On the brink of self-hydration: the water heptadecamer

For pure, neutral, isolated molecular clusters, (H2O)17 marks the transition from structures with all water molecules on the cluster surface to water self-hydration, i.e., cluster structures around one central water molecule. Getting this right with water model potentials turns out to be challenging. Even the best water potentials currently available, which reproduce collective properties very well, still deliver contradicting results for (H2O)17, when different low-energy isomers from global structure optimizations are examined. Interestingly, ab initio quantum chemistry also struggles with the only seemingly simple question if (H2O)17 is all-surface or water-centered. Hence, although the long history of water potential development may be entering its final phase, it is not quite finished yet.

The performance of OPC and OPC3 water models in predictions of 2D structures under nanoconfinement

Nanoconfined water plays an important role in broad fields of science and engineering. Classical molecular dynamics (MD) simulations have been widely used to investigate water phases under nanoconfinement. The key ingredient of MD is the force field. In this study, we systematically investigated the performance of a recently introduced family of globally optimal water models, OPC and OPC3, and TIP4P/2005 in describing nanoconfined two-dimensional (2D) water ice. Our studies show that the melting points of the monolayer square ice (MSI) of all three water models are higher than the melting points of the corresponding bulk ice Ih. Under the same conditions, the melting points of MSI of OPC and TIP4P/2005 are the same and are ∼90 K lower than that of the OPC3 water model. In addition, we show that OPC and TIP4P/2005 water models are able to form a bilayer AA-stacked structure and a trilayer AAA-stacked structure, which are not the cases for the OPC3 model. Considering the available experimental data and first-principles simulations, we consider the OPC water model as a potential water model for 2D water ice MD studies.

Accuracy of TIP4P/2005 and SPC/Fw Water Models

Water is used as the main solvent in model systems containing bioorganic molecules. Choosing the right water model is an important step in the study of the biophysical and biochemical processes that occur in cells. In the present work, we perform molecular dynamics simulations using two distinct force fields for water: the rigid model TIP4P/2005, where only intermolecular interactions are considered, and the flexible model SPC/Fw, where intramolecular interactions are also taken into account. The simulations aim to determine the effect of the inclusion of intramolecular interactions on the accuracy of calculated properties of bulk water (density and thermal expansion coefficient, self-diffusion coefficients, shear viscosity, radial distribution functions, and dielectric constant), as compared to experimental results, over a temperature range between 250 and 370 K. We find that the results of the rigid model present the smallest deviations relative to experiments for most of the calculated quantities, except for the shear viscosity of supercooled water and the water dielectric constant, where the flexible model presents better agreement with experiments.

Simulations of disordered matter in 3D with the morphological autoregressive protocol (MAP) and convolutional neural networks

Disordered molecular systems, such as amorphous catalysts, organic thin films, electrolyte solutions, and water, are at the cutting edge of computational exploration at present. Traditional simulations of such systems at length scales relevant to experiments in practice require a compromise between model accuracy and quality of sampling. To address this problem, we have developed an approach based on generative machine learning called the Morphological Autoregressive Protocol (MAP), which provides computational access to mesoscale disordered molecular configurations at linear cost at generation for materials in which structural correlations decay sufficiently rapidly. The algorithm is implemented using an augmented PixelCNN deep learning architecture that, as we previously demonstrated, produces excellent results in 2 dimensions (2D) for mono-elemental molecular systems. Here, we extend our implementation to multi-elemental 3D and demonstrate performance using water as our test system in two scenarios: (1) liquid water and (2) samples conditioned on the presence of pre-selected motifs. We trained the model on small-scale samples of liquid water produced using path-integral molecular dynamics simulations, including nuclear quantum effects under ambient conditions. MAP-generated water configurations are shown to accurately reproduce the properties of the training set and to produce stable trajectories when used as initial conditions in quantum dynamics simulations. We expect our approach to perform equally well on other disordered molecular systems in which structural correlations decay sufficiently fast while offering unique advantages in situations when the disorder is quenched rather than equilibrated.

The Magnetic Field Freezes the Mercedes-Benz Water Model

In this study, we investigate the impact of magnetic fields on the structural and thermodynamic properties of water. To accomplish this, we employed the Mercedes-Benz (MB) model, a two-dimensional representation of water using Lennard-Jones disks with angle-dependent interactions that closely mimic hydrogen bond formation. We extended the MB model by introducing two charges to enable interaction with the magnetic field. Employing molecular dynamics simulations, we thoroughly explored the thermodynamic properties concerning various magnetic flux intensities. As a result, we observed that under a weak magnetic flux, the property of water remained unaltered, while a stronger flux astonishingly led to the freezing of water molecules. Furthermore, our study revealed that once a specific flux magnitude was reached, the density anomaly disappeared, and an increase in flux caused the MB particles to form a glassy state.

Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study

Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.

Stereoelectronic Switches of Single-Molecule Junctions through Conformation-Modulated Intramolecular Coupling Approaches

Stereoelectronic effects in single-molecule junctions have been widely utilized to achieve a molecular switch, but high-efficiency and reproducible switching remain challenging. Here, we demonstrate that there are three stable intramolecular conformations in the 9,10-diphenyl-9,10-methanoanthracen-11-one (DPMAO) systems due to steric effect. Interestingly, different electronic coupling approaches including weak coupling (through-space), decoupling, and strong coupling (through-bond) between two terminal benzene rings are accomplished in the three stable conformations, respectively. Theoretical calculations show that the molecular conductance of three stable conformations differs by more than 1 order of magnitude. Furthermore, the populations of the three stable conformations are highly dependent on the solvent effect and the external electric field. Therefore, an excellent molecular switch can be achieved using the DPMAO molecule junctions and external stimuli. Our findings reveal that modulating intramolecular electronic coupling approaches may be a useful manner to enable molecular switches with high switching ratios. This opens up a new route for building high-efficiency molecular switches in single-molecular junctions.

Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents

We develop a Stockmayer fluid model that accounts for the dielectric responses of polar solvents (water, MeOH, EtOH, acetone, 1-propanol, DMSO, and DMF) and NaCl solutions. These solvent molecules are represented by Lennard-Jones (LJ) spheres with permanent dipole moments and the ions by charged LJ spheres. The simulated dielectric constants of these liquids are comparable to experimental values, including the substantial decrease in the dielectric constant of water upon the addition of NaCl. Moreover, the simulations predict an increase in the dielectric constant when considering the influence of ion translations in addition to the orientation of permanent dipoles.

Supercooled solutions of sodium perchlorate in TIP4P/2005 water: The effect of martian solutes on thermodynamics and structure

We study the thermodynamic behavior of sodium perchlorate solutions in supercooled water through molecular dynamics numerical simulations. These solutions are of special interest because of the recent experimental results that led to hypothesize the presence of liquid water in perchlorate solutions beneath the Martian soil. We model water using the TIP4P/2005 potential. The results we obtain for solutions with concentrations 1.63 and 15.4 wt% are in agreement with those of a system undergoing a liquid-liquid phase transition where the liquid-liquid critical point shifts to slightly higher temperatures and lower pressures. The structure of the system is also analyzed, and we come to the conclusion that, even at the highest concentration considered, water retains its anomalous behavior.

Impact of hierarchical water dipole orderings on the dynamics of aqueous salt solutions

Ions exhibit highly ion-specific complex behaviours when solvated in water, which remains a mystery despite the fundamental importance of ion solvation in nature, science, and technology. Here we explain these ion-specific properties by the ion-induced hierarchical dipolar, translational, and bond-orientational orderings of ion hydration shell under the competition between ion-water electrostatic interactions and inter-water hydrogen bonding. We first characterise this competition by a new length λHB(q), explaining the ion-specific effects on solution dynamics. Then, by continuously tuning ion size and charge, we find that the bond-orientational order of the ion hydration shell highly develops for specific ion size and charge combinations. This ordering drastically stabilises the hydration shell; its degree changes the water residence time around ions by 11 orders of magnitude for main-group ions. These findings are fundamental to ionic processes in aqueous solutions, providing a physical principle for electrolyte design and application.

A Neural-Network-Optimized Hydrogen Peroxide Pairwise Additive Model for Classical Simulations

We have developed an all-atom pairwise additive model for hydrogen peroxide using an optimization procedure based on artificial neural networks (ANNs). The model is based on experimental molecular geometry and includes a dihedral potential that hinders the cis-type configuration and allows for crossing the trans one, defined between the planes that have the two oxygen atoms and each hydrogen. The model's parametrization is achieved by training simple ANNs to minimize a target function that measures the differences between various thermodynamic and transport properties and the corresponding experimental values. Finally, we evaluated a range of properties for the optimized model and its mixtures with SPC/E water, including bulk-liquid properties (density, thermal expansion coefficient, adiabatic compressibility, etc.) and properties of systems at equilibrium (vapor and liquid density, vapor pressure and composition, surface tension, etc.). Overall, we obtained good agreement with experimental data.

Ben Naim's four-arm model with density anomaly: Theory and computer simulations

Molecular dynamics, Wertheim's integral equation theory (IET), and thermodynamics perturbation theory (TPT) were used to study the thermodynamics and structure of particles interacting through angle-dependent potential. The particles are modeled as two-dimensional Lennard-Jones disks with four hydrogen bonding arms arranged symmetrically. The model was introduced by Ben-Naim and we call it the BN4 model. The BN4 model exhibits density anomaly and other anomalous properties similar to those in water and in the Mercedes-Benz (MB) model. The IET is based on the orientationally averaged version of the Ornstein-Zernike equation and correctly predicts the pair correlation function of the model at high temperatures. Both TPT and IET are in semiquantitative agreement with the simulation values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity.

