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DOE OSTI2018

Role of the Anion on the Transport and Structure of Organic Mixed Conductors

Abstract Organic mixed conductors are increasingly employed in electrochemical devices operating in aqueous solutions that leverage simultaneous transport of ions and electrons. Indeed, their mode of operation relies on changing their doping (oxidation) state by the migration of ions to compensate for electronic charges. Nevertheless, the structural and morphological changes that organic mixed conductors experience when ions and water penetrate the material are not fully understood. Through a combination of electrochemical, gravimetric, and structural characterization, the effects of water and anions with a hydrophilic conjugated polymer are elucidated. Using a series of sodium‐ion aqueous salts of varying anion size, hydration shells, and acidity, the links between the nature of the anion and the transport and structural properties of the polymer are systematically studied. Upon doping, ions intercalate in the crystallites, permanently modifying the lattice spacings, and residual water swells the film. The polymer, however, maintains electrochemical reversibility. The performance of electrochemical transistors reveals that doping with larger, less hydrated, anions increases their transconductance but decreases switching speed. This study highlights the complexity of electrolyte‐mixed conductor interactions and advances materials design, emphasizing the coupled role of polymer and electrolyte (solvent and ion) in device performance.

Cendra, Camila↗

DOE OSTI2026

Diffusion and Solvation Dynamics of Ions in Water: Beyond the Brownian Approximation

The coupled dynamics of ions and water molecules in their first hydration shell impact a variety of processes including ion diffusion, selective ion transport in water-filled nanopores, and the kinetics of ion-pairing, ion adsorption, and metal-ligand binding reactions. In this work, we study these coupled dynamics for alkali metals (Li, Na, K, Rb, Cs), alkaline Earth metals (Mg, Ca, Sr, Ba), and chloride through the lens of their dependence on ion isotopic mass. Results are validated against previous measurements of the isotopic mass-dependence of ion diffusion coefficients in water and previous ab initio calculations of ion high-frequency dynamics in water. We find that the vibrational power spectra of ions in water consistently exhibit either two or three peaks, i.e., ions have several rattling frequencies within their solvations shells as previously reported for a subset of the species examined here. These frequencies have different sensititivies to isotopic mass that may serve as signatures of ion solvation processes (such as the tendency of ions to orient their first-shell water molecules) and that also may relate to Hofmeister-like effects including the relative affinity of different metals for ribonucleic acid (RNA).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Hydrated Metal and Metal-Nitrate Complexes in Water: Full Lanthanide(III) Series plus Miscellaneous Metal Ions

This is a dataset of hydrated metal complexes and metal–nitrate hydrated complexes intended for public use, reproducibility, and downstream structural analysis. A key feature is coverage across the full lanthanide(III) series (La–Lu), enabling systematic comparisons of coordination motifs and bonding trends across the entire lanthanide sequence. In addition to the lanthanides, the dataset also includes other metal ions such as UO2(VI), Fe(II), and Fe(III). The dataset provides optimized geometries for hydrated and nitrate-containing hydrated complexes, together with representative ab initio molecular dynamics (AIMD) trajectories saved in standard XYZ formats. The accompanying NWChem input decks enable reproduction of the reported calculations and provide a starting point for extending the simulations to related coordination environments. Computationally, DFT calculations employ the B3LYP functional with DFT-D3BJ dispersion corrections and a COSMO continuum solvent model (dielectric constant 78.4) to represent solvation beyond the explicitly treated first hydration shell. AIMD simulations are performed with the NWChem qmd module at 298 K, integrating nuclear motion with the velocity-Verlet algorithm and controlling temperature using a Nosé–Hoover thermostat. Trajectories are approximately 4.8 ps in length and are used primarily to assess short-time stability of candidate coordination motifs, including (for lanthanides) differences between 8- versus 9-water coordination and comparisons between nitrate-bound and nitrate-free hydrated complexes.

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗

DOE OSTI2016

Lutetium(III) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex

The structure and dynamics of the lutetium(III) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(III) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(III) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1984

Solution influence on biomolecular equilibria - Nucleic acid base associations

Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

Pohorille, A.↗

DOE OSTI2017

Water and chloride ions migration in porous cementitious materials: An experimental and molecular dynamics investigation

The interactions of water and chloride ions penetration into porous mortar have been investigated experimentally and modelled by molecular dynamics. The water distribution visualized by neutron radiography and chloride penetration by Electron Probe Micro-Analysis indicate that separation of chloride ions from water during the penetration process took place and water ran much deeper into the material than chloride ions. The relationship between the penetration depth of water and chloride ions can be described by a linear function despite different water-cement ratio. Furthermore, molecular dynamics attributes the different transport mechanisms of water and ions in porous cementitious materials to three reasons: the nanostructure of hydration product play filtering role to screen chloride ions with larger hydration shell; as compared with water, ions reside in the calcium silicate surface for longer time due to the strong interfacial bonding; chloride ions accumulate and form CaCl ionic cluster, slowing down the migrating rate.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Fate of Methane Emitted from Dissociating Marine Hydrates: Modeling, Laboratory, and Field Constraints

The overall goals of this research are: (1) to determine the physical fate of single and multiple methane bubbles emitted to the water column by dissociating gas hydrates at seep sites deep within the hydrate stability zone or at the updip limit of gas hydrate stability, and (2) to quantitatively link theoretical and laboratory findings on methane transport to the analysis of real-world field-scale methane plume data placed within the context of the degrading methane hydrate province on the US Atlantic margin. The project is arranged to advance on three interrelated fronts (numerical modeling, laboratory experiments, and analysis of field-based plume data) simultaneously. The fundamental objectives of each component are the following: Numerical modeling: Constraining the conditions under which rising bubbles become armored with hydrate, the impact of hydrate armoring on the eventual fate of a bubble’s methane, and the role of multiple bubble interactions in survival of methane plumes to very shallow depths in the water column. Laboratory experiments: Exploring the parameter space (e.g., bubble size, gas saturation in the liquid phase, “proximity” to the stability boundary) for formation of a hydrate shell around a free bubble in water, the rise rate of such bubbles, and the bubble’s acoustic characteristics using field-scale frequencies. Field component: Extending the results of numerical modeling and laboratory experiments to the field-scale using brand new, existing, public-domain, state-of-the-art real world data on US Atlantic margin methane seeps, without acquiring new field data in the course of this particular project. This component quantitatively analyzes data on Atlantic margin methane plumes and place those new plumes and their corresponding seeps within the context of gas hydrate degradation processes on this margin.

03 NATURAL GAS↗

DOE OSTI2022

Control of Structural Hydrophobicity and Cation Solvation on Interlayer Water Transport during Clay Dehydration

Swelling clay hydration/dehydration is important to many environmental and industrial processes. Experimental studies usually probe equilibrium hydration states in an averaged manner and thus cannot capture the fast water transport and structural change in interlayers during hydration/dehydration. Using molecular simulations and thermogravimetric analyses, we observe a two-stage dehydration process. The first stage is controlled by evaporation at the edges: water molecules near hydrophobic sites and the first few water molecules of the hydration shell of cations move fast to particle edges for evaporation. The second stage is controlled by slow desorption of the last 1–2 water molecules from the cations and slow transport through the interlayers. The two-stage dehydration is strongly coupled with interlayer collapse and the coordination number changes of cations, all of which depend on layer charge distribution. Furthermore, this mechanistic interpretation of clay dehydration can be key to the coupled chemomechanical behavior in natural/engineered barriers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Structural, dynamical, and transport properties of the hydrated halides: How do At{sup −} bulk properties compare with those of the other halides, from F{sup −} to I{sup −}?

The properties of halides from the lightest, fluoride (F{sup −}), to the heaviest, astatide (At{sup −}), have been studied in water using a polarizable force-field approach based on molecular dynamics (MD) simulations at the 10 ns scale. The selected force-field explicitly treats the cooperativity within the halide-water hydrogen bond networks. The force-field parameters have been adjusted to ab initio data on anion/water clusters computed at the relativistic Möller-Plesset second-order perturbation theory level of theory. The anion static polarizabilities of the two heaviest halides, I{sup −} and At{sup −}, were computed in the gas phase using large and diffuse atomic basis sets, and taking into account both electron correlation and spin-orbit coupling within a four-component framework. Our MD simulation results show the solvation properties of I{sup −} and At{sup −} in aqueous phase to be very close. For instance, their first hydration shells are structured and encompass 9.2 and 9.1 water molecules at about 3.70 ± 0.05 Å, respectively. These values have to be compared to the F{sup −}, Cl{sup −}, and Br{sup −} ones, i.e., 6.3, 8.4, and 9.0 water molecules at 2.74, 3.38, and 3.55 Å, respectively. Moreover our computations predict the solvation free energy of At{sup −} in liquid water at ambient conditions to be 68 kcal mol{sup −1}, a value also close the I{sup −} one, about 70 kcal mol{sup −1}. In all, our simulation results for I{sup −} are in excellent agreement with the latest neutron- and X-ray diffraction studies. Those for the At{sup −} ion are predictive, as no theoretical or experimental data are available to date.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Thermal Responsive Ion Selectivity of Uranyl Peroxide Nanocages: An Inorganic Mimic of K + Ion Channels

Abstract An actinyl peroxide cage cluster, Li 48+ m K 12 (OH) m [UO 2 (O 2 )(OH)] 60 (H 2 O) n ( m ≈20 and n ≈310; U 60 ), discriminates precisely between Na + and K + ions when heated to certain temperatures, a most essential feature for K + selective filters. The U 60 clusters demonstrate several other features in common with K + ion channels, including passive transport of K + ions, a high flux rate, and the dehydration of U 60 and K + ions. These qualities make U 60 (a pure inorganic cluster) a promising ion channel mimic in an aqueous environment. Laser light scattering (LLS) and isothermal titration calorimetry (ITC) studies revealed that the tailorable ion selectivity of U 60 clusters is a result of the thermal responsiveness of the U 60 hydration shells.

Gao, Yunyi↗

DOE OSTI2016

Thermal Responsive Ion Selectivity of Uranyl Peroxide Nanocages: An Inorganic Mimic of K + Ion Channels

Gao, Yunyi↗

DOE OSTI2022

Determination of the Structures of Lignin Subunits and Nanoparticles in Solution by Small‐Angle Neutron Scattering: Towards Improving Lignin Valorization

Abstract Lignin nanoparticles (LNPs) are usually produced from lignin solution through supersaturation. The structure of the lignin in solution is still poorly understood due to structural variability of isolated lignins. Here, lignins were extracted from different plants to establish a general pattern of their structure in several lignin solvents. Lignin molecules (lignin subunits) and larger aggregates were observed in dimethyl sulfoxide (DMSO), ethylene glycol (EG) and 0.1 N NaOD solutions by small‐angle neutron scattering (SANS). It was proposed that the aggregates were composed of lignin subunits with a higher molecular weight and a higher ratio of the aliphatic to phenolic hydroxyl groups. The size, shape, and compactness are important factors that affect the uses of the LNPs, which were obtained from the SANS data for the first time. A discrepancy in the radius between SANS and DLS was discovered, pointing to a large hydration shell around the LNPs in aqueous solutions. The cytotoxicity of the corncob lignin, kraft lignin, and their LNPs were measured and compared.

Zhang, Xin↗

DOE OSTI2019

DRoP: Automated detection of conserved solvent‐binding sites on proteins

Abstract Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X‐ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein‐protein or protein‐ligand interactions, as well as conserved water‐binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.

Kearney, Bradley M.↗

DOE OSTI2016

High-resolution Measurement of Contact Ion-pair Structures in Aqueous RbCl Solutions from the Simultaneous Corefinement of their Rb and Cl K-edge XAFS and XRD Spectra

Abstract not provided

Pham, Van-Thai↗

DOE OSTI2025

Molecular insights into Yb(III) speciation in sulfate-bearing hydrothermal fluids from X-ray absorption spectra informed by ab initio molecular dynamics

Rare earth elements (REEs) are critical for advanced technologies, yet in hydrothermal aqueous solutions the molecular level details of their interaction with ligands that control their geochemical transport and deposition remain poorly understood. Here, this study elucidates the coordination behavior of Yb 3+ in sulfate-rich hydrothermal fluids using in situ extended X-ray absorption fine structure (EXAFS) spectroscopy and ab initio molecular dynamics (AIMD) simulations. By integrating multi-angle EXAFS with AIMD-derived constraints, we precisely resolve Yb 3+ coordination structures and ligand interactions under hydrothermal conditions. At room temperature, Yb 3+ is coordinated by five water molecules and two sulfate ligands (coordination number, CN = 8), forming a distorted square antiprism geometry. Increasing temperature induces progressive dehydration, reducing the hydration shell and favoring stronger sulfate complexation. At 200°C, sulfate ligands reorganize around Yb 3+ , shifting its geometry to a capped octahedron (CN = 7). At 300 °C, sulfate binding dominates, leading to structural reorganization that parallels the onset of sulfate mineral precipitation, consistent with the retrograde solubility of REE sulfates. These findings provide direct molecular-scale evidence that sulfate acts as both a transport and deposition ligand, critically influencing REE mobility in geochemical environments. Our results can also help to refine thermodynamic models of REE speciation in high-temperature hydrothermal fluids and improve our understanding of REE ore formation processes in nature.

