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Correction to Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study
This errata is to correct the acknowledgment in the original published article. G.B. (partial support), V.-A.G., M.-T.N., and R.R. were supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. Computer resources were provided by Research Computing at Pacific Northwest National Laboratory and the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231. PNNL is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. G.B. acknowledges the EPSRC for partial support in PhD funding. The authors acknowledge the use of the IRIDIS High Performance Computing Facility (IRIDIS 5) and associated support services at the University of Southampton in the completion of this work. We are grateful to the UK Materials and Molecular Modeling Hub (Thomas HPC) for computational resources, which is partially funded by EPSRC (EP/P020194/1).
DRIFT: Diffusivity Regulation of Isotopes by nanoconFinementT
Spontaneous isotope fractionation has been reported under nanoconfinement conditions in naturally occurring systems, but the origin of this phenomena is currently unknown. Two existing hypotheses have been proposed, one based on changes in the solvation environment of the isotopes that reduces the non-mass dependent hydrodynamics contribution to diffusion. The other is that isotopes have mass-dependent surface adsorption, varying their total diffusion through nanoconfined channels. To investigate these hypotheses, benchtop experiments, nuclear magnetic resonance (NMR) spectroscopy, and molecule scale modeling were applied. Classical molecular dynamics simulations identified that the Na + and Cl - hydration shells across the three different salt solutions ( 22 Na 35 Cl, 23 Na 35 Cl, 24 Na 35 Cl) did not vary as a function of the Na + isotope, but that there was a significant pore size effect, with larger hydration shells at larger pore sizes. Additionally, while total adsorption times did not vary as a function of the Na + isotope or pore size, the free ion concentration, or those adsorbed on the surface for <5% of the simulation time did exhibit isotope dependence. Experimentally, challenges occurred developing a repeatable experiment, but NMR characterization of water diffusion rates through ordered alumina membranes was able to identify the existence of two distinct water environments associated with water inside and outside the pore. Further NMR studies could be used to confirm variation in hydration shells and diffusion rates of dissolved ions in water. Ultimately, mass-dependence adsorption is a primary driver of variations in isotope diffusion rates, rather than variation in hydration shells that occur under nanoconfinement.
Interaction of a Model Peptide with a Water--Bilayer System
We discuss a molecular dynamics study of the alanine dipeptide at the interface between water and a glycerol-1-monooleate (GMO) bilayer. The dipeptide is interfacially active and incorporates into the bilayer without disrupting its structure. The interfacial region that is readily penetrated by the dipeptide spans the entire head group portion of the bilayer. The polar groups of the alanine dipeptide mostly remain well solvated by water and the oxygen atoms of GMO, and conformations of the dipeptide are characterized by (phi, psi) angles typical of alpha-helix and beta-sheet structures. When the molecule is deeper in the bilayer, the C(sub 7eq) state also becomes stable. The barrier to the isomerization reaction at the interface is lower than in bulk phases. After 7 ns of trajectories, the system is not fully equilibrated, due to slow collective motions involving GMO head groups. These result in decreased mobility and lower rates of isomerization of the dipeptide at the interface.
Selectivity in gas–liquid interactions: Molecular beam scattering of CD 4 and ND 3 from an aqueous flat liquid jet
The dynamics of polar and nonpolar molecules colliding with an aqueous surface are characterized by scattering molecular beams of deuterated methane and ammonia, CD 4 and ND 3 (E i = 28.9 and 30.3 kJ mol −1 , respectively), from a flat liquid jet of cold salty water (8 m LiBr, 230 K). Translational energy distributions of scattered species collected as a function of collision geometry probe both impulsive scattering (IS) and thermal desorption (TD) mechanisms. Here, we find that CD 4 scattering is dominated by IS and exhibits a super-specular angular distribution. The fraction of TD scattering events is notably smaller for cold salty water than for dodecane, consistent with a higher free energy of solvation for CD 4 in the water jet. In contrast, no scattering signal is seen for ND 3 from the water jet, a result attributed to the high solubility and efficient protonation of ND 3 in liquid water. The IS channel for CD 4 was analyzed using a soft-sphere model, yielding a higher internal energy (E int ) and lower effective surface mass (m eff ) than was seen for Ne/water; the higher value of E int is attributed to rotational excitation of the scattered CD 4 . These findings demonstrate that the outcomes of a gas–liquid collision—scattering trajectory, surface adherence, and energy transfer—are directed at the molecular level by both the gaseous scatterer and liquid surface.
