Mild-Temperature Supercritical Water Confined in Hydrophobic Metal-Organic Frameworks.

Fluids under extreme confinement show characteristics significantly different from those of their bulk counterpart. This work focuses on water confined within the complex cavities of highly hydrophobic metal-organic frameworks (MOFs) at high pressures. A combination of high-pressure intrusion-extrusion experiments with molecular dynamic simulations and synchrotron data reveals that supercritical transition for MOF-confined water takes place at a much lower temperature than in bulk water, ∼250 K below the reference values. This large shifting of the critical temperature (Tc) is attributed to the very large density of confined water vapor in the peculiar geometry and chemistry of the cavities of Cu2tebpz (tebpz = 3,3',5,5'-tetraethyl-4,4'-bipyrazolate) hydrophobic MOF. This is the first time the shift of Tc is investigated for water confined within highly hydrophobic nanoporous materials, which explains why such a large reduction of the critical temperature was never reported before, neither experimentally nor computationally.

Multiscale biomolecular simulations in the exascale era.

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in developing a versatile and high-performance multiscale simulation framework with the aim of efficient utilization of state-of-the-art supercomputers. We showcase its application in uncovering complex biological mechanisms and its potential for leveraging exascale computing.

Exploring the Heat of Water Intrusion into a Metal-Organic Framework by Experiment and Simulation.

Wetting of a solid by a liquid is relevant for a broad range of natural and technological processes. This process is complex and involves the generation of heat, which is still poorly understood especially in nanoconfined systems. In this article, scanning transitiometry was used to measure and evaluate the pressure-driven heat of intrusion of water into solid ZIF-8 powder within the temperature range of 278.15-343.15 K. The conditions examined included the presence and absence of atmospheric gases, basic pH conditions, solid sample origins, and temperature. Simultaneously with these experiments, molecular dynamics simulations were conducted to elucidate the changing behavior of water as it enters into ZIF-8. The results are rationalized within a temperature-dependent thermodynamic cycle. This cycle describes the temperature-dependent process of ZIF-8 filling, heating, emptying, and cooling with respect to the change of internal energy of the cycle from the calculated change in the specific heat capacity of the system. At 298 K the experimental heat of intrusion per gram of ZIF-8 was found to be -10.8 ± 0.8 J·g-1. It increased by 19.2 J·g-1 with rising temperature to 343 K which is in a reasonable match with molecular dynamic simulations that predicted 16.1 J·g-1 rise. From these combined experiments, the role of confined water in heat of intrusion of ZIF-8 is further clarified.

Tuning Wetting-Dewetting Thermomechanical Energy for Hydrophobic Nanopores via Preferential Intrusion.

Heat and the work of compression/decompression are among the basic properties of thermodynamic systems. Being relevant to many industrial and natural processes, this thermomechanical energy is challenging to tune due to fundamental boundaries for simple fluids. Here via direct experimental and atomistic observations, we demonstrate, for fluids consisting of nanoporous material and a liquid, one can overcome these limitations and noticeably affect both thermal and mechanical energies of compression/decompression exploiting preferential intrusion of water from aqueous solutions into subnanometer pores. We hypothesize that this effect is due to the enthalpy of dilution manifesting itself as the aqueous solution concentrates upon the preferential intrusion of pure water into pores. We suggest this genuinely subnanoscale phenomenon can be potentially a strategy for controlling the thermomechanical energy of microporous liquids and tuning the wetting/dewetting heat of nanopores relevant to a variety of natural and technological processes spanning from biomedical applications to oil-extraction and renewable energy.

Effect of Crystallite Size on the Flexibility and Negative Compressibility of Hydrophobic Metal-Organic Frameworks.

Flexible nanoporous materials are of great interest for applications in many fields such as sensors, catalysis, material separation, and energy storage. Of these, metal-organic frameworks (MOFs) are the most explored thus far. However, tuning their flexibility for a particular application remains challenging. In this work, we explore the effect of the exogenous property of crystallite size on the flexibility of the ZIF-8 MOF. By subjecting hydrophobic ZIF-8 to hydrostatic compression with water, the flexibility of its empty framework and the giant negative compressibility it experiences during water intrusion were recorded via in operando synchrotron irradiation. It was observed that as the crystallite size is reduced to the nanoscale, both flexibility and the negative compressibility of the framework are reduced by ∼25% and ∼15%, respectively. These results pave the way for exogenous tuning of flexibility in MOFs without altering their chemistries.