Realistic phase diagram of water from "first principles" data-driven quantum simulations

Since the experimental characterization of the low-pressure region of water's phase diagram in the early 1900s, scientists have been on a quest to understand the thermodynamic stability of ice polymorphs on the molecular level. In this study, we demonstrate that combining the MB-pol data-driven many-body potential for water, which was rigorously derived from "first principles" and exhibits chemical accuracy, with advanced enhanced-sampling algorithms, which correctly describe the quantum nature of molecular motion and thermodynamic equilibria, enables computer simulations of water's phase diagram with an unprecedented level of realism. Besides providing fundamental insights into how enthalpic, entropic, and nuclear quantum effects shape the free-energy landscape of water, we demonstrate that recent progress in "first principles" data-driven simulations, which rigorously encode many-body molecular interactions, has opened the door to realistic computational studies of complex molecular systems, bridging the gap between experiments and simulations.

Density anomaly in water-alcohol mixtures: Minimum model for structure makers and breakers

We modeled the change in the temperature of maximum density (TMD) of a waterlike solvent when small amounts of solute are added to the mixture. The solvent is modeled as a two length scales potential, which is known to exhibit waterlike characteristic anomalies, while the solute is chosen to have an attractive interaction with the solvent which is tuned from small to large attractive potential. We show that if the solute exhibits high attraction with the solvent it behaves as a structure maker and the TMD increases with the addition of solute, while if the solute shows a low attraction with the solvent the TMD decreases, with the solute behaving as a structure breaker.

Self-diffusion and shear viscosity for the TIP4P/Ice water model

With an ever-increasing interest in water properties, many intermolecular force fields have been proposed to describe the behavior of water. Unfortunately, good models for liquid water usually cannot provide simultaneously an accurate melting point for ice. For this reason, the TIP4P/Ice model was developed for targeting the melting point and has become the preferred choice for simulating ice at coexistence. Unfortunately, available data for its dynamic properties in the liquid state are scarce. Therefore, we demonstrate a series of simulations aimed at the calculation of transport coefficients for the TIP4P/Ice model over a large range of thermodynamic conditions, ranging from T = 245 K to T = 350 K, for the temperature, and from p = 0 to p = 500 MPa, for the pressure. We have found that the self-diffusion (shear viscosity) exhibits smaller (increased) values than TIP4P/2005 and experiments. However, rescaling the temperature with respect to the triple point temperature, as in a corresponding states plot, we find that TIP4P/Ice compares very well with TIP4P/2005 and experiment. Such observations allow us to infer that despite the different original purposes of these two models examined here, one can benefit from a vast number of reports regarding the behavior of transport coefficients for the TIP4P/2005 model and utilize them following the routine described in this paper.

The electric field changes the anomalous properties of the Mercedes Benz water model

The influence of a homogeneous constant electric field on water properties was assessed. We used a simple two-dimensional statistical mechanical model called the Mercedes-Benz (MB) model of water in the study. The MB water molecules are two-dimensional disks with Gaussian arms that mimic the formation of hydrogen bonds. The model is modified with added charges for interaction with the electric field. The influence of the strength of the electric field on the water's properties was studied using Monte Carlo simulations. The structure and thermodynamics of the water were determined as a function of the strength of the electric field. We observed that the properties and phase transitions of the water in the low strength electric field does not change. In contrast, the high strength electric field shifts boiling and melting points as well as the position of the density maxima. After further increasing the strength of the electric field the density anomaly disappears.

Molecular Dynamics Simulation of the Synergistic Effect of Alkali/Surfactant/Polymer on the Formation and Stabilization of Water-Based Foam Systems

The stable maintenance effect of a chemical oil displacement agent on a foam liquid film usually creates problems with the oilfields surface system. To achieve comprehensive insights into the influence mechanism of these chemical agent components on the foam liquid film, an "SDBS/HPAM/OH^-" water-based foam simulation system and corresponding control systems were constructed by adjusting the categories and quantities of component molecules by molecular dynamics (MD) simulation. The simulated results indicated that the foam stability follows the order of "SDBS/HPAM/OH^-" system > "SDBS/HPAM" system > "SDBS" system. The smaller the inclination angle of the SDBS molecular tail chain, the greater the tendency of the SDBS molecular configuration to be "upright" at the gas-liquid interface, which is not conducive to preventing the aggregation and penetration of gas molecules at the gas-liquid interface. Although the presence of HPAM molecules can significantly enhance the stability of the liquid film by restricting the liquid film's drainage and the diffusion of gas molecules, the addition of HPAM molecules would weaken the formation ability of the foam liquid film. Through decreasing the aggregation of cations around the co-adsorption layer, OH^- not only enhances the interfacial activity of SDBS molecules, but also reduces the electrostatic repulsion between -COO^- groups on the HPAM molecular chain, which makes the foam more stable. With an increase in the pH, SDBS concentration, and HPAM concentration, the stability of foam liquid film was strengthened. These results are helpful in facilitating new insights into the formation and stabilization mechanism of water-based foams. In particular, they provide support for the development and application of new defoaming technologies.