Computing the solubility of argon and xenon in molten sodium chloride and potassium chloride salts
Molten salt reactors (MSRs) offer significant advancements in nuclear reactor safety and efficiency by operating at higher temperatures and lower pressures compared to traditional reactors. A critical aspect of MSR operation involves understanding the solubility of fission byproducts, particularly noble gases, in the molten salts used. This study employs molecular dynamics (MD) simulations to compute Henry’s law constants and enthalpies of solvation for argon and xenon in molten sodium chloride (NaCl) and potassium chloride (KCl). We developed a new pairwise potential for the noble gas and salt interactions based on first principles calculations. We then used this potential to calculate Henry’s law constants of the two gases in the molten salts, which were modeled using both a rigid ion model (RIM) and a polarizable ion model (PIM). The solubility calculations, performed using the Widom insertion method, show qualitative agreement with limited experimental data, highlighting the temperature dependence and greater solubility of both gases in KCl compared to NaCl. Additionally, free volume analysis elucidated the role of available space within the molten salts in governing solubility trends. Our findings suggest that PIM trajectories provide more reliable predictions for noble gas solubility than RIM due to their accurate density representation. Furthermore, these results enhance understanding of gas solubility in MSR environments, and the methods can be readily extended to other systems.
The First X-ray Diffraction Patterns of Clay Minerals from Gale Crater
The Mars Science Laboratory (MSL) Rover, Curiosity spent approx 150 sols at Yellowknife Bay (YKB) studying a section of fluvio-lacustrine sedimentary rocks (with potential indications of volcanic influence), informally known as the Yellowknife Bay formation. YKB lies in a distal region of the Peace Vallis alluvial fan, which extends from the northern rim of Gale Crater toward the dune field at the base of Mt Sharp. Sedimentological and stratigraphic observations are consistent with the Yellowknife Bay formation being part of a distal fan deposit, which could be as young as middle Hesperian to even early Amazonian in age (approx 3.5 to 2.5 Ga). The Yellowknife Bay formation hosts a unit of mudstone called the Sheepbed member. Curiosity obtained powdered rock samples from two drill holes in the Sheepbed Member, named John Klein and Cumberland, and delivered them to instruments in Curiosity. Data from CheMin, a combined X-ray diffraction (XRD)/X-ray fluorescence instrument (XRF), has allowed detailed mineralogical analysis of mudstone powders revealing a clay mineral component of approx 20 wt.% in each sample. The clay minerals are important indicators of paleoenvironmental conditions and sensitive recorders of post-depositional alteration processes. The XRD pattern of John Klein reveals a 021 band consistent with a trioctahedral phyllosilicate. A broad peak at approx 10A with a slight inflexion at approx 12A indicates the presence of 2:1 type clay minerals in the John Klein sample. The trioctahedral nature of the clay minerals, breadth of the basal reflection, and presence of a minor component with larger basal spacing suggests that John Klein contains a trioctahedral smectite (probably saponite), whose interlayer is largely collapsed because of the low-humidity conditions. The XRD patterns show no evidence of corrensite (mixed-layer chlorite/smectite) or chlorite, which are typical diagenetic products of trioctahedral smectites when subjected to burial and heating >60degC in the presence of water. Given estimated geothermal gradients on Mars temperatures <60 degC might still be consistent with (but do not require) moderate burial. However, our ability to identify interstratified minerals is greatly limited by the lack of access to traditional treatments methods used in the lab (e.g., ethylene glycol solvation). Our preferred explanation for the origin of trioctahedral smectites in Sheepbed mudstone is in situ production via reaction of olivine, water and Si-bearing amorphous material, an important mudstone component detected by XRD. Elevated levels of magnetite in the Sheepbed and the trioctahedral monomineralic nature of the clay minerals support this model. These observations, combined with previous studies of olivine stability, support the persistence of circum-neutral hydrous conditions for thousands of years at YKB.
