Temperature Dependence of Non-Condon Effects in Two-Dimensional Vibrational Spectroscopy of Water

Non-Condon effects in vibrational spectroscopy refers to the dependence of a molecule's vibrational transition dipole and polarizability on the coordinates of the surrounding environment. Earlier studies have shown that such effects can be pronounced for hydrogen-bonded systems like liquid water. Here, we present a theoretical study of two-dimensional vibrational spectroscopy under the non-Condon and Condon approximations at varying temperatures. We have performed calculations of both two-dimensional infrared and two-dimensional vibrational Raman spectra to gain insights into the temperature dependence of non-Condon effects in nonlinear vibrational spectroscopy. The two-dimensional spectra are calculated for the OH vibration of interest in the isotopic dilution limit where the coupling between the oscillators is ignored. Generally, both the infrared and Raman line shapes undergo red shifts with decrease in temperature due to strengthening of hydrogen bonds and decrease in the fraction of OH modes with weaker or no hydrogen bonds. The infrared line shape is further red-shifted under the non-Condon effects at a given temperature, while the Raman line shape does not show any such red shift due to non-Condon effects. The spectral dynamics becomes slower on decrease of temperature due to slower hydrogen bond relaxation and, for a given temperature, the spectral diffusion occurs at a faster rate upon inclusion of non-Condon effects. The time scales of spectral diffusion extracted from different metrics agree well with each other and also with experiments. The changes in the spectrum due to non-Condon effects are found to be more significant at lower temperatures.

Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel

Connexin 36 (Cx36) is responsible for signal transmission in electrical synapses by forming interneuronal gap junctions. Despite the critical role of Cx36 in normal brain function, the molecular architecture of the Cx36 gap junction channel (GJC) is unknown. Here, we determine cryo-electron microscopy structures of Cx36 GJC at 2.2-3.6 Å resolutions, revealing a dynamic equilibrium between its closed and open states. In the closed state, channel pores are obstructed by lipids, while N-terminal helices (NTHs) are excluded from the pore. In the open state with pore-lining NTHs, the pore is more acidic than those in Cx26 and Cx46/50 GJCs, explaining its strong cation selectivity. The conformational change during channel opening also includes the α-to-π-helix transition of the first transmembrane helix, which weakens the protomer-protomer interaction. Our structural analyses provide high resolution information on the conformational flexibility of Cx36 GJC and suggest a potential role of lipids in the channel gating.

Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset

Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.

Fluorescent Probes cis- and trans-Parinaric Acids in Fluid and Gel Lipid Bilayers: A Molecular Dynamics Study

Fluorescence probes are indispensable tools in biochemical and biophysical membrane studies. Most of them possess extrinsic fluorophores, which often constitute a source of uncertainty and potential perturbation to the host system. In this regard, the few available intrinsically fluorescent membrane probes acquire increased importance. Among them, cis- and trans-parinaric acids (c-PnA and t-PnA, respectively) stand out as probes of membrane order and dynamics. These two compounds are long-chained fatty acids, differing solely in the configurations of two double bonds of their conjugated tetraene fluorophore. In this work, we employed all-atom and coarse-grained molecular dynamics simulations to study the behavior of c-PnA and t-PnA in lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), representative of the liquid disordered and solid ordered lipid phases, respectively. All-atom simulations indicate that the two probes show similar location and orientation in the simulated systems, with the carboxylate facing the water/lipid interface and the tail spanning the membrane leaflet. The two probes establish interactions with the solvent and lipids to a similar degree in POPC. However, the almost linear t-PnA molecules have tighter lipid packing around them, especially in DPPC, where they also interact more with positively charged lipid choline groups. Probably for these reasons, while both probes show similar partition (assessed from computed free energy profiles across bilayers) to POPC, t-PnA clearly partitions more extensively than c-PnA to the gel phase. t-PnA also displays more hindered fluorophore rotation, especially in DPPC. Our results agree very well with experimental fluorescence data from the literature and allow deeper understanding of the behavior of these two reporters of membrane organization.