Phase diagrams-Why they matter and how to predict them

Understanding the thermodynamic stability and metastability of materials can help us to, for example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to be durable. It can also help us to design experimental routes to novel phases with potentially interesting properties. In this Perspective, we provide an overview of how thermodynamic phase behavior can be quantified both in computer simulations and machine-learning approaches to determine phase diagrams, as well as combinations of the two. We review the basic workflow of free-energy computations for condensed phases, including some practical implementation advice, ranging from the Frenkel-Ladd approach to thermodynamic integration and to direct-coexistence simulations. We illustrate the applications of such methods on a range of systems from materials chemistry to biological phase separation. Finally, we outline some challenges, questions, and practical applications of phase-diagram determination which we believe are likely to be possible to address in the near future using such state-of-the-art free-energy calculations, which may provide fundamental insight into separation processes using multicomponent solvents.

Free energy calculations and unbiased molecular dynamics targeting the liquid-liquid transition in water no man's land

The existence of a first-order phase transition between a low-density liquid (LDL) and a high-density liquid (HDL) form of supercooled water has been a central and highly debated issue of physics and chemistry for the last three decades. We present a computational study that allows us to determine the free-energy landscapes of supercooled water over a wide range of pressure and temperature conditions using the TIP4P/2005 force field. Our approach combines topology-based structural transformation coordinates, state-of-the-art free-energy calculation methods, and extensive unbiased molecular dynamics. All our diverse simulations cannot detect any barrier within the investigated timescales and system size, for a discontinuous transition between the LDL and HDL forms throughout the so-called "no man's land," until the onset of the solid, non-diffusive amorphous forms.

Densities, Viscosities, Thermal Expansivities, and Isothermal Compressibilities of Carbonated Hydroalcoholic Solutions for Applications in Sparkling Beverages

Densities, viscosities, isothermal compressibilities, and thermal expansivities of carbonated hydroalcoholic solutions relevant for sparkling beverages are evaluated by molecular dynamics simulations as a function of temperature and alcoholic degree. They are compared with available experimental data, among which new measurements of densities and viscosities are performed in that respect. The OPC water model seems to yield the most accurate results, and the choice of CO₂ model has little influence on the results. Theoretical densities obtained with the OPC model typically deviate by ∼2 kg m^-3 from experimental data. At low alcoholic degrees (<9% EtOH vol), experimental viscosities lie in between theoretical values derived from the Stokes-Einstein formula and the calculation of transverse current autocorrelation functions, but at higher alcoholic degrees (≥9% EtOH vol), the Stokes-Einstein relation leads to viscosities in quantitative agreement with experiments. Isothermal compressibilities estimated with a fluctuation formula roughly extend from 0.40 to 0.49 GPa^-1 in close agreement with the experimental range of values. However, thermal expansivities are found to significantly overestimate experimental data, a behavior that is partly attributed to the low temperature of maximum density of the OPC model. Despite this discrepancy, our molecular model seems to be suitable for describing several transport and thermodynamic properties of carbonated hydroalcoholic solutions. It could therefore serve as a starting point to build more realistic models for carbonated beverages, from fizzy drinks to sparkling wines.

Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field

We introduce a new parametrization of the AMOEBA polarizable force field for water denoted Q-AMOEBA, for use in simulations that explicitly account for nuclear quantum effects (NQEs). This study is made possible thanks to the recently introduced adaptive Quantum Thermal Bath (adQTB) simulation technique which computational cost is comparable to classical molecular dynamics. The flexible Q-AMOEBA model conserves the initial AMOEBA functional form, with an intermolecular potential including an atomic multipole description of electrostatic interactions (up to quadrupole), a polarization contribution based on the Thole interaction model and a buffered 14-7 potential to model van der Waals interactions. It has been obtained by using a ForceBalance fitting strategy including high-level quantum chemistry reference energies and selected condensed-phase properties targets. The final Q-AMOEBA model is shown to accurately reproduce both gas-phase and condensed-phase properties, notably improving the original AMOEBA water model. This development allows the fine study of NQEs on water liquid phase properties such as the average H-O-H angle compared to its gas-phase equilibrium value, isotope effects, and so on. Q-AMOEBA also provides improved infrared spectroscopy prediction capabilities compared to AMOEBA03. Overall, we show that the impact of NQEs depends on the underlying model functional form and on the associated strength of hydrogen bonds. Since adQTB simulations can be performed at near classical computational cost using the Tinker-HP package, Q-AMOEBA can be extended to organic molecules, proteins, and nucleic acids opening the possibility for the large-scale study of the importance of NQEs in biophysics.