Paleoenvironmental Implications of Clay Minerals at Yellowknife Bay, Gale Crater, Mars
The Mars Science Laboratory (MSL) Rover, Curiosity spent approx 150 sols at Yellowknife Bay (YKB) studying a section of fluvio-lacustrine sedimentary rocks (with potential indications of volcanic influence), informally known as the Yellowknife Bay formation. YKB lies in a distal region of the Peace Vallis alluvial fan, which extends from the northern rim of Gale Crater toward the dune field at the base of Mt Sharp. Sedimentological and stratigraphic observations are consistent with the Yellowknife Bay formation being part of a distal fan deposit, which could be as young as middle Hesperian to even early Amazonian in age (approx. 3.5 to 2.5 Ga). The Yellowknife Bay formation hosts a unit of mudstone called the Sheepbed member. Curiosity obtained powdered rock samples from two drill holes in the Sheepbed Member, named John Klein and Cumberland, and delivered them to instruments in Curiosity. Data from CheMin, a combined X-ray diffraction (XRD)/X-ray fluorescence instrument (XRF), has allowed detailed mineralogical analysis of mudstone powders revealing a clay mineral component of approx. 20 wt.% in each sample. The clay minerals are important indicators of paleoenvironmental conditions and sensitive recorders of post-depositional alteration processes. The XRD pattern of John Klein reveals a 02l band consistent with a trioctahedral phyllosilicate. A broad peak at approx. 10A with a slight inflexion at approx. 12A indicates the presence of 2:1 type clay minerals in the John Klein sample. The trioctahedral nature of the clay minerals, breadth of the basal reflection, and presence of a minor component with larger basal spacing suggests that John Klein contains a trioctahedral smectite (probably saponite), whose interlayer is largely collapsed because of the low-humidity conditions. The XRD patterns show no evidence of corrensite (mixed-layer chlorite/smectite) or chlorite, which are typical diagenetic products of trioctahedral smectites when subjected to burial and heating >60 C in the presence of water. Given estimated geothermal gradients on Mars temperatures <60 C might still be consistent with (but do not require) moderate burial. However, our ability to identify interstratified minerals is greatly limited by the lack of access to traditional treatments methods used in the lab (e.g., ethylene glycol solvation). Our preferred explanation for the origin of trioctahedral smectites in Sheepbed mudstone is in situ production via reaction of olivine, water and Si-bearing amorphous material, an important mudstone component detected by XRD. Elevated levels of magnetite in the Sheepbed and the trioctahedral monomineralic nature of the clay minerals support this model. These observations, combined with previous studies of olivine stability, support the persistence of circum-neutral hydrous conditions for thousands of years at YKB.
A Theoretical Model for Computing Freezing Point Depression of Lithium-Ion Battery Electrolytes
Reliable prediction of freezing point depression in liquid electrolytes will accelerate the development of improved Li-ion batteries which can operate in low temperature environments. In this work we establish a computational methodology to calculate activity coefficients and liquidus lines for battery-relevant liquid electrolytes. Electronic structure methods are used in conjuction with classical molecular dynamics simulations and theoretical expressions for Born solvation energy, ion-atmosphere effects from Debye-Hückel theory and solvent entropic effects. The framework uses no a priori knowledge beyond neat solvent properties and the concentration of salt. LiPF 6 in propylene carbonate (PC), LiPF 6 in dimethyl carbonate (DMC) and LiClO 4 in DMC are investigated up to 1 molal with accuracy better than 3 °C when compared to experimental freezing point measurements. Finally, we find that the difference in freezing point depression between the propylene carbonate-based electrolyte and the dimethyl carbonate electrolytes originates from the difference in the solvent dielectric constant.