AIMD↗

DOE OSTI2023

Distance-dependent dielectric constant at the calcite/electrolyte interface: Implication for surface complexation modeling

Hypothesis: The electrical double layer formed at the mineral/electrolyte interface is often modeled using mean-field approaches based on a continuum description of the solvent whose dielectric constant is assumed to decrease monotonically with decreasing distance to the surface. In contrast, molecular simulations show that the solvent polarizability oscillates near the surface similar to the water density profile - as shown previously, for example, by Bonthuis et al. (D.J. Bonthuis, S. Gekle, R.R. Netz, Dielectric Profile of Interfacial Water and its Effect on Double-Layer Capacitance, Phys Rev Lett 107(16) (2011) 166102). Here, we showed that molecular and mesoscale pictures agree by spatially averaging the dielectric constant obtained from molecular dynamics simulations over the distances relevant to the mean-field representation. In addition, the values of capacitances used to describe the electrical double layer in Surface Complexation Models (SCMs) of the mineral/electrolyte interface can be estimated using molecularly informed spatially averaged dielectric constants and positions of hydration layers. Experiments: First, we used molecular dynamics simulations to model the calcite 101¯4/electrolyte interface. Next, by using atomistic trajectories, we calculated the distance-dependent static dielectric constant and water density in the direction normal to the. Finally, we applied spatial compartmentalization consistent with the model of parallel-plate capacitors connected in series to estimate SCM capacitances. Findings: Computationally expensive simulations are required to determine the dielectric constant profile of interfacial water near the mineral surface. On the other hand, water density profiles are readily assessable from much shorter simulation trajectories. Our simulations confirmed that dielectric and water density oscillations at the interface are correlated. Here, we parametrized linear regression models to estimate the dielectric constant directly from the local water density. This is a significant computational shortcut compared to slowly converging calculations relying on total dipole moment fluctuations. The amplitude of the interfacial dielectric constant oscillation can exceed the dielectric constant of the bulk water, suggesting an ice-like frozen state, but only if there are no electrolyte ions. The interfacial accumulation of electrolyte ions causes a decrease in the dielectric constant due to the reduction of water density and re-orientation of water dipoles in ion hydration shells. Finally, we show how to use the computed dielectric properties to estimate SCM's capacitances.

58 GEOSCIENCES↗

DOE OSTI2024

Physicochemical control of solvation and molecular assembly of charged amphiphilic oligomers at air-aqueous interfaces

Hypothesis : Understanding the rules that control the assembly of nanostructured soft materials at interfaces is central to many applications. We hypothesize that electrolytes can be used to alter the hydration shell of amphiphilic oligomers at the air-aqueous interface of Langmuir films, thereby providing a means to control the formation of emergent nanostructures. Experiments : Three representative salts – (NaF, NaCl, NaSCN) were studied for mediating the self-assembly of oligodimethylsiloxane methylimidazolium (ODMS-MIM + ) amphiphiles in Langmuir films. The effects of the different salts on the nanostructure assembly of these films were probed using vibrational sum frequency generation (SFG) spectroscopy and Langmuir trough techniques. Experimental data were supported by atomistic molecular dynamic simulations. Findings : Langmuir trough surface pressure – area isotherms suggested a surprising effect on oligomer assembly, whereby the presence of anions affects the stability of the interfacial layer irrespective of their surface propensities. In contrast, SFG results implied a strong anion effect that parallels the surface activity of anions. These seemingly contradictory trends are explained by anion driven tail dehydration resulting in increasingly heterogeneous systems with entangled ODMS tails and appreciable anion penetration into the complex interfacial layer comprised of headgroups, tails, and interfacial water molecules. These findings provide physical and chemical insight for tuning a wide range of interfacial assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Molecular Design of Functional Polymers for Silica Scale Inhibition

Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Finally, our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