Scaled charges for ions: An improvement but not the final word for modeling electrolytes in water

In this work, we discuss the use of scaled charges when developing force fields for NaCl in water. We shall develop force fields for Na⁺ and Cl^- using the following values for the scaled charge (in electron units): ±0.75, ±0.80, ±0.85, and ±0.92 along with the TIP4P/2005 model of water (for which previous force fields were proposed for q = ±0.85 and q = ±1). The properties considered in this work are densities, structural properties, transport properties, surface tension, freezing point depression, and maximum in density. All the developed models were able to describe quite well the experimental values of the densities. Structural properties were well described by models with charges equal to or larger than ±0.85, surface tension by the charge ±0.92, maximum in density by the charge ±0.85, and transport properties by the charge ±0.75. The use of a scaled charge of ±0.75 is able to reproduce with high accuracy the viscosities and diffusion coefficients of NaCl solutions for the first time. We have also considered the case of KCl in water, and the results obtained were fully consistent with those of NaCl. There is no value of the scaled charge able to reproduce all the properties considered in this work. Although certainly scaled charges are not the final word in the development of force fields for electrolytes in water, its use may have some practical advantages. Certain values of the scaled charge could be the best option when the interest is to describe certain experimental properties.

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.

Dynamics of Aqueous Electrolyte Solutions: Challenges for Simulations

This Perspective article focuses on recent simulation work on the dynamics of aqueous electrolytes. It is well-established that full-charge, nonpolarizable models for water and ions generally predict solution dynamics that are too slow in comparison to experiments. Models with reduced (scaled) charges do better for solution diffusivities and viscosities but encounter issues describing other dynamic phenomena such as nucleation rates of crystals from solution. Polarizable models show promise, especially when appropriately parametrized, but may still miss important physical effects such as charge transfer. First-principles calculations are starting to emerge for these properties that are in principle able to capture polarization, charge transfer, and chemical transformations in solution. While direct ab initio simulations are still too slow for simulations of large systems over long time scales, machine-learning models trained on appropriate first-principles data show significant promise for accurate and transferable modeling of electrolyte solution dynamics.

Atmospheric water harvesting using functionalized carbon nanocones

In this work, we propose a method to harvest liquid water from water vapor using carbon nanocones. The condensation occurs due to the presence of hydrophilic sites at the nanocone entrance. The functionalization, together with the high mobility of water inside nanostructures, leads to a fast water flow through the nanostructure. We show using molecular dynamics simulations that this device is able to collect water if the surface functionalization is properly selected.

Hydrophilic Versus Hydrophobic Coupling in the Pressure Dependence of the Chemical Potential of Alkali Metal and Halide Ions in Water

We computed the chemical potential for some alkali metal ions (K⁺, Rb⁺, and Cs⁺) and two halide ions (Br^- and I^-) in aqueous solution at ambient T and various pressures in the range 1-8000 atm. Results were obtained from classic Monte Carlo simulations in the NPT ensemble by means of the free energy perturbation method. Here, the chemical potential is computed as the sum of a term relative to a Lennard-Jones solute and a term relative to the process in which this solute is transformed into the ion. Hydrophobic and hydrophilic features of these two components of the chemical potential show opposite behaviors under isothermal compression. The increase in pressure determines an increase in the hydrophobic component, which becomes more positive with a stronger effect for larger ions. Correspondingly, the values of the hydrophilic component become more negative for alkali ions, whereas they are only slightly affected by compression for halide ions. Hydrophobic-hydrophilic quasi-compensation in the slopes is observed for Rb⁺. For a smaller ion, such as K⁺, the dependence on pressure of the hydrophilic component is slightly dominant. For a larger ion, as observed in the cases of Cs⁺, Br^-, and I^-, the hydrophobic component assumes the determinant role. Pressure dependence of the chemical potential is little affected by corrections introduced for molecular potential truncation. This view can change for possible boundary artifacts that could have affected the static electrostatic potential. Some inference is obtained from comparison with experimental data at 1 atm on the free energy of hydration. Discrepancies show the characteristic asymmetry between cations and anions. The further addition of a correction based on the static potential significantly reduces these discrepancies with important error cancellation on the sum of chemical potentials of ions of opposite charge. The correction is applied also at higher pressures, and results are compared with those obtained by adding an alternative correction that is based on the water number density. Regardless of the ion, changes of the chemical potential induced by an increase in pressure appear to be dominated by the hydrophobic component, in particular when using the alternative correction. For bromide and iodide electrolytes, the two corrections give chemical potentials in good agreement.