GNN for Deep Full Event Interpretation and Hierarchical Reconstruction of Heavy-Hadron Decays in Proton-Proton Collisions.

The LHCb experiment at the Large Hadron Collider (LHC) is designed to perform high-precision measurements of heavy-hadron decays, which requires the collection of large data samples and a good understanding and suppression of multiple background sources. Both factors are challenged by a fivefold increase in the average number of proton-proton collisions per bunch crossing, corresponding to a change in the detector operation conditions for the LHCb Upgrade I phase, recently started. A further tenfold increase is expected in the Upgrade II phase, planned for the next decade. The limits in the storage capacity of the trigger will bring an inverse relationship between the number of particles selected to be stored per event and the number of events that can be recorded. In addition the background levels will rise due to the enlarged combinatorics. To tackle both challenges, we propose a novel approach, never attempted before in a hadronic collider: a Deep-learning based Full Event Interpretation (DFEI), to perform the simultaneous identification, isolation and hierarchical reconstruction of all the heavy-hadron decay chains per event. This strategy radically contrasts with the standard selection procedure used in LHCb to identify heavy-hadron decays, that looks individually at subsets of particles compatible with being products of specific decay types, disregarding the contextual information from the rest of the event. Following the DFEI approach, once the relevant particles in each event are identified, the rest can be safely removed to optimise the storage space and maximise the trigger efficiency. We present the first prototype for the DFEI algorithm, that leverages the power of Graph Neural Networks (GNN). This paper describes the design and development of the algorithm, and its performance in Upgrade I simulated conditions.

Hydrophobicity of molecular-scale textured surfaces: The case of zeolitic imidazolate frameworks, an atomistic perspective.

Hydrophobicity has proven fundamental in an inexhaustible amount of everyday applications. Material hydrophobicity is determined by chemical composition and geometrical characteristics of its macroscopic surface. Surface roughness or texturing enhances intrinsic hydrophilic or hydrophobic characteristics of a material. Here we consider crystalline surfaces presenting molecular-scale texturing typical of crystalline porous materials, e.g., metal-organic frameworks. In particular, we investigate one such material with remarkable hydrophobic qualities, ZIF-8. We show that ZIF-8 hydrophobicity is driven not only by its chemical composition but also its sub-nanoscale surface corrugations, a physical enhancement rare amongst hydrophobes. Studying ZIF-8's hydrophobic properties is challenging as experimentally it is difficult to distinguish between the materials' and the macroscopic corrugations' contributions to the hydrophobicity. The computational contact angle determination is also difficult as the standard "geometric" technique of liquid nanodroplet deposition is prone to many artifacts. Here, we characterise ZIF-8 hydrophobicity via: (i) the "geometric" approach and (ii) the "energetic" method, utilising the Young-Dupré formula and computationally determining the liquid-solid adhesion energy. Both approaches reveal nanoscale Wenzel-like bathing of the corrugated surface. Moreover, we illustrate the importance of surface linker termination in ZIF-8 hydrophobicity, which reduces when varied from sp3 N to sp2 N termination. We also consider halogenated analogues of the methyl-imidazole linker, which promote the transition from nanoWenzel-like to nanoCassie-Baxter-like states, further enhancing surface hydrophobicity. Present results reveal the complex interface physics and chemistry between water and complex porous, molecular crystalline surfaces, providing a hint to tune their hydrophobicity.

Mechanism of Water Intrusion into Flexible ZIF-8: Liquid Is Not Vapor.

Zeolitic Imidazolate Frameworks (ZIF) find application in storage and dissipation of mechanical energy. Their distinctive properties linked to their (sub)nanometer size and hydrophobicity allow for water intrusion only under high hydrostatic pressure. Here we focus on the popular ZIF-8 material investigating the intrusion mechanism in its nanoscale cages, which is the key to its rational exploitation in target applications. In this work, we used a joint experimental/theoretical approach combining in operando synchrotron experiments during high-pressure intrusion experiments, molecular dynamics simulations, and stochastic models to reveal that water intrusion into ZIF-8 occurs by a cascade filling of connected cages rather than a condensation process as previously assumed. The reported results allowed us to establish structure/function relations in this prototypical microporous material, representing an important step to devise design rules to synthesize porous media.

Optimization of the wetting-drying characteristics of hydrophobic metal organic frameworks via crystallite size: The role of hydrogen bonding between intruded and bulk liquid.

HYPOTHESIS: The behavior of Heterogeneous Lyophobic Systems (HLSs) comprised of a lyophobic porous material and a corresponding non-wetting liquid is affected by a variety of different structural parameters of the porous material. Dependence on exogenic properties such as crystallite size is desirable for system tuning as they are much more facilely modified. We explore the dependence of intrusion pressure and intruded volume on crystallite size, testing the hypothesis that the connection between internal cavities and bulk water facilitates intrusion via hydrogen bonding, a phenomenon that is magnified in smaller crystallites with a larger surface/volume ratio. EXPERIMENTS: Water intrusion/extrusion pressures and intrusion volume were experimentally measured for ZIF-8 samples of various crystallite sizes and compared to previously reported values. Alongside the practical research, molecular dynamics simulations and stochastic modeling were performed to illustrate the effect of crystallite size on the properties of the HLSs and uncover the important role of hydrogen bonding within this phenomenon. FINDINGS: A reduction in crystallite size led to a significant decrease of intrusion and extrusion pressures below 100 nm. Simulations indicate that this behavior is due to a greater number of cages being in proximity to bulk water for smaller crystallites, allowing cross-cage hydrogen bonds to stabilize the intruded state and lower the threshold pressure of intrusion and extrusion. This is accompanied by a reduction in the overall intruded volume. Simulations demonstrate that this phenomenon is linked to ZIF-8 surface half-cages exposed to water being occupied by water due to non-trivial termination of the crystallites, even at atmospheric pressure.

Classical nucleation of vapor between hydrophobic plates.

In this work, an extended classical nucleation theory (CNT), including line tension, is used to disentangle classical and non-classical effects in the nucleation of vapor from a liquid confined between two hydrophobic plates at a nanometer distance. The proposed approach allowed us to gauge, from the available simulation work, the importance of elusive nanoscale effects, such as line tension and non-classical modifications of the nucleation mechanism. Surprisingly, the purely macroscopic theory is found to be in quantitative accord with the microscopic data, even for plate distances as small as 2 nm, whereas in extreme confinement (<1.5 nm), the CNT approximations proved to be unsatisfactory. These results suggest how classical nucleation theory still offers a computationally inexpensive and predictive tool useful in all domains where nanoconfined evaporation occurs-including nanotechnology, surface science, and biology.

Effect of coarse graining in water models for the study of kinetics and mechanisms of clathrate hydrates nucleation and growth.

Clathrate hydrates are crystalline inclusion compounds wherein a water framework encages small guest atoms/molecules within its cavities. Among the others, methane clathrates are the largest fossil fuel resource still available. They can also be used to safely transport gases and can also form spontaneously under suitable conditions plugging pipelines. Understanding the crystallization mechanism is very important, and given the impossibility of experimentally identifying the atomistic path, simulations played an important role in this field. Given the large computational cost of these simulations, in addition to all-atom force fields, scientists considered coarse-grained water models. Here, we have investigated the effect of coarse-graining, as implemented in the water model mW, on the crystallization characteristics of methane clathrate in comparison with the all-atom TIP4P force field. Our analyses revealed that although the characteristics directly depending on the energetics of the water models are well reproduced, dynamical properties are off by the orders of magnitude. Being crystallization a non-equilibrium process, the altered kinetics of the process results in different characteristics of crystalline nuclei. Both TIP4P and mW water models produce methane clathrate nuclei with some amount of the less stable (in the given thermodynamic conditions) structure II phase and an excess of pentagonal dodecahedral cages over the tetrakaidecahedral ones regarding the ideal ratio in structure I. However, the dependence of this excess on the methane concentration in solution is higher with the former water model, whereas with the latter, the methane concentration in solution dependence is reduced and within the statistical error.

Effect of the Topology on Wetting and Drying of Hydrophobic Porous Materials.