Double universality of the transition in the supercritical state

Universality aids consistent understanding of physical properties and states of matter where a theory predicts how a property of a phase (solid, liquid, and gas) changes with temperature or pressure. Here, we show that the matter above the critical point has a remarkable double universality. The first universality is the transition between the liquid-like and gas-like states seen in the crossover of the specific heat on the dynamical length with a fixed inversion point. The second universality is the operation of this effect in many supercritical fluids, including N₂, CO₂, Pb, H₂O, and Ar. Despite different structure and chemical bonding, the transition has the same fixed inversion point deep in the supercritical state. This advances our understanding of the supercritical state previously considered to be a featureless area on the phase diagram and a theoretical guide for improved deployment of supercritical fluids in green and environmental applications.

Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations

Water freezing is the most common liquid-to-crystal phase transition on Earth, however, despite its critical implications on climate change and cryopreservation among other disciplines, its characterization through experimental and computational techniques remains elusive. In this work, we make use of computer simulations to measure the nucleation rate (J) of water at normal pressure under different supercooling conditions, ranging from 215 to 240K. We employ two different water models, mW, a coarse-grained potential for water, and TIP4P/ICE, an atomistic non-polarizable water model that provides one of the most accurate representations of the different ice phases. To evaluate J, we apply the Lattice Mold technique, a computational method based on the use of molds to induce the nucleus formation from the metastable liquid under conditions at which observing spontaneous nucleation would be unfeasible. With this method, we obtain estimates of the nucleation rate for ice Ih, Ic and a stacking mixture of ice Ih/Ic; reaching consensus with most of the previously reported rates, although differing with some others. Furthermore, we confirm that the predicted nucleation rates by the TIP4P/ICE model are in better agreement with experimental data than those obtained through the mW potential. Taken together, our study provides a reliable methodology to measure nucleation rates in a simple and computationally efficient manner which contributes to benchmarking the freezing behaviour of two popular water models.

Ab initio machine learning of phase space averages

Equilibrium structures determine material properties and biochemical functions. We here propose to machine learn phase space averages, conventionally obtained by ab initio or force-field-based molecular dynamics (MD) or Monte Carlo (MC) simulations. In analogy to ab initio MD, our ab initio machine learning (AIML) model does not require bond topologies and, therefore, enables a general machine learning pathway to obtain ensemble properties throughout the chemical compound space. We demonstrate AIML for predicting Boltzmann averaged structures after training on hundreds of MD trajectories. The AIML output is subsequently used to train machine learning models of free energies of solvation using experimental data and to reach competitive prediction errors (mean absolute error ∼ 0.8 kcal/mol) for out-of-sample molecules-within milliseconds. As such, AIML effectively bypasses the need for MD or MC-based phase space sampling, enabling exploration campaigns of Boltzmann averages throughout the chemical compound space at a much accelerated pace. We contextualize our findings by comparison to state-of-the-art methods resulting in a Pareto plot for the free energy of solvation predictions in terms of accuracy and time.

The pressure induced phase diagram of double-layer ice under confinement: a first-principles study

Here, we present double-layer ice confined within various carbon nanotubes (CNTs) using state-of-the-art pressure induced (-5 GPa to 5 GPa) dispersion corrected density functional theory (DFT) calculations. We find that the double-layer ice exhibits remarkably rich and diverse phase behaviors as a function of pressure with varying CNT diameters. The lattice cohesive energies for various pure double layer ice phases follow the order of hexagonal > pentagonal > square tube > hexagonal-close-packed (HCP) > square > buckled-rhombic (b-RH). The confinement width was found to play a crucial role in the square and square tube phases in the intermediate pressure range of about 0-1 GPa. Unlike the phase transition in pure bilayer ice structures, the relative enthalpies demonstrate that the pentagonal phase, rather than the hexagonal structure, is the most stable ice polymorph at ambient pressure as well as in a deep negative pressure region, whereas the b-RH phase dominates under high pressure. The relatively short O⋯O distance of b-RH demonstrates the presence of a strong hydrogen bonding network, which is responsible for stabilizing the system.

Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks

Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.