Orcinol and resorcinol induce local ordering of water molecules near the liquid-vapor interface

Resorcinol and orcinol are simple members of the family of phenolic compounds present in particulate matter in the atmosphere; they are amphiphilic in nature and thus surface active in aqueous solution. Here, we used X-ray photoelectron spectroscopy to probe the concentration of resorcinol (benzene-1,3-diol) and orcinol (5-methylbenzene-1,3-diol) at the liquid-vapor interface of aqueous solutions. Qualitatively consistent surface propensity and preferential orientation was obtained by molecular dynamics simulations. Auger electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy was used to probe the hydrogen bonding (HB) structure, indicating that the local structure of water molecules near the surface of the resorcinol and orcinol solutions tends towards a larger fraction of tetrahedrally coordinated molecules than observed at the liquid-vapor interface of pure water. The order parameter obtained from the molecular dynamics simulations confirm these observations. This effect is being discussed in terms of the formation of an ordered structure of these molecules at the surface leading to patterns of hydrated OH groups with distances among them that are relatively close to those in ice. These results suggest that the self-assembly of phenolic species at the aqueous solution-air interface could induce freezing similar to the case of fatty alcohol monolayers and, thus, be of relevance for ice nucleation in the atmosphere. We also attempted at looking at the changes of the O 1b₁, 3a₂ and 1b₂ molecular orbitals of liquid water, which are known to be sensitive to the HB structure as well, in response to the presence of resorcinol and orcinol. However, these changes remained negligible within uncertainty for both experimentally obtained valence spectra and theoretically calculated density of states.

Fast Polarizable Water Model for Atomistic Simulations

Simulating water accurately has been a major challenge in atomistic simulations for decades. Inclusion of electronic polarizability effects holds considerable promise, yet existing approaches suffer from significant computational overheads compared to the widely used nonpolarizable water models. We have developed a globally optimal polarizable water model, OPC3-pol, that explicitly accounts for electronic polarizability with minimal impact on the computational efficiency. OPC3-pol reproduces five key bulk water properties at room temperature with an average relative error of 0.6%. In atomistic simulations, OPC3-pol's computational efficiency is in between that of 3- and 4-point nonpolarizable models; the model supports increased (4 fs) integration time step. OPC3-pol is tested in simulations of globular protein ubiquitin and a B-DNA dodecamer with several AMBER force fields, ff99SB, ff14SB, ff19SB, and OL15, demonstrating structure stability close to reference on multi-microsecond time scale. Simulation of an intrinsically disordered amyloid β-peptide yields an ensemble with the radius of gyration of a random coil. The proposed water model can be trivially adopted by any package that supports standard nonpolarizable force fields and water models; its intended use is in long classical atomistic simulations where water polarization effects are expected to be important.

Pharmacological mechanism and therapeutic efficacy of Icariside II in the treatment of acute ischemic stroke: a systematic review and network pharmacological analysis

Background and objective

Epimedii has long been used as a traditional medicine in Asia for the treatment of various common diseases, including Alzheimer's disease, cancer, erectile dysfunction, and stroke. Studies have reported the ameliorative effects of Icariside II (ICS II), a major metabolite of Epimedii, on acute ischemic stroke (AIS) in animal models. Based on network pharmacology, molecular docking, and molecular dynamics (MD) simulations, we conducted a systematic review to evaluate the effects and neuroprotective mechanisms of ICS II on AIS.

Methods

First, we have searched 6 databases using studies with ICS II treatment on AIS animal models to explore the efficacy of ICS II on AIS in preclinical studies. The literature retrieval time ended on March 8, 2022 (Systematic Review Registration ID: CRD42022306291). There were no restrictions on the language of the search strategy. Systematic review follows the Patient, Intervention, Comparison and Outcome (PICO) methodology and framework. SYCLE's RoB tool was used to evaluate the the risk of bias. In network pharmacology, AIS-related genes were identified and the target-pathway network was constructed. Then, these targets were used in the enrichments of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene ontology (GO). Molecular docking and MD simulation were finally employed between ICS II and the potential target genes.

Results

Twelve publications were included describing outcomes of 1993 animals. The literature details, animal strains, induction models, doses administered, duration of administration, and outcome measures were extracted from the 12 included studies. ICS II has a good protective effect against AIS. Most of the studies in this systematic review had the appropriate methodological quality, but some did not clearly state the controlling for bias of potential study. Network pharmacology identified 246 targets with SRC, CTNNB1, HSP90AA1, MAPK1, and RELA as the core target proteins. Besides, 215 potential pathways of ICS II were identified, such as PI3K-Akt, MAPK, and cGMP-PKG signaling pathway. GO enrichment analysis showed that ICS II was significantly enriched in subsequent regulation such as MAPK cascade. Molecular docking and MD simulations showed that ICS II can closely bind with important targets.

