamellar from the disordered liquid is the easiest and the nucleation of gyroid the most challenging. This poses the question of what are the factors that determine the rates of nucleation of the mesophases and whether they are controlled by the complexity of the structures or the thermodynamics of nucleation. Here, we use molecular simulations to investigate the nucleation and thermodynamics of lamellar, hexagonal, and gyroid in a binary mixture of particles that produces the same mesophases as those of surfactants and block copolymers. We demonstrate that a combination of averaged bond-order parameters q̅₂ and q̅₈ identifies and distinguishes the three mesophases. We use these parameters to track the microscopic process of nucleation of each mesophase and investigate the existence of heterogeneous nucleation (cross-nucleation) between mesophases. We estimate the surface tensions of the liquid/mesophase interfaces from nucleation rates using classical nucleation theory and find that they are comparable for the three mesophases with values that are about a third of those expected for liquid-crystal interfaces. The driving forces for nucleation, on the other hand, are quite different and increase in the order gyroid < hexagonal < lamellar at any temperature. We find that the nucleation rates of the mesophases follow the order of their driving forces. We conclude that the difficulty to nucleate the gyroid originates in its lower temperature of melting and extremely low entropy of melting compared to those of the hexagonal and lamellar mesophases.

What Controls the Limit of Supercooling and Superheating of Pinned Ice Surfaces?

Cold-adapted organisms produce antifreeze proteins and glycoproteins to control the growth, melting and recrystallization of ice. It has been proposed that these molecules pin the crystal surface, creating a curvature that arrests the growth and melting of the crystal. Here we use thermodynamic modeling and molecular simulations to demonstrate that the curvature of the superheated or supercooled surface depends on the temperature and distances between ice-binding molecules, but not the details of their interactions with ice. We perform simulations of ice pinned with the antifreeze protein TmAFP, polyvinyl alcohol with different degrees of polymerization, and model ice-binding molecules to determine the thermal hystereses on melting and freezing, i.e. the maximum curvature that can be attained before, respectively, ice melts or grows irreversibly over the ice-binding molecules. We find that the thermal hysteresis is controlled by the bulkiness of the ice-binding molecules and their footprint at the ice surface. We elucidate the origin of the asymmetry between freezing and melting hysteresis found in experiments and propose guidelines to design synthetic antifreeze molecules with potent thermal hysteresis activity.

Ice-Nucleating and Antifreeze Proteins Recognize Ice through a Diversity of Anchored Clathrate and Ice-like Motifs

Cold-adapted organisms produce antifreeze and ice-nucleating proteins to prevent and promote ice formation. The crystal structure of hyperactive bacterial antifreeze protein (AFP) MpAFP suggests that this protein binds ice through an anchored clathrate motif. It is not known whether other hyperactive AFPs and ice-nucleating proteins (INPs) use the same motif to recognize or nucleate ice. Here we use molecular simulations to elucidate the ice-binding motifs of hyperactive insect AFPs and a model INP of Pseudomonas syringae. We find that insect AFPs recognize ice through anchored clathrate motifs distinct from that of MpAFP. By performing simulations of ice nucleation by PsINP, we identify two distinct ice-binding sites on opposite sides of the β-helix. The ice-nucleating sequences identified in the simulations agree with those previously proposed for the closely related INP of Pseudomonas borealis based on the structure of the protein. The simulations indicate that these sites have comparable ice-nucleating efficiency, but distinct binding motifs, controlled by the amino acid sequence: one is an anchored clathrate and the other ice-like. We conclude that anchored clathrate and ice-like motifs can be equally effective for binding proteins to ice and promoting ice nucleation.

Antifreeze Glycoproteins Bind Reversibly to Ice via Hydrophobic Groups

Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.

Is Water at the Graphite Interface Vapor-like or Ice-like?