Melting points of water models: Current situation

By using the direct coexistence method, we have calculated the melting points of ice I h at normal pressure for three recently proposed water models, namely, TIP3P-FB, TIP4P-FB, and TIP4P-D. We obtained T m = 216 K for TIP3P-FB, T m = 242 K for TIP4P-FB, and T m = 247 K for TIP4P-D. We revisited the melting point of TIP4P/2005 and TIP5P obtaining T m = 250 and 274 K, respectively. We summarize the current situation of the melting point of ice I h for a number of water models and conclude that no model is yet able to simultaneously reproduce the melting temperature of ice I h and the temperature of the maximum in density at room pressure. This probably points toward our both still incomplete knowledge of the potential energy surface of water and the necessity of incorporating nuclear quantum effects to describe both properties simultaneously.

Freezing point depression of salt aqueous solutions using the Madrid-2019 model

Salt aqueous solutions are relevant in many fields, ranging from biological systems to seawater. Thus, the availability of a force-field that is able to reproduce the thermodynamic and dynamic behavior of salt aqueous solutions would be of great interest. Unfortunately, this has been proven challenging, and most of the existing force-fields fail to reproduce much of their behavior. In particular, the diffusion of water or the salt solubility are often not well reproduced by most of the existing force-fields. Recently, the Madrid-2019 model was proposed, and it was shown that this force-field, which uses the TIP4P/2005 model for water and non-integer charges for the ions, provides a good description of a large number of properties, including the solution densities, viscosities, and the diffusion of water. In this work, we assess the performance of this force-field on the evaluation of the freezing point depression. Although the freezing point depression is a colligative property that at low salt concentrations depends solely on properties of pure water, a good model for the electrolytes is needed to accurately predict the freezing point depression at moderate and high salt concentrations. The coexistence line between ice and several salt aqueous solutions (NaCl, KCl, LiCl, MgCl₂, and Li₂SO₄) up to the eutectic point is estimated from direct coexistence molecular dynamics simulations. Our results show that this force-field reproduces fairly well the experimentally measured freezing point depression with respect to pure water freezing for all the salts and at all the compositions considered.

Temperature dependence of thermodynamic, dynamical, and dielectric properties of water models

We investigate the temperature dependence of thermodynamic (density and isobaric heat capacity), dynamical (self-diffusion coefficient and shear viscosity), and dielectric properties of several water models, such as the commonly employed TIP3P water model, the well-established four-point water model TIP4P-2005, and the recently developed four-point water model TIP4P-D. We focus on the temperature range of interest for the field of computational biophysics and soft matter (280–350 K). The four-point water models lead to a spectacularly improved agreement with experimental data, strongly suggesting that the use of more modern parameterizations should be favored compared to the more traditional TIP3P for modeling temperature-dependent phenomena in biomolecular systems.

In Silico Drug Design of Benzothiadiazine Derivatives Interacting with Phospholipid Cell Membranes

The use of drugs derived from benzothiadiazine, a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension, low blood sugar or the human immunodeficiency virus, among others. In this work we have investigated the interactions of benzothiadiazine and four of its derivatives designed in silico with model zwitterionic cell membranes formed by dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine and cholesterol at the liquid–crystal phase inside aqueous potassium chloride solution. We have elucidated the local structure of benzothiadiazine by means of microsecond molecular dynamics simulations of systems including a benzothiadiazine molecule or one of its derivatives. Such derivatives were obtained by the substitution of a single hydrogen site of benzothiadiazine by two different classes of chemical groups, one of them electron-donating groups (methyl and ethyl) and another one by electron-accepting groups (fluorine and trifluoromethyl). Our data have revealed that benzothiadiazine derivatives have a strong affinity to stay at the cell membrane interface although their solvation characteristics can vary significantly—they can be fully solvated by water in short periods of time or continuously attached to specific lipid sites during intervals of 10–70 ns. Furthermore, benzothiadiazines are able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of characteristic lengths between 1.6 and 2.1 Å.

Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments

The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.

Surface tension of liquids and binary mixtures from molecular dynamics simulations

In this work we assess and extend strategies for calculating surface tension of complex liquids from molecular dynamics simulations: the mechanical route and the instantaneous liquid interface (ILI) approach. The former employs the connection between stress tensor and surface tension, whereas the latter involves computation of instantaneous density field. Whereas the mechanical route is general, the ILI method involves system-dependent parameters restricting its original application to liquid water only. Here we generalize the approach to complex molecular liquids using atomic van der Waals radii. The performance of the approaches is evaluated on two liquid systems: acetonitrile and water-methanol mixture. In addition, we compare the effect of the computational models for interaction potentials based on semi-empirical electronic structure theory and classical force fields on the estimate of the surface tension within both stress tensor and ILI approaches.

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

Water models with realistic physical–chemical properties are essential to study a variety of biomedical processes or engineering technologies involving molecules or nanomaterials. Atomistic models of water are constrained by the feasible computational capacity, but calibrated coarse-grained (CG) ones can go beyond these limits. Here, we compare three popular atomistic water models with their corresponding CG model built using finite-size particles such as ellipsoids. Differently from previous approaches, short-range interactions are accounted for with the generalized Gay–Berne potential, while electrostatic and long-range interactions are computed from virtual charges inside the ellipsoids. Such an approach leads to a quantitative agreement between the original atomistic models and their CG counterparts. Results show that a timestep of up to 10 fs can be achieved to integrate the equations of motion without significant degradation of the physical observables extracted from the computed trajectories, thus unlocking a significant acceleration of water-based mesoscopic simulations at a given accuracy.

Soluble State of Villin Headpiece Protein as a Tool in the Assessment of MD Force Fields

Protein self-assembly plays an important role in cellular processes. Whereas molecular dynamics (MD) represents a powerful tool in studying assembly mechanisms, its predictions depend on the accuracy of underlying force fields, which are known to overly promote protein assembly. We here examine villin headpiece domain, HP36, which remains soluble at concentrations amenable to MD studies. The experimental characterization of soluble HP36 at concentrations of 0.05 to 1 mM reveals concentration-independent 90% monomeric and 10% dimeric populations. Extensive all-atom MD simulations at two protein concentrations, 0.9 and 8.5 mM, probe the HP36 dimer population, stability, and kinetics of dimer formation within two MD force fields, Amber ff14SB and CHARMM36m. MD results demonstrate that whereas CHARMM36m captures experimental HP36 monomer populations at the lower concentration, both force fields overly promote HP36 association at the higher concentration. Moreover, contacts stabilizing HP36 dimers are force-field-dependent. CHARMM36m produces consistently higher HP36 monomer populations, lower association rates, and weaker dependence of these quantities on the protein concentration than Amber ff14SB. Nonetheless, the highest monomer populations and dissociation constants are observed when the TIP3P water model in Amber ff14SB is replaced by TIP4P/2005, showcasing the critical role of the water model in addressing the protein solubility problem in MD.

A Review of Recent Developments in Molecular Dynamics Simulations of the Photoelectrochemical Water Splitting Process

In this review, we provide a short overview of the Molecular Dynamics (MD) method and how it can be used to model the water splitting process in photoelectrochemical hydrogen production. We cover classical non-reactive and reactive MD techniques as well as multiscale extensions combining classical MD with quantum chemical and continuum methods. Selected examples of MD investigations of various aqueous semiconductor interfaces with a special focus on TiO2 are discussed. Finally, we identify gaps in the current state-of-the-art where further developments will be needed for better utilization of MD techniques in the field of water splitting.

Dipole ordering of water molecules in cordierite: Monte Carlo simulations

Electric dipoles of water molecules, enclosed singly in regularly spaced nanopores of a cordierite crystal, become ordered at low temperature due to their mutual interaction and show the frequency dependence of their dielectric susceptibility, typical for relaxor ferroelectrics, according to recent experimental data. The corresponding phase transition is accompanied by anomalies in thermodynamic quantities, such as heat capacity and dielectric susceptibility, which are calculated here using the Monte Carlo method, and their agreement with the experimental data is discussed. Despite the increase in the correlation length, the partially filled dipole lattice at low temperatures, according to the calculations, does not have long-range order and corresponds to a dipole glass. This simulation gives a microscopical insight into the formation of polar nanoregions in relaxor ferroelectrics and the temperature dependence of their size.

Structural and topological changes across the liquid-liquid transition in water

It has recently been shown that the TIP4P/Ice model of water can be studied numerically in metastable equilibrium at and below its liquid-liquid critical temperature. We report here simulations along a subcritical isotherm, for which two liquid states with the same pressure and temperature but different density can be equilibrated. This allows for a clear visualization of the structural changes taking place across the transition. We specifically focus on how the topological properties of the H-bond network change across the liquid-liquid transition. Our results demonstrate that the structure of the high-density liquid, characterized by the existence of interstitial molecules and commonly explained in terms of the collapse of the second neighbor shell, actually originates from the folding back of long rings, bringing pairs of molecules separated by several hydrogen-bonds close by in space.