Establishing molecular mechanisms of wetting and drying of hydrophobic porous materials is a general problem for science and technology within the subcategories of the theory of liquids, chromatography, nanofluidics, energy storage, recuperation, and dissipation. In this article, we demonstrate a new way to tackle this problem by exploring the effect of the topology of pure silica nanoparticles, nanotubes, and zeolites. Using molecular dynamics simulations, we show how secondary porosity promotes the intrusion of water into micropores and affects the hydrophobicity of materials. It is demonstrated herein that for nano-objects, the hydrophobicity can be controlled by changing the ratio of open to closed nanometer-sized lateral pores. This effect can be exploited to produce new materials for practical applications when the hydrophobicity needs to be regulated without significantly changing the chemistry or structure of the materials. Based on these simulations and theoretical considerations, for pure silica zeolites, we examined and then classified the experimental database of intrusion pressures, thus leading to the prediction of any zeolite's intrusion pressure. We show a correlation between the intrusion pressure and the ratio of the accessible pore surface area to total pore volume. The correlation is valid for some zeolites and mesoporous materials. It can facilitate choosing prospective candidates for further investigation and possible exploitation, especially for energy storage, recuperation, and dissipation.

Turning Molecular Springs into Nano-Shock Absorbers: The Effect of Macroscopic Morphology and Crystal Size on the Dynamic Hysteresis of Water Intrusion-Extrusion into-from Hydrophobic Nanopores.

Controlling the pressure at which liquids intrude (wet) and extrude (dry) a nanopore is of paramount importance for a broad range of applications, such as energy conversion, catalysis, chromatography, separation, ionic channels, and many more. To tune these characteristics, one typically acts on the chemical nature of the system or pore size. In this work, we propose an alternative route for controlling both intrusion and extrusion pressures via proper arrangement of the grains of the nanoporous material. To prove the concept, dynamic intrusion-extrusion cycles for powdered and monolithic ZIF-8 metal-organic framework were conducted by means of water porosimetry and in operando neutron scattering. We report a drastic increase in intrusion-extrusion dynamic hysteresis when going from a fine powder to a dense monolith configuration, transforming an intermediate performance of the ZIF-8 + water system (poor molecular spring) into a desirable shock-absorber with more than 1 order of magnitude enhancement of dissipated energy per cycle. The obtained results are supported by MD simulations and pave the way for an alternative methodology of tuning intrusion-extrusion pressure using a macroscopic arrangement of nanoporous material.

Double Life of Methanol: Experimental Studies and Nonequilibrium Molecular-Dynamics Simulation of Methanol Effects on Methane-Hydrate Nucleation.

We have investigated systematically and statistically methanol-concentration effects on methane-hydrate nucleation using both experiment and restrained molecular-dynamics simulation, employing simple observables to achieve an initially homogeneous methane-supersaturated solution particularly favorable for nucleation realization in reasonable simulation times. We observe the pronounced "bifurcated" character of the nucleation rate upon methanol concentration in both experiments and simulation, with promotion at low concentrations and switching to industrially familiar inhibition at higher concentrations. Higher methanol concentrations suppress hydrate growth by in-lattice methanol incorporation, resulting in the formation of "defects", increasing the energy of the nucleus. At low concentrations, on the contrary, the detrimental effect of defects is more than compensated for by the beneficial contribution of CH3 in easing methane incorporation in the cages or replacing it altogether.

Subnanometer Topological Tuning of the Liquid Intrusion/Extrusion Characteristics of Hydrophobic Micropores.

Intrusion (wetting)/extrusion (drying) of liquids in/from lyophobic nanoporous systems is key in many fields, including chromatography, nanofluidics, biology, and energy materials. Here we demonstrate that secondary topological features decorating main channels of porous systems dramatically affect the intrusion/extrusion cycle. These secondary features, allowing an unexpected bridging with liquid in the surrounding domains, stabilize the water stream intruding a micropore. This reduces the intrusion/extrusion barrier and the corresponding pressures without altering other properties of the system. Tuning the intrusion/extrusion pressures via subnanometric topological features represents a yet unexplored strategy for designing hydrophobic micropores. Though energy is not the only field of application, here we show that the proposed tuning approach may bring 20-75 MPa of intrusion/extrusion pressure increase, expanding the applicability of hydrophobic microporous materials.

Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC.