Conclusions

ICS II is a promising drug in the treatment of AIS. However, this systematic review reveals key knowledge gaps (i.e., the protective role of ICS II in women) that ICS II must address before it can be used for the treatment of human AIS. Our study shows that ICS II plays a protective role in AIS through multi-target and multi-pathway characteristics, providing ideas for the development of drugs for the treatment of AIS.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03732-9.

Effect of sodium chloride adsorption on the surface premelting of ice

We characterise the structural properties of the quasi-liquid layer (QLL) at two low-index ice surfaces in the presence of sodium chloride (Na⁺/Cl^-) ions by molecular dynamics simulations. We find that the presence of a high surface density of Na⁺/Cl^- pairs changes the surface melting behaviour from step-wise to gradual melting. The ions lead to an overall increase of the thickness and the disorder of the QLL, and to a low-temperature roughening transition of the air-ice interface. The local molecular structure of the QLL is similar to that of liquid water, and the differences between the basal and primary prismatic surface are attenuated by the presence of Na⁺/Cl^- pairs. These changes modify the crystal growth rates of different facets and the solvation environment at the surface of sea-water ice with a potential impact on light scattering and environmental chemical reactions.

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.

Molecular dynamics analysis of elastic properties and new phase formation during amorphous ices transformations

Unlike conventional first-order phase transitions, the kinetics of amorphous-amorphous transitions has been much less studied. The ultrasonic experiments on the transformations between low-density and high-density amorphous ice induced by pressure or heating provided the pressure and temperature dependencies of elastic moduli. In this article, we make an attempt to build a microscopic picture of these experimentally studied transformations using the molecular dynamics method with the TIP4P/Ice water model. We study carefully the dependence of the results of elastic constants calculations on the deformation rates. The system size effects are considered as well. The comparison with the experimental data enriches our understanding of the transitions observed. Our modeling gives new information about the formation mechanisms of new phase clusters during the transition between low-density and high-density amorphous ices. We analyse the applicability of the term “nucleation” for these processes.

Modeling Gd3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of MRI Contrast Agents

The correct parametrization of lanthanide complexes is of the utmost importance for their characterization using computational tools such as molecular dynamics simulations. This allows the optimization of their properties for a wide range of applications, including medical imaging. Here we present a systematic study to establish the best strategies for the correct parametrization of lanthanide complexes using [Gd(DOTA)]^- as a reference, which is used as a contrast agent in MRI. We chose the bonded model to parametrize the lanthanide complexes, which is especially important when considering the study of the complex as a whole (e.g., for the study of the dynamics of its interaction with proteins or membranes). We followed two strategies: a so-called heuristic approach employing strategies already published by other authors and another based on the more recent MCPB.py tool. Adjustment of the Lennard-Jones parameters of the metal was required. The final topologies obtained with both strategies were able to reproduce the experimental ion to oxygen distance, vibrational frequencies, and other structural properties. We report a new strategy to adjust the Lennard-Jones parameters of the metal ion in order to capture dynamic properties such as the residence time of the capping water (τ_m). For the first time, the correct assessment of the τ_m value for Gd-based complexes was possible by recording the dissociative events over up to 10 μs all-atom simulations. The MCPB.py tool allowed the accurate parametrization of [Gd(DOTA)]^- in a simpler procedure, and in this case, the dynamics of the water molecules in the outer hydration sphere was also characterized. This sphere was divided into the first hydration layer, an intermediate region, and an outer hydration layer, with a residence time of 18, 10 and 19 ps, respectively, independent of the nonbonded parameters chosen for Gd³⁺. The Lennard-Jones parameters of Gd³⁺ obtained here for [Gd(DOTA)]^- may be used with similarly structured gadolinium MRI contrast agents. This allows the use of molecular dynamics simulations to characterize and optimize the contrast agent properties. The characterization of their interaction with membranes and proteins will permit the design of new targeted contrast agents with improved pharmacokinetics.

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.

Quantum simulations of neutral water clusters and singly-charged water cluster anions

We report a computational study of the structural and energetic properties of water clusters and singly-charged water cluster anions containing from 20 to 573 water molecules. We have used both a classical and a quantum description of the molecular degrees of freedom. Water intra and inter-molecular interactions have been modelled through the SPC/F model, while the water-excess electron interaction has been described via the well-known Turi-Borgis potential. We find that in general the quantum effects of the water degrees of freedom are small, but they do influence the cluster-size at which the excess electron stabilises inside the cluster, which occurs at smaller cluster sizes when quantum effects are taken into consideration.

Water Diffusion Proceeds via a Hydrogen-Bond Jump Exchange Mechanism

The self-diffusion of water molecules plays a key part in a broad range of essential processes in biochemistry, medical imaging, material science, and engineering. However, its molecular mechanism and the role played by the water hydrogen-bond network rearrangements are not known. Here we combine molecular dynamics simulations and analytic modeling to determine the molecular mechanism of water diffusion. We establish a quantitative connection between the water diffusion coefficient and hydrogen-bond jump exchanges, and identify the features that determine the underlying energetic barrier. We thus provide a unified framework to understand the coupling between translational, rotational, and hydrogen-bond dynamics in liquid water. It explains why these different dynamics do not necessarily exhibit identical temperature dependences although they all result from the same hydrogen-bond exchange events. The consequences for the understanding of water diffusion in supercooled conditions and for water transport in complex aqueous systems, including ionic, biological, and confined solutions, are discussed.

The lung surfactant activity probed with molecular dynamics simulations

The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.

Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization

The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca²⁺ than Mg²⁺, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg²⁺). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.

The "good," the "bad," and the "hidden" in neutron scattering and molecular dynamics of ionic aqueous solutions

We characterize a concentrated 7.3 m CaCl₂ solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca²⁺-Cl^- interactions were primarily "hidden" in the Ca-NDIS signal due to overlapping with Ca²⁺-O_w and Ca²⁺-H_w contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models "on average," the question "which model is the best" has not been answered but replaced by the question "which model is better for a given research." An overall "good" model can still be inappropriate or, in some instances, "bad" and, unfortunately, produce erroneous results. The accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.

Can molecular simulations reliably compare homogeneous and heterogeneous ice nucleation?

In principle, the answer to the posed titular question is undoubtedly "yes." But in practice, requisite reference data for homogeneous systems have been obtained with a treatment of intermolecular interactions that is different from that typically employed for heterogeneous systems. In this article, we assess the impact of the choice of truncation scheme when comparing water in homogeneous and inhomogeneous environments. Specifically, we use explicit free energy calculations and a simple mean field analysis to demonstrate that using the "cut-and-shift" version of the Lennard-Jones potential (common to most simple point charge models of water) results in a systematic increase in the melting temperature of ice I_h. In addition, by drawing an analogy between a change in cutoff and a change in pressure, we use existing literature data for homogeneous ice nucleation at negative pressures to suggest that enhancements due to heterogeneous nucleation may have been overestimated by several orders of magnitude.

Maximum in density of electrolyte solutions: Learning about ion-water interactions and testing the Madrid-2019 force field

In this work, we studied the effect of Li⁺, Na⁺, K⁺, Mg²⁺, and Ca²⁺ chlorides and sulfates on the temperature of maximum density (TMD) of aqueous solutions at room pressure. Experiments at 1 molal salt concentration were carried out to determine the TMD of these solutions. We also performed molecular dynamics simulations to estimate the TMD at 1 and 2 m with the Madrid-2019 force field, which uses the TIP4P/2005 water model and scaled charges for the ions, finding an excellent agreement between experiment and simulation. All the salts studied in this work shift the TMD of the solution to lower temperatures and flatten the density vs temperature curves (when compared to pure water) with increasing salt concentration. The shift in the TMD depends strongly on the nature of the electrolyte. In order to explore this dependence, we have evaluated the contribution of each ion to the shift in the TMD concluding that Na⁺, Ca²⁺, and SO₄ ^2- seem to induce the largest changes among the studied ions. The volume of the system has been analyzed for salts with the same anion and different cations. These curves provide insight into the effect of different ions upon the structure of water. We claim that the TMD of electrolyte solutions entails interesting physics regarding ion-water and water-water interactions and should, therefore, be considered as a test property when developing force fields for electrolytes. This matter has been rather unnoticed for almost a century now and we believe it is time to revisit it.

The coexistence curve and surface tension of a monatomic water model

We study the monatomic water model of Molinero and Moore the grand canonical ensemble Monte Carlo simulation. Measurements of the probability distribution of the number density obtained via multicanonical sampling and histogram reweighting provide accurate estimates of the temperature dependence of both the liquid-vapor coexistence densities and the surface tension. Using finite-size scaling methods, we locate the liquid-vapor critical point at T_c = 917.6 K, ρ_c = 0.311 g cm^-3. When plotted in scaled variables, in order to test the law of corresponding states, the coexistence curve of monatomic water is close to that of real water. In this respect, it performs better than extended simple point charge (SPC/E), TIP4P, and TIP4P/2005 water.

Molecular dynamics simulations of the evaporation of hydrated ions from aqueous solution

Although important for atmospheric processes and gas-phase catalysis, very little is known about the hydration state of ions in the vapor phase. Here we study the evaporation energetics and kinetics of a chloride ion from liquid water by molecular dynamics simulations. As chloride permeates the interface, a water finger forms and breaks at a chloride separation of ≈ 2.8 nm from the Gibbs dividing surface. For larger separations from the interface, about 7 water molecules are estimated to stay bound to chloride in saturated water vapor, as corroborated by continuum dielectrics and statistical mechanics models. This ion hydration significantly reduces the free-energy barrier for evaporation. The effective chloride diffusivity in the transition state is found to be about 6 times higher than in bulk, which reflects the highly mobile hydration dynamics as the water finger breaks. Both effects significantly increase the chloride evaporation flux from the quiescent interface of an electrolyte solution, which is predicted from reaction kinetic theory.

Field-Induced Electron Generation in Water: Solvation Dynamics and Many-Body Interactions

The solvated electron represents an elementary quantum system in a liquid environment. Electrons solvated in water have raised strong interest because of their prototypical properties, their role in radiation chemistry, and their relevance for charge separation and transport. Nonequilibrium dynamics of photogenerated electrons in water occur on ultrafast time scales and include charge transfer, localization, and energy dissipation processes. We present new insight into the role of fluctuating electric fields of the liquid for generating electrons in the presence of an external terahertz field and address polaronic many-body properties of solvated electrons. This Perspective combines a review of recent results from experiment and theory with a discussion of basic electric interactions of electrons in water.

Dipolar Relaxation of Water Protons in the Vicinity of a Collagen-like Peptide

Quantitative magnetic resonance imaging is one of the few available methods for noninvasive diagnosis of degenerative changes in articular cartilage. The clinical use of the imaging data is limited by the lack of a clear association between structural changes at the molecular level and the measured magnetic relaxation times. In anisotropic, collagen-containing tissues, such as articular cartilage, the orientation dependency of nuclear magnetic relaxation can obscure the content of the images. Conversely, if the molecular origin of the phenomenon would be better understood, it would provide opportunities for diagnostics as well as treatment planning of degenerative changes in these tissues. We study the magnitude and orientation dependence of the nuclear magnetic relaxation due to dipole–dipole coupling of water protons in anisotropic, collagenous structures. The water–collagen interactions are modeled with molecular dynamics simulations of a small collagen-like peptide dissolved in water. We find that in the vicinity of the collagen-like peptide, the dipolar relaxation of water hydrogen nuclei is anisotropic, which can result in orientation-dependent relaxation times if the water remains close to the peptide. However, the orientation-dependency of the relaxation is different from the commonly observed magic-angle phenomenon in articular cartilage MRI.

A molecular simulation study into the stability of hydrated graphene nanochannels used in nanofluidics devices

Graphene-based nanochannels are a popular choice in emerging nanofluidics applications because of their tunable and nanometer-scale channels. In this work, molecular dynamics (MD) simulations were employed both to (i) assess the stability of dry and hydrated graphene nanochannels and (ii) elucidate the properties of water confined in these channels, using replica-scale models with 0.66-2.38 nm channel heights. The use of flexible nanochannel walls allows the nanochannel height to relax in response to the solvation forces arising from the confined fluid and the forces between the confining surfaces, without the need for application of arbitrarily high external pressures. Dry nanochannels were found to completely collapse if the initial nanochannel height was less than 2 nm, due to attractive van der Waals interactions between the confining graphene surfaces. However, the presence of water was found to prevent total nanochannel collapse, due to repulsive hydration forces opposing the attractive van der Waals force. For nanochannel heights less than ∼1.7 nm, the confining surfaces must be relaxed to obtain accurate hydration pressures and water diffusion coefficients, by ensuring commensurability between the number of confined water layers and the channel height. For very small (∼0.7 nm), hydrated channels a pressure of 231 MPa due to the van der Waals forces was obtained. In the same system, the confined water forms a mobile, liquid monolayer with a diffusion coefficient of 4.0 × 10^-5 cm² s^-1, much higher than bulk liquid water. Although this finding conflicts with most classical MD simulations, which predict in-plane order and arrested dynamics, it is supported by experiments and recently published first-principles MD simulations. Classical simulations can therefore be used to predict the properties of water confined in sub-nanometre graphene channels, providing sufficiently realistic molecular models and accurate intermolecular potentials are employed.

A Benchmark Protocol for DFT Approaches and Data-Driven Models for Halide-Water Clusters

Dissolved ions in aqueous media are ubiquitous in many physicochemical processes, with a direct impact on research fields, such as chemistry, climate, biology, and industry. Ions play a crucial role in the structure of the surrounding network of water molecules as they can either weaken or strengthen it. Gaining a thorough understanding of the underlying forces from small clusters to bulk solutions is still challenging, which motivates further investigations. Through a systematic analysis of the interaction energies obtained from high-level electronic structure methodologies, we assessed various dispersion-corrected density functional approaches, as well as ab initio-based data-driven potential models for halide ion-water clusters. We introduced an active learning scheme to automate the generation of optimally weighted datasets, required for the development of efficient bottom-up anion-water models. Using an evolutionary programming procedure, we determined optimized and reference configurations for such polarizable and first-principles-based representation of the potentials, and we analyzed their structural characteristics and energetics in comparison with estimates from DF-MP2 and DFT+D quantum chemistry computations. Moreover, we presented new benchmark datasets, considering both equilibrium and non-equilibrium configurations of higher-order species with an increasing number of water molecules up to 54 for each F, Cl, Br, and I anions, and we proposed a validation protocol to cross-check methods and approaches. In this way, we aim to improve the predictive ability of future molecular computer simulations for determining the ongoing conflicting distribution of different ions in aqueous environments, as well as the transition from nanoscale clusters to macroscopic condensed phases.

Structural characteristics of low-density environments in liquid water

The existence of two structural forms in liquid water has been a point of discussion for a long time. A phase transition between these two forms of liquid water has been proposed based on evidence from molecular simulations, and experiments have also been very recently able to track the proposed transition of the low-density liquid form to the high-density liquid form. We propose to use the average angle an oxygen atom makes with its neighbors to describe the structural environment of a water molecule. The distribution of this order parameter is observed to have two peaks with one peak at ∼109.5^{∘}, corresponding to the internal angle of a regular tetrahedron, indicating tetrahedral arrangement. The other peak corresponds to an environment with a tighter arrangement of neighboring molecules. The distribution of O-O-O angles is decomposed into two skewed distributions to estimate the fractions of the two liquid forms in water. A good similarity is observed between the temperature and pressure trends of fractions of locally favored tetrahedral structure (LFTS) form estimated using the new order parameter and the reports in the literature, over a range of temperatures and pressures. We also compare the structural environments indicated by different order parameters and find that the order parameter proposed in this paper captures the structure of first solvation shell of the LFTS accurately.

Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E

Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using twelve different Mg2+ parameter sets, that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygens on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.

Molecular dynamics simulations of structural and dynamical aspects of DNA hydration water

Water is a remarkable liquid, both because of it is intriguing but also because of its importance. Water plays a key role on the structure and function of biological molecules, but on the other hand also the structure and dynamics of water are deeply influenced by its interactions with biological molecules, specially at low temperatures, where water's anomalies are enhanced. Here we present extensive molecular dynamics simulations of water hydrating a oligonucleotide down to very low temperatures (supercooled water), comparing four water models and analyzing the water structure and dynamics in different domains: water in the minor groove, water in the major groove and bulk water. We found that the water in the grooves is slowed down by the interactions with the nucleic acid and a hints of a dynamic transition regarding translational and orientational dynamics were found, specially for the water models TIP4P/2005 and TIP4P-Ew, which also showed the closest agreement with available experimental data. The behavior of water in such extreme conditions is relevant for the study of cryopreservation of biological tissues.

Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA

Magnesium is an indispensable cofactor in countless vital processes. In order to understand its functional role, the characterization of the binding pathways to biomolecules such as RNA is crucial. Despite the importance, a molecular description is still lacking since the transition from the water-mediated outer-sphere to the direct inner-sphere coordination is on the millisecond time scale and therefore out of reach for conventional simulation techniques. To fill this gap, we use transition path sampling to resolve the binding pathways and to elucidate the role of the solvent in the binding process. The results reveal that the molecular void provoked by the leaving phosphate oxygen of the RNA is immediately filled by an entering water molecule. In addition, water molecules from the first and second hydration shell couple to the concerted exchange. To capture the intimate solute-solvent coupling, we perform a committor analysis as the basis for a machine learning algorithm that derives the optimal deep learning model from thousands of scanned architectures using hyperparameter tuning. The results reveal that the properly optimized deep network architecture recognizes the important solvent structures, extracts the relevant information, and predicts the commitment probability with high accuracy. Our results provide detailed insights into the solute-solvent coupling which is ubiquitous for kosmotropic ions and governs a large variety of biochemical reactions in aqueous solutions.

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D

Magnesium is essential in many vital processes. To correctly describe Mg2+ in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput. 2021, 17, 2530-2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg2+ parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg2+ force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 106 to 108 exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg2+, or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs.

The physics of empty liquids: from patchy particles to water

Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.

Appraising the potency of small molecule inhibitors and their graphene surface-mediated organizational attributes on uric acid-melamine clusters

Uric acid (UA) and melamine (MM) crystallization in humans is associated with adverse medical conditions, including the germination of kidney stones, because of their low solubility. The growth of kidney stones, usually formed on renal papillary facades, is accomplished on the matrix-coated surface by the aggregation of preformed crystals or secondary crystal nucleation. Therefore, the effects of inhibitors such as theobromine (TB) and allopurinol (AP) on MM-UA aggregation are investigated by employing classical molecular dynamics simulations on a graphene surface. This impersonates the exact essence of the precipitation of kidney stones. The interaction between MM-UA is very intense and, thus, large clusters are formed on the surface. The presence of TB and AP will, however, substantially inhibit their aggregation. TB and AP significantly impede UA aggregation in particular. Therefore, lower order UA clusters are formed. These smaller UA clusters then pull a lower number of MM towards themselves, resulting in a smaller order UA-MM cluster. MM and UA aggregation on a 2D graphene surface is found to be spontaneous. There is no difference in these molecules' adsorption with a change in the force field parameters (i.e., GAFF and OPLS-AA) for graphene. Moreover, the greater the surface area of graphene, the more molecules are absorbed. The solute-surface van der Waals interaction energy plays a driving force in the adsorption of solute molecules on the surface. In addition, interactions like hydrogen bonding and π-stacking over the graphene surface involve binding all like molecules. These aggregated solute molecules strongly attract more like molecules until all solute molecules are adsorbed on the graphene surface, as estimated by enhanced sampling. The molecular origin of graphene exfoliation by MM is also described here. The present work helps to design novel kidney stone inhibitors.

Site-Specific Water Dynamics in the First Hydration Layer of an Anti-Freeze Glyco-Protein: A Simulation Study

Antifreeze glycoproteins (AFGPs) inhibit ice recrystallization by a mechanism remaining largely elusive. Dynamics of AFGPs’ hydration water and its involvement in the antifreeze activity, for instance, have not been identified...

Polarisation of water under thermal fields: the effect of the molecular dipole and quadrupole moments

The investigation of the behaviour of water under thermal fields is important to understand thermoelectricity of solutions, aqueous suspensions, bioelectric effects or the properties of wet materials under spatially inhomogeneous...

Universal Two-Component Dynamics in Supercritical Fluids

Despite the technological importance of supercritical fluids, controversy remains about the details of their microscopic dynamics. In this work, we study four supercritical fluid systems—water, Si, Te, and Lennard-Jones fluid—via classical molecular dynamics simulations. A universal two-component behavior is observed in the intermolecular dynamics of these systems, and the changing ratio between the two components leads to a crossover from liquidlike to gaslike dynamics, most rapidly around the Widom line. We find evidence to connect the liquidlike component dominating at lower temperatures with intermolecular bonding and the component prominent at higher temperatures with free-particle, gaslike dynamics. The ratio between the components can be used to describe important properties of the fluid, such as its self-diffusion coefficient, in the transition region. Our results provide an insight into the fundamental mechanism controlling the dynamics of supercritical fluids and highlight the role of spatiotemporally inhomogeneous dynamics even in thermodynamic states where no large-scale fluctuations exist in the fluid.