Effect of Water Content on Thermodynamic Properties of Compressed Hydrogen

Force field-based molecular simulations were used to calculate thermal expansivities, heat capacities, and Joule-Thomson coefficients of binary (standard) hydrogen-water mixtures for temperatures between 366.15 and 423.15 K and pressures between 50 and 1000 bar. The mole fraction of water in saturated hydrogen-water mixtures in the gas phase ranges from 0.004 to 0.138. The same properties were calculated for pure hydrogen at 323.15 K and pressures between 100 and 1000 bar. Simulations were performed using the TIP3P and a modified TIP4P force field for water and the Marx, Vrabec, Cracknell, Buch, and Hirschfelder force fields for hydrogen. The vapor-liquid equilibria of hydrogen-water mixtures were calculated along the melting line of ice Ih, corresponding to temperatures between 264.21 and 272.4 K, using the TIP3P force field for water and the Marx force field for hydrogen. In this temperature range, the solubilities and the chemical potentials of hydrogen and water were obtained. Based on the computed solubility data of hydrogen in water, the freezing-point depression of water was computed ranging from 264.21 to 272.4 K. The modified TIP4P and Marx force fields were used to improve the solubility calculations of hydrogen-water mixtures reported in our previous study [Rahbari A.;J. Chem. Eng. Data2019, 64, 4103-4115] for temperatures between 323 and 423 K and pressures ranging from 100 to 1000 bar. The chemical potentials of ice Ih were calculated as a function of pressure between 100 and 1000 bar, along the melting line for temperatures between 264.21 and 272.4 K, using the IAPWS equation of state for ice Ih. We show that at low pressures, the presence of water has a large effect on the thermodynamic properties of compressed hydrogen. Our conclusions may have consequences for the energetics of a hydrogen refueling station using electrochemical hydrogen compressors.

Effect of trehalose on protein cryoprotection: Insights into the mechanism of slowing down of hydration water

We study, with molecular dynamics simulations, a lysozyme protein immersed in a water-trehalose solution upon cooling. The aim is to understand the cryoprotectant role played by this disaccharide through the modifications that it induces on the slow dynamics of protein hydration water with its presence. The α-relaxation shows a fragile to strong crossover about 20° higher than that in the bulk water phase and 15° higher than that in lysozyme hydration water without trehalose. The protein hydration water without trehalose was found to show a second slower relaxation exhibiting a strong to strong crossover coupled with the protein dynamical transition. This slower relaxation time importantly appears enormously slowed down in our cryoprotectant solution. On the other hand, this long-relaxation in the presence of trehalose is also connected with a stronger damping of the protein structural fluctuations than that found when the protein is in contact with the pure hydration water. Therefore, this appears to be the mechanism through which trehalose manifests its cryoprotecting function.

Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water

There are a large number of force fields available to model water in molecular dynamics simulations, which each have their own strengths and weaknesses in describing the behavior of the liquid. One particular weakness in many of these models is their description of dynamics away from ambient conditions, where their ability to reproduce measurements is mixed. To investigate this issue, we use the recently developed fluctuation theory for dynamics to directly evaluate measures of the local temperature and pressure dependence: the activation energy and the activation volume. We examine these activation parameters for hydrogen-bond jump exchange times, OH reorientation times, and diffusion coefficients calculated from the SPC/E, SPC/Fw, TIP3P-PME, TIP3P-PME/Fw, OPC3, TIP4P/2005, TIP4P/Ew, E3B2, and E3B3 water models. Activation energy decompositions available through the fluctuation theory approach provide mechanistic insight into the origins of different temperature dependences between the various models, as well as the influence of three-body effects and flexibility.

Bulk supercooled water versus adsorbed films on silica surfaces: specific heat by Monte Carlo simulation

Between 150 and 230.6 K, bulk supercooled water freezes upon cooling, and amorphous ice crystallizes upon heating: bulk water thus exists only in its stable ice form. To circumvent this problem, experiments are generally performed on water adsorbed in SiO2 based porous systems. In this work, we take advantage of Monte Carlo simulations to explore this metastable supercooled region inaccessible to experiments. Using three rigid, non-polarizable water models, namely SPC, TIP4P and TIP4P/2005, we investigate the isobaric specific heat capacity (Cp), between 100 and 300 K, of bulk water and water films of few monolayers adsorbed on different SiO2 surfaces: a smooth surface, a non-hydroxylated (0001) surface of quartz, and a fully hydroxylated (001) surface of cristobalite. As Cp is directly related to the entropy fluctuations and we focus on low temperatures, the convergence of the Monte Carlo simulations is a critical point of this work. Also, due to the small mass of the hydrogen atoms, quantum corrections are taken into account, and lead to an excellent agreement of the simulated and experimental Cp values at low temperature (100 K region). Altogether, we conclude that, in bulk, Cp is shown to exhibit a broad peak around 225 K for the SPC and TIP4P models, and around 250 K for the TIP4P/2005 model, in qualitative agreement with the experimentally observed features in Cp measurements. For interfacial water, in all cases, the broad Cp peak disappears. This result, at odds with experimental observations, suggests that disorder and hydrogen bonding at the interface (not yet taken into account) have a fundamental role in confined water transitions.

Quantum-mechanical exploration of the phase diagram of water

The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.