Understanding why constant energy or constant temperature may affect nucleation behavior in MD simulations: A study of gas hydrate nucleation.

Molecular dynamics simulations have been widely used in exploring the nucleation behavior of many systems, including gas hydrates. Gas hydrates are ice-like solids in which gas molecules are trapped in water cages. During hydrate formation, a considerable amount of heat is released, and previous work has reported that the choice of temperature control scheme may affect the behavior of hydrate formation. The origins of this effect have remained an open question. To address this question, extensive NVE simulations and thermostatted (NPT and NVT) simulations with different temperature coupling strengths have been performed and compared for systems where a water nanodroplet is immersed in a H2S liquid. Detailed analysis of the hydrate structures and their mechanisms of formation has been carried out. Slower nucleation rates in NVE simulations in comparison to NPT simulations have been observed in agreement with previous studies. Probability distributions for various temperature measures along with their spatial distributions have been examined. Interestingly, a comparison of these temperature distributions reveals a small yet noticeable difference in the widths of the distributions for water. The somewhat reduced fluctuations in the temperature for the water species in the NVE simulations appear to be responsible for reducing the hydrate nucleation rate. We further conjecture that the NVE-impeded nucleation rate may be the result of the finite size of the surroundings (here the liquid H2S portion of the system). Additionally, a local spatial temperature gradient arising from the heat released during hydrate formation could not be detected.

Mixed Hydrate Nucleation: Molecular Mechanisms and Cage Structures.

The molecular-level details of the formation of mixed gas hydrates remain elusive despite their significance for a variety of scientific and industrial applications. In this study, extensive molecular simulations have been performed to examine the behavior of CH4/H2S mixed hydrate nucleation utilizing two different simulation setups varying in compositions and temperatures. The observed behavior exhibits similar phenomenology across the various systems once differences in nucleation rates and guest uptake are accounted for. We find that CH4 is always enriched in the hydrate phase while the aqueous phase is enriched in H2S. Even with H2S as a minor component (i.e., 10% mole fraction), the system can mirror the overall nucleation kinetics of pure H2S hydrate systems with CH4-dominant nuclei. Through analyses of cages and their transitions, nonstandard cages, particularly those with 12 faces (e.g., 51062), have been found to be key intermediate cage types in the early stage of nucleation. Additionally, we present previously unreported cage types comprising heptagonal faces (e.g., 596271) as having a significant role in the early-stage gas hydrate structural transitions.

Massive generation of metastable bulk nanobubbles in water by external electric fields.

Nanobubbles (NBs) are nanoscopic gaseous domains than can exist on solid surfaces or in bulk liquids. They have attracted substantial attention due to their long-time (meta)stability and a high potential for real-world applications. Using an approach not previously investigated, we exploit surface-electrostatic NB formation and stabilization via application of external electric fields in gas-liquid systems, with the marked result of massively increased gas uptake into the liquid in NB form. The de facto gas solubility enhancement (over many months) ranges from 2.5-fold for oxygen to 30-fold for methane vis-à-vis respective Henry's law values for gas solubility; the more hydrophobic the gas, the more spectacular the increase. Molecular dynamics simulations reveal that the origin of NBs' movement lies in dielectrophoresis, while substantial NB stabilization arises from a surface-polarization interaction.

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'.

Does Local Structure Bias How a Crystal Nucleus Evolves?

The broad scientific and technological importance of crystallization has led to significant research probing and rationalizing crystal nucleation processes. Previous work has generally neglected the possibility of the molecular-level dynamics of individual crystal nuclei coupling to local structures. However, recent experimental work has conjectured that this can occur. Therefore, to address a deficiency in scientific understanding of crystallization, we have probed the nucleation of prototypical single and multicomponent crystals (specifically, ice and mixed gas hydrates). We establish that local structures can bias the evolution of nascent crystal phases on a nanosecond time scale by, for example, promoting the appearance or disappearance of specific crystal motifs and thus reveal a new facet of crystallization behavior. Moreover, we demonstrate structural biases are likely present during crystallization processes beyond ice and gas hydrate formation. Structurally biased dynamics are a lens for understanding existing computational and experimental results while pointing to future opportunities.

Bridging solution properties to gas hydrate nucleation through guest dynamics.

By investigating the aqueous solution properties of several hydrate guests with molecular simulations, we find that with increasing guest concentration, the guest's hydration shell becomes more ordered and the system entropy decreases. A common critical value of the self-diffusion coefficient of different guest molecules is identified, below which hydrates will nucleate very readily.

Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence.

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

Probing Molecular Mechanisms of Self-Assembly in Metal-Organic Frameworks.

Metal-organic framework materials (MOFs) are a class of nanoporous materials, important to many applications (e.g., gas storage, separation), and their synthesis has received considerable attention. Yet, very little is known about the mechanisms of self-assembly of MOFs. Here, we provide molecular-level insights into the previously unexplored behavior of the self-assembly process, through molecular dynamics simulations, for an archetypal Zn-carboxylate MOF system exhibiting complex vertex topologies (e.g., paddle-wheel clusters). A key finding of this study is the characterization of a stochastic and multistage ordering process intrinsic to self-assembly of the Zn-carboxylate MOF system. A variety of transient intermediate structures consisting of various types of Zn-ion clusters and carboxylate-ligand coordination, and featuring a range of geometric arrangements, are observed during structural evolution. The general features deduced here for the mechanism of the self-assembly of this archetypal MOF system expose the complexities of the various molecular-level events that can occur during the early stages of this process spanning time scales of nano- to microseconds. More generally, we provide fundamental insights that elucidate key aspects of the early stages of the self-assembly mechanism for an important class of nanoporous materials, and of experimental studies exploring nucleation and growth processes in such materials.

Unraveling Mixed Hydrate Formation: Microscopic Insights into Early Stage Behavior.

The molecular-level details of mixed hydrate nucleation remain unclear despite the broad implications of this process for a variety of scientific domains. Through analysis of mixed hydrate nucleation in a prototypical CH4/H2S/H2O system, we demonstrate that high-level kinetic similarities between mixed hydrate systems and corresponding pure hydrate systems are not a reliable basis for estimating the composition of early stage mixed hydrate nuclei. Moreover, we show that solution compositions prior to and during nucleation are not necessarily effective proxies for the composition of early stage mixed hydrate nuclei. Rather, microscopic details, (e.g., guest-host interactions and previously neglected cage types) apparently play key roles in determining early stage behavior of mixed hydrates. This work thus provides key foundational concepts and insights for understanding mixed hydrate nucleation.

Evidence from mixed hydrate nucleation for a funnel model of crystallization.

The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological similarities between protein folding and crystallization. Such funnel-shaped potential energy landscapes may be typical of broad classes of molecular ordering processes, and can provide a new perspective for both studying and understanding these processes.

Ordering effects of conjugate thermal fields in simulations of molecular liquids: Carbon dioxide and water.

As shown previously, it is possible to apply configurational and kinetic thermostats simultaneously in order to induce a steady thermal flux in molecular dynamics simulations of many-particle systems. This flux appears to promote motion along potential gradients and can be utilized to enhance the sampling of ordered arrangements, i.e., it can facilitate the formation of a critical nucleus. Here we demonstrate that the same approach can be applied to molecular systems, and report a significant enhancement of the homogeneous crystal nucleation of a carbon dioxide (EPM2 model) system. Quantitative ordering effects and reduction of the particle mobilities were observed in water (TIP4P-2005 model) and carbon dioxide systems. The enhancement of the crystal nucleation of carbon dioxide was achieved with relatively small conjugate thermal fields. The effect is many orders of magnitude bigger at milder supercooling, where the forward flux sampling method was employed, than at a lower temperature that enabled brute force simulations of nucleation events. The behaviour exhibited implies that the effective free energy barrier of nucleation must have been reduced by the conjugate thermal field in line with our interpretation of previous results for atomic systems.

Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges.

Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water's properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water's quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water's isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research.

Mechanism of O((3)P) formation from a hydroxyl radical pair in aqueous solution.

The reaction mechanism for the rapid formation of a triplet oxygen atom, O((3)P), from a pair of triplet-state hydroxyl radicals in liquid water is explored utilizing extensive Car-Parrinello MD simulations and advanced visualization techniques. The local solvation structures, the evolution of atomic charges, atomic separations, spin densities, electron localization functions, and frontier molecular orbitals, as well as free energy profiles, evidence that the reaction proceeds through a hybrid (hydrogen atom transfer and electron-proton transfer) and hemibond-assisted reaction mechanism. A benchmarking study utilizing high-level ab initio calculations to examine the interactions of a hydroxyl radical pair in the gas phase and the influence of a hemibonded water is also provided. The results presented here should serve as a foundation for further experimental and theoretical studies aimed at better understanding the role and potential applications of the triplet oxygen atom as a potent reactive oxygen species.

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation.

For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular dynamics (MD) simulations. In the case of nucleation of methane hydrate from enhanced-sampling simulation, we notice that already at the transition state, ∼80% of the enclathrated CH4 molecules are contained in a well-structured (sII) clathrate-like crystallite. For direct MD simulation of nucleation of H2S hydrate, some sI/sII polymorphic diversity was encountered, and it was found that a realistic dissipation of the nucleation energy (in view of non-equilibrium relaxation to either microcanonical (NVE) or isothermal-isobaric (NPT) distributions) is important to determine the relative propensity to form sI versus sII motifs.

Communication: structural interconversions between principal clathrate hydrate structures.

Gas clathrate hydrates formed with most gases belong to three common and well characterized crystalline structures known as sI, sII, and sH, although molecular mechanisms for their structural interconversions have remained poorly understood. Here, we present potential mechanisms for the interconversions between sI and sH and sII and sH, as observed within molecular simulations of the cross-nucleation of different methane hydrate phases. We find that a 4(1)5(10)6(2) cage intermediates the structural interconversion between sI and sH, while a sII crystal can form on a sH template directly. These structural interconversion pathways emphasize the diversity of possible clathrate hydrate phases characterized by a variety of tetrahedrally hydrogen-bonded structures.

Aqueous production of oxygen atoms from hydroxyl radicals.

The behavior of the hydroxyl radical (OH*) in solution is significant to a broad range of scientific and technological fields. OH* is considered a highly reactive, short-lived species and previous studies have neglected the possibility of encounters of two OH* in solution. However, these encounters may be nonnegligible in environments with elevated local OH* concentrations, such as under many in vivo processes and within nuclear infrastructure. High concentrations of OH* in vivo are considered to be very dangerous; OH* has been related to many ailments ranging from cancer to Alzheimer's disease. Here we probe details of the reactions and interactions that can occur between two OH* in water by utilizing Car-Parrinello molecular dynamics simulations and advanced visualization techniques. The recombination reaction to form hydrogen peroxide is confirmed for the singlet electronic state. In contrast, the triplet state yields an oxygen atom, O(aq). This species has been previously detected in experimental water-radiolysis studies, but its origin could not be determined. O(aq) is a much more potent biradical than its parent OH* and its presence can impact many in vivo processes. This study also reveals that the hemibonded interaction plays key role in the behavior of OH*(aq). Our findings have major implications to the scientific understanding of the impacts of high local OH* concentrations, such during oxidative stress and in aging processes. Given its importance, this study will form the basis of further experimental and theoretical investigations exploring the role of O(aq) in a number of contexts.

Driving ordering processes in molecular-dynamics simulations.

Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized.

Density equalisation in supercooled high- and low-density water mixtures.

The temporal evolution of two model high-density/low-density (HDL/LDL) interfaces was examined from molecular dynamics (MD) calculations at temperatures close to the predicted second critical point of water for three water models. In all cases, interfacial density equalisation occurred rapidly showing no preference for inhomogenous distribution. A uniform density (of ca. 0.99-1.067 g/cm(3), depending on the potential) was always observed at the interface, indicating the free energy of water in low- and high-density forms is metastable, and that LDL and HDL should not coexist as independent entities at thermodynamic equilibrium. It is reckoned that previous MD studies supporting the "two-liquid" model have an explicit, if inappropriate, assumption of mechanical equilibrium between the two phases. The present result challenges the notion that a second critical point exists, and that LDL/HDL mixtures could be even kinetically metastable.