We present an interface of the wavefunction-based quantum chemical software CFOUR to the multiscale modeling framework MiMiC. Electrostatic embedding of the quantum mechanical (QM) part is achieved by analytic evaluation of one-electron integrals in CFOUR, while the rest of the QM/molecular mechanical (MM) operations are treated according to the previous MiMiC-based QM/MM implementation. Long-range electrostatic interactions are treated by a multipole expansion of the potential from the QM electron density to reduce the computational cost without loss of accuracy. Testing on model water/water systems, we verified that the CFOUR interface to MiMiC is robust, guaranteeing fast convergence of the self-consistent field cycles and optimal conservation of the energy during the integration of the equations of motion. Finally, we verified that the CFOUR interface to MiMiC is compatible with the use of a QM/QM multiple time-step algorithm, which effectively reduces the cost of ab initio MD (AIMD) or QM/MM-MD simulations using higher level wavefunction-based approaches compared to cheaper density functional theory-based ones. The new wavefunction-based AIMD and QM/MM-MD implementations were tested and validated for a large number of wavefunction approaches, including Hartree-Fock and post-Hartree-Fock methods like Møller-Plesset, coupled-cluster, and complete active space self-consistent field.

Crystal-Size-Induced Band Gap Tuning in Perovskite Films.

A comprehensive picture explaining the effect of the crystal size in metal halide perovskite films on their opto-electronic characteristics is currently lacking. We report that perovskite nanocrystallites exhibit a wider band gap due to concurrent quantum confinement and size dependent structural effects, with the latter being remarkably distinct and attributed to the perturbation from the surface of the nanocrystallites affecting the structure of their core. This phenomenon might assist in the photo-induced charge separation within the perovskite in devices employing mesoporous layers as they restrict the size of nanocrystallites present in them. We demonstrate that the crystal size effect is widely applicable as it is ubiquitous in different compositions and deposition methods employed in the fabrication of state-of-the-art perovskite solar cells. This effect is a convenient and effective way to tune the band gap of perovskites.

Giant Negative Compressibility by Liquid Intrusion into Superhydrophobic Flexible Nanoporous Frameworks.

Materials or systems demonstrating negative linear compressibility (NLC), whose size increases (decreases) in at least one of their dimensions upon compression (decompression) are very rare. Materials demonstrating this effect in all their dimensions, negative volumetric compressibility (NVC), are exceptional. Here, by liquid porosimetry and in situ neutron diffraction, we show that one can achieve exceptional NLC and NVC values by nonwetting liquid intrusion in flexible porous media, namely in the ZIF-8 metal-organic framework (MOF). Atomistic simulations show that the volumetric expansion is due to the presence of liquid in the windows connecting the cavities of ZIF-8. This discovery paves the way for designing novel materials with exceptional NLC and NVC at reasonable pressures suitable for a wide range of applications.

The interplay among gas, liquid and solid interactions determines the stability of surface nanobubbles.

Surface nanobubbles are gaseous domains found at immersed substrates, whose remarkable persistence is still not fully understood. Recently, it has been observed that the formation of nanobubbles is often associated with a local high gas oversaturation at the liquid-solid interface. Tan, An and Ohl have postulated the existence of an effective potential attracting the dissolved gas to the substrate and producing a local oversaturation within 1 nm from it that can stabilize nanobubbles by preventing outgassing in the region where gas flow would be maximum. It is this effective solid-gas potential - which is not the intrinsic, mechanical interaction between solid and gas atoms - its dependence on chemical and physical characteristics of the substrate, gas and liquid, that controls the stability and the other characteristics of surface nanobubbles. Here, we perform free energy atomistic calculations to determine, for the first time, the effective solid-gas interaction that allows us to identify the molecular origin of the stability and other properties of surface nanobubbles. By combining the Tan-An-Ohl model and the present results, we provide a comprehensive theoretical framework allowing, among others, the interpretation of recent unexplained experimental results, such as the stability of surface nanobubbles in degassed liquids, the very high gas concentration in the liquid surrounding nanobubbles, and nanobubble instability in organic solvents with high gas solubility.

Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study.

The koff values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-infrequent metadynamics, based on the AMBER force field-to compute the koff of the ligand iperoxo (in clinical use) targeting the muscarinic receptor M2. The ligand charges are calculated by either (i) the Amber standard procedure or (ii) B3LYP-DFT. The calculations using (i) turn out not to provide a reasonable estimation of the transition-state free energy. Those using (ii) differ from experiment by 2 orders of magnitude. On the basis of B3LYP DFT QM/MM simulations, we suggest that the observed discrepancy in (ii) arises, at least in part, from the lack of electronic polarization and/or charge transfer in biomolecular force fields. These issues might be present in other systems, such as DNA-protein complexes.