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning
Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.
Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study
Implicit solvent models are a computationally efficient method of representing solid/liquid interfaces prevalent in electrocatalysis, energy storage, and materials science. However, electronic structure changes induced at the metallic surface by the dielectric continuum are not fully understood. To address this, we perform DFT calculations for the Pt(111)/water interface, in order to compare Poisson–Boltzmann continuum solvation methods with ab initio molecular dynamics (AIMD) simulations of explicit solvent. We show that the implicit solvent cavity can be parametrized in terms of the electric dipole moment change at the equilibrated explicit Pt/water interface to obtain the potential of zero charge (PZC). We also compare the accuracy of aqueous enthalpies of adsorption of phenol on Pt(111) using geometry and charge density based dielectric cavitation methods. The ability to parametrize the cavity according to individual atoms, as afforded in the geometry based approach, is key to obtaining accurate enthalpy changes of adsorption under aqueous conditions. Additionally, we show that the electronic structure changes induced by explicit solvent and our proposed implicit solvent parametrization scheme yield comparable density difference profiles and d-band projected density of states. We therefore demonstrate the capability of implicit solvent approaches to capture both the energetics of adsorption processes and the main electronic effects of aqueous solvent on the metallic surface. Therefore, this work provides a scheme for computationally efficient simulations of interfacial processes for applications in areas such as heterogeneous catalysis and electrochemistry.
Theoretical Examination of the Hydroxide Transport in Cobaltocenium-Containing Polyelectrolytes
Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. We find that the hydroxide diffusion depends on the channel size, modulation of the electrostatic interactions by the solvation shell, and its rearrangement ability. Hydroxide diffusion proceeds via both the vehicular and structural diffusion mechanisms with the latter playing a larger role at low diffusion coefficients. The highest diffusion coefficient is observed under moderate water densities (around half the density of liquid water) when there are enough water molecules to form the solvation shell, reducing the electrostatic interaction between ions, yet there is enough space for the water rearrangements during the proton hopping. Furthermore, the effects of cobaltocenium separation, orientation, chemical modifications, and the role of nuclear quantum effects are also discussed.
Propagation of positive discharges in an air bubble having an embedded water droplet
Low temperature plasmas generated inside gas bubbles immersed in water is an effective method of rapidly transferring plasma generated reactive species to the water for applications in biomedicine, agriculture and environment. Reactive species are generally produced in the gas phase plasma and then solvate into the liquid. The large surface-to-volume ratio (SVR) of the bubble accelerates this process. In generating bubbles in water, aerosols and droplets are also contained within the bubble. These droplets also have a large SVR and so can be rapidly plasma activated. However, the presence of the droplets can also impact the propagation of the plasma in the bubble. In this paper, results are discussed from computational and experimental investigations of the formation and evolution of discharges in an air bubble immersed in water with an embedded water droplet. The computations were performed with a two-dimensional plasma hydrodynamics model. Experiments were performed with a quasi-2D bubble apparatus. In bubbles having a droplet, a plasma filament typically bridges from the powered electrode to the droplet, and then from the droplet to the bubble surface. A surface-hugging streamer also occurs on the inner bubble surface and on the surface of the droplet. Both surface streamers result in part from surface charge accumulation and can dominate the formation of reactive species that transport into the droplet. Increasing droplet conductivity suppresses propagation of the surface discharge and leads to a lower density of aqueous reactive species. Increasing conductivity of the surrounding water does not change the overall structure of the discharge but does slightly elevate the discharge intensity. Finally, the size and shape of the embedded droplet can significantly affect the formation and propagation of the streamer.