Graphitic surfaces are the main component of soot, a major constituent of atmospheric aerosols. Experiments indicate that soots of different origins display a wide range of abilities to heterogeneously nucleate ice. The ability of pure graphite to nucleate ice in experiments, however, seems to be almost negligible. Nevertheless, molecular simulations with the monatomic water model mW with water-carbon interactions parameterized to reproduce the experimental contact angle of water on graphite predict that pure graphite nucleates ice. According to classical nucleation theory, the ability of a surface to nucleate ice is controlled by the binding free energy between ice immersed in liquid water and the surface. To establish whether the discrepancy in freezing efficiencies of graphite in mW simulations and experiments arises from the coarse resolution of the model or can be fixed by reparameterization, it is important to elucidate the contributions of the water-graphite, water-ice, and ice-water interfaces to the free energy, enthalpy, and entropy of binding for both water and the model. Here we use thermodynamic analysis and free energy calculations to determine these interfacial properties. We demonstrate that liquid water at the graphite interface is not ice-like or vapor-like: it has similar free energy, entropy, and enthalpy as water in the bulk. The thermodynamics of the water-graphite interface is well reproduced by the mW model. We find that the entropy of binding between graphite and ice is positive and dominated, in both experiments and simulations, by the favorable entropy of reducing the ice-water interface. Our analysis indicates that the discrepancy in freezing efficiencies of graphite in experiments and the simulations with mW arises from the inability of the model to simultaneously reproduce the contact angle of liquid water on graphite and the free energy of the ice-graphite interface. This transferability issue is intrinsic to the resolution of the model, and arises from its lack of rotational degrees of freedom.

Soluble Oligomeric Nucleants: Simulations of Chain Length, Binding Strength, and Volume Fraction Effects

Recent theories and simulations suggest that molecular additives can bind to the surfaces of nuclei, lower the surface energy, and accelerate nucleation. Experiments have shown that oligomeric and polymeric additives can also modify nucleation rates of proteins, ice, and minerals; however, general design principles for oligomeric or polymeric promoters do not yet exist. Here we investigate oligomeric additives for which each segment of the oligomer can bind to surfaces of nuclei. We use semigrand canonical Monte Carlo simulations in a Potts lattice gas model to study the effects of oligomer chain length, volume fraction, and binding strength. We find that increasing each of those parameters lowers the nucleation barrier. At extremely low oligomer concentrations, the nucleation kinetics can be modeled as though each oligomer is a heterogeneous nucleation site in solution.

Promotion of Homogeneous Ice Nucleation by Soluble Molecules

Atmospheric aerosols nucleate ice in clouds, strongly impacting precipitation and climate. The prevailing consensus is that ice nucleation is promoted heterogeneously by the surface of ice nucleating particles in the aerosols. However, recent experiments indicate that water-soluble molecules, such as polysaccharides of pollen and poly(vinyl alcohol) (PVA), increase the ice freezing temperature. This poses the question of how do flexible soluble molecules promote the formation of water crystals, as they do not expose a well-defined surface to ice. Here we use molecular simulations to demonstrate that PVA promotes ice nucleation through a homogeneous mechanism: PVA increases the nucleation rate by destabilizing water in the solution. This work demonstrates a novel paradigm for understanding ice nucleation by soluble molecules and provides a new handle to design additives that promote crystallization.

Self-Assembly of Mesophases from Nanoparticles

A growing number of crystalline and quasi-crystalline structures have been formed by coating nanoparticles with ligands, polymers, and DNA. The design of nanoparticles that assemble into mesophases, such as those formed by block copolymers, would combine the order, mobility, and stimuli responsive properties of mesophases with the electronic, magnetic, and optical properties of nanoparticles. Here we use molecular simulations to demonstrate that binary mixtures of unbound particles with simple short-ranged pair interactions produce the same mesophases as block copolymers and surfactants, including lamellar, hexagonal, gyroid, body-centered cubic, face-centered cubic, perforated lamellar, and semicrystalline phases. The key to forming the mesophases is the frustrated attraction between particles of different types, achieved through control over interparticle size and over strength and softness of the interaction. Experimental design of nanoparticles with effective interactions described by the potentials of this work would provide a distinct, robust route to produce ordered tunable liquid crystalline mesophases from nanoparticles.

Reaction Coordinate for Ice Crystallization on a Soft Surface

The control of assembly and crystallization of molecules is becoming increasingly important in chemistry, engineering, and materials sciences. Crystallization is also central to understand natural processes that include the formation of atmospheric ice and biomineralization. Organic surfaces, biomolecules, and even liquid/vapor interfaces can promote the nucleation of crystals. These soft surfaces present significant structural fluctuations, which have been shown to strongly impact the rate of crystallization. This raises the question of whether degrees of freedom of soft surfaces play a role in the reaction coordinate for crystal nucleation. Here we use molecular simulations to investigate the mechanism of ice nucleation promoted by an alcohol monolayer. Our analysis indicates that while the flexibility of the surface strongly depresses its ice nucleation ability, it does not play a role in the coordinate that controls the transformation from liquid to ice. We find that the variable that drives the transformation is the size of the crystalline cluster, the same as that for the homogeneous crystallization. We argue that this is a general result that arises from the separation of time scales between surface fluctuations and the crossing of the transition state barrier for crystallization.

Stability and Vapor Pressure of Aqueous Aggregates and Aerosols Containing a Monovalent Ion

The incidence of charged particles on the nucleation and the stability of aqueous aggregates and aerosols was reported more than a century ago. Many studies have been conducted ever since to characterize the stability, structure, and nucleation barrier of ion-water droplets. Most of these studies have focused on the free-energy surface as a function of cluster size, with an emphasis on the role of ionic charge and radius. This knowledge is fundamental to go beyond the rudimentary ion-induced classical nucleation theory. In the present article, we address this problem from a different perspective, by computing the vapor pressures of (H₂O)_nLi⁺ and (H₂O)_nCl^- aggregates using molecular simulations. Our calculations shed light on the structure, the critical size, the range of stability, and the role of ion-water interactions in aqueous clusters. Moreover, they allow one to assess the accuracy of the classical thermodynamic model, highlighting its strengths and weaknesses.

Ice Nucleation Efficiency of Hydroxylated Organic Surfaces Is Controlled by Their Structural Fluctuations and Mismatch to Ice

Heterogeneous nucleation of ice induced by organic materials is of fundamental importance for climate, biology, and industry. Among organic ice-nucleating surfaces, monolayers of long chain alcohols are particularly effective, while monolayers of fatty acids are significantly less so. As these monolayers expose to water hydroxyl groups with an order that resembles the one in the basal plane of ice, it was proposed that lattice matching between ice and the surface controls their ice-nucleating efficiency. Organic monolayers are soft materials and display significant fluctuations. It has been conjectured that these fluctuations assist in the nucleation of ice. Here we use molecular dynamic simulations and laboratory experiments to investigate the relationship between the structure and fluctuations of hydroxylated organic surfaces and the temperature at which they nucleate ice. We find that these surfaces order interfacial water to form domains with ice-like order that are the birthplace of ice. Both mismatch and fluctuations decrease the size of the preordered domains and monotonously decrease the ice freezing temperature. The simulations indicate that fluctuations depress the freezing efficiency of monolayers of alcohols or acids to half the value predicted from lattice mismatch alone. The model captures the experimental trend in freezing efficiencies as a function of chain length and predicts that alcohols have higher freezing efficiency than acids of the same chain length. These trends are mostly controlled by the modulation of the structural mismatch to ice. We use classical nucleation theory to show that the freezing efficiencies of the monolayers are directly related to their free energy of binding to ice. This study provides a general framework to relate the equilibrium thermodynamics of ice binding to a surface and the nonequilibrium ice freezing temperature and suggests that these could be predicted from the structure of interfacial water.

Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake

The coarse-grained model FF_pvap reproduces the experimental activity coefficient of water in tetramethylammonium chloride solutions over a wide range of concentrations, with a hundred-fold gain in computing efficiency with respect to atomistic models.

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions

Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.