Superatomic nature of metal encapsulated dodecahedrane: The case of M@ C 20 H 20 (M = Li, Na, Mg + )
The idea of designing unprecedented materials made of superatomic building blocks, motivated the present study on endohedral M@C 20 H 20 (M = Li, Na, Mg + ) species. Here, ground and excited electronic structures of M@C 20 H 20 (M = Li, Na, Mg + ) were analyzed by means of high-level quantum calculations. In their ground states, one electron occupies a defuse superatomic s-orbital that lies around the C 20 H 20 cage. These entities populate higher angular momentum p-, d-, f-, g-superatomic orbitals in their low-lying electronic states. The proposed superatomic Aufbau shell model for Li@C 20 H 20 and Na@C 20 H 20 is 1s, 1p, 1d, 2s, 1f, 2p, 2d, 1g, 2f slightly different from that of Mg@C 20 H 20 + which is 1s, 1p, 1d, 2s, 1f, 2p, 2d, 1g, 3s, 2f, 2g, 3p. These introduced superatomic orbital series resemble the Aufbau principle of solvated electron precursors.
Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects
The identity of metal ions surrounding DNA is key to its biological function and materials applications. In this work, we compare atomistic molecular dynamics simulations of double strand DNA (dsDNA) with four alkaline earth metal ions (Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ ) to elucidate the physical interactions that govern DNA–ion binding. Simulations accurately model the ion–phosphate distance of Mg 2+ and reproduce ion counting experiments for Ca 2+ , Sr 2+ , and Ba 2+ . Our analysis shows that alkaline earth metal ions prefer to bind at the phosphate backbone compared to the major groove and negligible binding occurs in the minor groove. Larger alkaline earth metal ions with variable first solvation shells (Ca 2+ , Sr 2+ , and Ba 2+ ) show both direct and indirect binding, where indirect binding increases with ion size. Mg 2+ does not fit this trend because the strength of its first solvation shell predicts indirect binding only. Ions bound to the phosphate backbone form fewer contacts per ion compared to the major groove. Within the major groove, metal ions preferentially bind to guanine–cystosine base pairs and form simultaneous contacts with the N7 and O6 atoms of guanine. Overall, we find that the interplay among ion size, DNA–ion interaction, and the size and flexibility of the first solvation shell are key to predicting how alkaline earth metal ions interact with DNA.
MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations
We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.
Solvation Environment and Interface Dynamics of Li 2 B 12 H 12 and Li 2 B 12 F 12 Electrolytes Uncovered by Theory and Operando Optical and FTIR Spectroelectrochemistry
In this work, we evaluated two closo-borate salts (Li 2 B 12 H 12 and Li 2 B 12 F 12 ) in propylene carbonate from theoretical and experimental perspectives to understand how the coordination environment influences their spectroscopic and electrochemical properties. The coordination environments of the closo-borate salts were modeled via density functional theory (DFT) and molecular dynamics (MD). Vibrational spectra calculated from the predicted coordination environments are in agreement with experimentally measured steady-state FTIR data. This theoretical investigation also suggested that Li 2 B 12 F 12 would possess a higher ionic conductivity than Li 2 B 12 H 12 , which was corroborated experimentally. Additionally, an electrochemical cell was designed and fabricated that enabled operando optical and FTIR spectroelectrochemical (OP-IR-SEC) measurements. This allowed for the simultaneous measurement of the relative changes of species at a lithium electrode-liquid electrolyte interface and the visualization of lithium plating at the electrode surface. This technique could provide new chemical insights and potentially link optical changes at the electrode–electrolyte interface to specific chemical species in similar electrochemical systems. The Li 2 B 12 F 12 electrolyte was found to have a higher thermal stability, which may find utility in applications for batteries that are subject to high-temperature conditions.
Toward a quantitative description of solvation structure: a framework for differential solution scattering measurements
Appreciating that the role of the solute–solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems in situ in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime—where sub-ångström spatial resolution is achieved—remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography.