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Results for “water structure and dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dynamic clay microstructures emerge via ion complexation waves

Clays control carbon, water and nutrient transport in the lithosphere, promote cloud formation5 and lubricate fault slip through interactions among hydrated mineral interfaces. Clay mineral properties are difficult to model because their structures are disordered, curved and dynamic. Consequently, interactions at the clay mineral-aqueous interface have been approximated using electric double layer models based on single crystals of mica and atomistic simulations. We discover that waves of complexation dipoles at dynamically curving interfaces create an emergent long-range force that drives exfoliation and restacking over time- and length-scales that are not captured in existing models. Curvature delocalizes electrostatic interactions in ways that fundamentally differ from planar surfaces, altering the ratio of ions bound to the convex and concave sides of a layer. Multiple-scattering reconstruction of low-dose energy-filtered cryo electron tomography enabled direct imaging of ion complexes and electrolyte distributions at hydrated and curved mineral interfaces with {\aa}ngstrom resolution over micron length scales. Layers exfoliate and restack abruptly and repeatedly over timescales that depend strongly on the counterion identity, demonstrating that the strong coupling between elastic, electrostatic and hydration forces in clays promote collective reorganization previously thought to be a feature only of active matter.

Whittaker, Michael L↗
DOE OSTI2022

Nucleation Rate Theory for Coordination Number: Elucidating Water-Mediated Formation of a Zigzag Na 2 SO 4 Morphology

Predicting and controlling nanostructure formation during nucleation can pave the way to synthesizing novel energy materials via crystallization. However, such control over nucleation and crystallization remains challenging due to an inadequate understanding of critical factors that govern evolving atomistic structures and dynamics. Here, in this paper, we utilize coordination number as a reaction coordinate and rate theory to investigate how sodium sulfate, commonly known as a phase-change energy material, nucleates in a supersaturated aqueous solution. In conjunction with ab initio and force field-based molecular dynamics simulation, the rate theoretical analysis reveals that sodium sulfate from an initially dissolved metastable state transits to a heterogeneous mixture of prenucleated clusters and finally to a large cylindrical zigzag morphology. Measurements of Raman spectra and their ab initio modeling confirm that this nucleated morphology contains a few waters for every sulfate. Rate processes such as solvent exchange and desolvation exhibit high sensitivity to the evolving prenucleation/nucleation structures, providing a means to distinguish between critical nucleation precursors. Desolvation and forming the first-shell interionic coordination structure via monomer-by-monomer addition around sulfates are found to explain the formation of large nuclei. Thus, a detailed understanding of the step-by-step structure formation across scales has been achieved. This can be leveraged to predict nucleation-related structures and dynamics and potentially control the synthesis of novel phase-change materials for energy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Charge accumulation and solvation in $β$-NiOOH: Surface chemistry of an OER catalyst from ML-aided simulations

Electrochemical water splitting is a key technology for a sustainable energy transition, providing a route to store surplus electricity from renewable sources. A central bottleneck is the sluggish oxygen evolution reaction (OER), which drives the search for catalysts that are active, stable, and inexpensive enough for large-scale deployment. Within this context, pure and doped NiO x H y combine high activity with low cost, making them prime candidates for alkaline OER. Yet, despite extensive study, the atomistic structure of NiOOH under operando conditions and the associated reaction mechanisms remain debated. Here, we investigate the structural complexity of pure β-NiOOH, the scaffold for its doped derivatives. We systematically investigate the oxidation of the surface adsorbates via proton-coupled electron transfer steps across relevant facets and sites, identifying the most probable sequence of deprotonation events. Our results reveal asymmetric charge accumulation on Wulff-relevant surfaces and show how applied potential can promote morphological restructuring. Explicit solvation is included through machine-learning interatomic potential molecular dynamics of the NiOOH/water interface, which allows us to resolve the hydrophobic and hydrophilic character of different surfaces and the associated interfacial water structure. Together, these insights demonstrate how surface chemistry and solvation jointly govern the stability of NiOOH and the accumulation of surface charge, with possible implications for catalytic performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure Function Studies of Photosystem II Using X-Ray Free Electron Lasers

The structure and mechanism of the water-oxidation chemistry that occurs in photosystem II have been subjects of great interest. The advent of X-ray free electron lasers allowed the determination of structures of the stable intermediate states and of steps in the transitions between these intermediate states, bringing a new perspective to this field. The room-temperature structures collected as the photosynthetic water oxidation reaction proceeds in real time have provided important novel insights into the structural changes and the mechanism of the water oxidation reaction. The time-resolved measurements have also given us a view of how this reaction—which involves multielectron, multiproton processes—is facilitated by the interaction of the ligands and the protein residues in the oxygen-evolving complex. These structures have also provided a picture of the dynamics occurring in the channels within photosystem II that are involved in the transport of the substrate water to the catalytic center and protons to the bulk.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Roles of Hydrogen Bonds and Alignment in Oriented Attachment of Gibbsite Nanoparticles: Insights from Molecular Dynamics

Oriented attachment (OA) of nanoparticles is an important crystal growth pathway in the synthesis of hierarchical structures. Although a significant understanding of OA has been made, the effect of atomistic misalignment and the roles of solvent/particle and particle/particle interactions on the structure–energy relationship during an OA remain elusive. In this study, we perform molecular dynamics simulations to calculate the potential of mean force (PMF) profile for gibbsite particle translation on a gibbsite slab with 1 or 2 intervening water layers (1W or 2W). The structures of the gibbsite surfaces and the confined water are analyzed to determine how the number and type of hydrogen bonds (H-bonds) influence the free energy profile during the translation. The PMF profile exhibits a periodicity of length 5.078 Å, consistent with the gibbsite unit cell size along the translation direction. The changes in the surface–water and water–water hydrogen bond network and water and surface OH groups’ orientations during the translation are strongly coupled with the changes in the PMF profile in the 1W case. However, when increasing the number of intervening water layers from 1W to 2W, the particle/slab misalignment becomes a dominant factor controlling the behavior of the PMF profile. We also establish a method to quantify misalignment between the particle and the slab, which exhibits a strong correlation with the free energy for the 2W case. These results shed more light into the roles of particle/slab misalignment and hydrogen bond network in the OA of mineral particles in aqueous solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Validating first-principles molecular dynamics calculations of oxide/water interfaces with x-ray reflectivity data

Metal oxide/water interfaces play a crucial role in many electrochemical and photocatalytic processes, such as photoelectrochemical water splitting, the creation of fuel from sunlight, and electrochemical CO 2 reduction. First-principles electronic structure calculations can reveal unique insights into these processes, such as the role of the alignment of the oxide electronic energy levels with those of liquid water. An essential prerequisite for the success of such calculations is the ability to predict accurate structural models of these interfaces, which in turn requires careful experimental validation. Here we report a general, quantitative validation protocol for first-principles molecular dynamics simulations of oxide/aqueous interfaces. The approach makes direct comparisons of interfacial x-ray reflectivity (XR) signals from experimental measurements and those obtained from ab initio simulations with semilocal and van der Waals functionals. The protocol is demonstrated here for the case of the Al 2 O 3 (001)/water interface, one of the simplest oxide/water interfaces. We discuss the technical requirements needed for validation, including the choice of the density functional, the simulation cell size, and the optimal choice of the thermodynamic ensemble. Our results establish a general paradigm for the validation of structural models and interactions at solid/water interfaces derived from first-principles simulations. Furthermore, while there is qualitative agreement between the simulated structures and the experimental best-fit structure, direct comparisons of simulated and measured XR intensities show quantitative discrepancies that derive from both bulk regions (i.e., alumina and water) as well as the interfacial region, highlighting the need for accurate density functionals to properly describe interfacial interactions. Our results show that XR data are sensitive not only to the atomic structure (i.e., the atom locations) but also to the electron-density distributions in both the substrate and at the interface.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Influence of Initial fabric and water-wetting on particle fracture and force chain evolution in natural silica sand

Particle fracture has a significant influence on the engineering behavior of granular materials. However, the combined influence of the initial fabric and wetting on particle fracture and force chain evolution in granular materials, particularly in sands, remains insufficiently explored in the current literature. Here, in this paper, one-dimensional (1D) confined compression experiments were conducted on dry and wet specimens, and particle-level fracture was captured using three-dimensional (3D) in-situ Synchrotron Micro-Computed Tomography (SMT). A quantitative assessment of particle fracture revealed that wet specimens, which have disturbed fabric, exhibited a higher fracture percentage in comparison to dry specimens. Complementary 3D finite element (FE) simulations were performed using dry and wet (only solid fabric was considered and the influence of pore water is not considered) sand assemblies to assess interparticle contact forces and particle-scale stress distributions within the specimens. Force chain analysis was subsequently conducted, encompassing quantification of interparticle forces, characterization of force network structures, and monitoring the dynamic evolution of force chains under different strain levels. The results show that the specimens with disturbed fabric led to a more dynamic and less persistent force network, more fabric instability, and thus more reorganization of force chain structures. In addition, the frequent rearrangement of the force network in the presence of water (with reduced inter-particle contact friction) likely exacerbates localized stress concentrations, promoting failure in previously unengaged or weakly connected particles. The results reported in this paper offer a new insight into how the initial fabric and wetting cause different fracture behavior. The findings can also pave the way for more in-depth future investigations into the mechanics governing particle fracture in granular assemblies.

Finite element analysis↗
DOE OSTI2023

Critical fluctuations in liquid–liquid extraction organic phases controlled by extractant and diluent molecular structure

Extractant aggregation in liquid–liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid–liquid phase transition known as third phase formation. Using small angle X-ray scattering, we find that structural heterogeneities across a wide range of compositions in binary mixtures of malonamide extractants and alkane diluents are well described by Ornstein–Zernike scattering. This suggests that structure in these simplified organic phases originates from the critical point associated with the liquid–liquid phase transition. To confirm this, we measure the temperature dependence of the organic phase structure, finding critical exponents consistent with the 3D Ising model. Molecular dynamics simulations were also consistent with this mechanism for extractant aggregation. Due to the absence of water or any other polar solutes required to form reverse-micellar-like nanostructures, these fluctuations are inherent to the binary extractant/diluent mixture. Further, we also show how the molecular structure of the extractant and diluent modulate these critical concentration fluctuations by shifting the critical temperature: critical fluctuations are suppressed by increasing extractant alkyl tail lengths or decreasing diluent alkyl chain lengths. This is consistent with how extractant and diluent molecular structure are known to impact metal and acid loading capacity in many-component LLE organic phases, suggesting phase behavior of practical systems may be effectively studied in simplified organic phases. Overall, the explicit connection between molecular structure, aggregation and phase behavior demonstrated here will enable the design of more efficient separations processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Using Neural Network Force Fields to Ascertain the Quality of Ab Initio Simulations of Liquid Water

Accurately simulating the properties of bulk water, despite the apparent simplicity of the molecule, is still a challenge. In order to fully understand and reproduce its complex phase diagram, it is necessary to perform simulations at the ab initio level, including quantum mechanical effects both for electrons and nuclei. This comes at a high computational cost, given that the structural and dynamical properties tend to require long timescales and large simulation cells. In this work, we evaluate the errors that density functional theory (DFT)-based simulations routinely incur into due time- and size-scale limitations. These errors are evaluated using neural-network-trained force fields that are accurate at the level of DFT methods. We compare different exchange and correlation potentials for properties of bulk water that require large timescales. Here we show that structural properties are less dependent on the system size and that dynamical properties such as the diffusion coefficient have a strong dependence on the simulation size and timescale. Our results facilitate comparisons of DFT-based simulation results with experiments and offer a path to discriminate between model and convergence errors in these simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Effect of Hydrophilicity and Interfacial Water Structure on Particle Attachment

Oriented attachment (OA) of nanoparticles is an important and common crystallization pathway. Efforts to isolate and quantify the interparticle forces that underlie OA have only recently been initiated and the role played by the interfacial solvent structure in the confined region between nanocrystal surfaces in enabling and controlling OA remains an open question. In this work, classical molecular dynamics (MD) simulations were performed to compute the free energy landscape of nanoparticles approaching mineral substrates in both vacuum and pure water. Periclase (MgO), muscovite (KAl 3 Si 3 O 10 (OH) 2 ), and pyrophyllite (Al 2 Si 4 O 10 (OH) 2 ) nanoparticles exposing the (100), (001), and (001) surfaces, respectively, were brought to contact with substrates exposing the same surfaces. These mineral surfaces were selected to investigate a range of hydrophilicities (periclase > muscovite > pyrophyllite). The MD simulations revealed that the interfacial water structure created free energy minima for nanoparticle approach that corresponded to integer numbers of intervening water layers. The depth of the free energy minima and the free energy barriers between minima correlated positively with the hydrophilicity of the mineral surface. While the range of solvent-mediated interactions was predicted to be short (a few intervening water layers at most for MgO), the free energy barriers were calculated to be large (fraction of an eV per nm 2 ) and the effect of misalignment diminished rapidly with the number of intervening water layers. The results help explain the formation of mesocrystals and the observed ability of nanoparticles to rotate before attachment while in a long-lived solvent-separated state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Quantification of hydraulic trait control on plant hydrodynamics and risk of hydraulic failure within a demographic structured vegetation model in a tropical forest (FATES–HYDRO V1.0)

Abstract. Vegetation plays a key role in the global carbon cycle and thus is an important component within Earth system models (ESMs) that project future climate. Many ESMs are adopting methods to resolve plant size and ecosystem disturbance history, using vegetation demographic models. These models make it feasible to conduct more realistic simulation of processes that control vegetation dynamics. Meanwhile, increasing understanding of the processes governing plant water use, and ecosystem responses to drought in particular, has led to the adoption of dynamic plant water transport (i.e., hydrodynamic) schemes within ESMs. However, the extent to which variations in plant hydraulic traits affect both plant water stress and the risk of mortality in trait-diverse tropical forests is understudied. In this study, we report on a sensitivity analysis of an existing hydrodynamic scheme (HYDRO) model that is updated and incorporated into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (FATES–HYDRO V1.0). The size- and canopy-structured representation within FATES is able to simulate how plant size and hydraulic traits affect vegetation dynamics and carbon–water fluxes. To better understand this new model system, and its functionality in tropical forest systems in particular, we conducted a global parameter sensitivity analysis at Barro Colorado Island, Panama. We assembled 942 observations of plant hydraulic traits on 306 tropical plant species for stomata, leaves, stems, and roots and determined the best-fit statistical distribution for each trait, which was used in model parameter sampling to assess the parametric sensitivity. We showed that, for simulated leaf water potential and loss of hydraulic conductivity across different plant organs, the four most important traits were associated with xylem conduit taper (buffers increasing hydraulic resistance with tree height), stomatal sensitivity to leaf water potential, maximum stem hydraulic conductivity, and the partitioning of total hydraulic resistance above vs. belowground. Our analysis of individual ensemble members revealed that trees at a high risk of hydraulic failure and potential tree mortality generally have a lower conduit taper, lower maximum xylem conductivity, lower stomatal sensitivity to leaf water potential, and lower resistance to xylem embolism for stem and transporting roots. We expect that our results will provide guidance on future modeling studies using plant hydrodynamic models to predict the forest responses to droughts and future field campaigns that aim to better parameterize plant hydrodynamic models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Moving beyond the Solvent-Tip Approximation to Determine Site-Specific Variations of Interfacial Water Structure through 3D Force Microscopy

Although interfacial solution structure impacts environmental, biological, and technological phenomena, including colloidal stability, protein assembly, heterogeneous nucleation, and water desalination, its molecular details remain poorly understood. Here, we visualize the three-dimensional (3D) hydration structure at the boehmite(010)-water interface using fast force mapping (FFM). Using a self-consistent scheme to decouple long-range tip-sample interactions from short-range solvation forces, we obtain the solution structure with lattice resolution. The results are benchmarked against molecular dynamics simulations that explicitly include the effects of the tip with different levels of approximation and systematically account for tip size, chemistry, and confinement effects. We find four laterally structured water layers within 1 nm of the surface, with the highest water densities at sites adjacent to hydroxyl groups. The key features beyond the first two layers can only be predicted using a full-scale simulation of the boehmite-water-silica system. Our findings further reveal a complex relationship between site-specific chemistry, water density, and long-range particle interactions; and present important advances toward quantitative data interpretation in 3D FFM.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Cyclic Peptides for Lanthanide Binding

Lanthanide ions are difficult to separate from one another due to their similar chemical properties. The discovery of lanthanide-binding peptides and proteins in nature has led to an increased interest in the possibility of utilizing the strong binding of peptides to lanthanide ions for their separations; as such, there has been an effort to identify or design peptides with improved lanthanide binding and selectivity toward particular lanthanide ions. Here, in this study, we designed and characterized lanthanide-binding cyclic peptides (LBCPs) with molecular dynamics simulations, electronic structure calculations, and emission spectroscopy. Luminescent decay measurements were done to determine the number of water molecules coordinated to the Eu 3+ ion in Eu-LBCP complexes and compare to the predicted number of water molecules by computation to assess the lanthanide-binding affinity of LBCPs. Measured stability constants show binding of the LBCPs to the Eu 3+ ion with stronger than micromolar affinity. We were able to identify multiple peptides that selectively bind to middle lanthanides. We describe the structural basis of the lanthanide-binding selectivity trend with strongest binding to the middle lanthanides, followed by the heavier lanthanides, and finally to the lighter ions.

ions↗
DOE OSTI2021

First-Principles Grand-Canonical Simulations of Water Adsorption in Proton-Exchanged Zeolites

Water appears by design or as impurities in many important reactive systems. For those catalyzed by porous solid acids, such as widely used zeolites, experimentally quantifying the amount or elucidating the structure of adsorbed water clusters at reaction conditions is challenging, while computational studies (e.g., first-principles molecular dynamics simulations) often need to assume the loading to examine solvation effects. Furthermore, we perform first-principles grand-canonical simulations to predict water adsorption to H-ZSM-5 zeolites under specified experimental conditions. Presampling with inexpensive force fields and a pool-based parallelization algorithm are used to improve simulation efficiency, while molecular dynamics is used to sample configurations involving hydronium species. We observe that H + exchange dramatically increases the hydrophilicity of zeolite MFI and an appreciable amount of water is present at very low relative humidities. At all conditions examined, the zeolitic protons are found to dissociate readily from the surface basic sites and become mobile by participating in the hydrogen-bonded chains of adsorbed water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Atomistic level aqueous dissolution dynamics of NASICON-Type Li 1+ x Al x Ti 2– x (PO 4 ) 3 (LATP)

Advancing the atomistic level understanding of aqueous dissolution of multicomponent materials is essential. Here, we combined ReaxFF and experiments to investigate the dissolution at the Li 1+ x Al x Ti 2– x (PO 4 ) 3 -water interface. We demonstrate that surface dissolution is a sequentially dynamic process. The phosphate dissolution destabilizes the NASICON structure, which triggers a titanium-rich secondary phase formation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

De novo design of drug-binding proteins with predictable binding energy and specificity

The de novo design of small molecule–binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase–1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free energy calculations performed directly on the designed models were in excellent agreement with the experimentally measured affinities. We conclude that de novo design of high-affinity small molecule–binding proteins with tuned interaction energies is feasible entirely from computation.

Science & Technology - Other Topics↗
DOE OSTI2021

Identification of Preferential Recharge Zones in Karst Systems Based on the Correlation between the Spring Level and Precipitation: A Case Study from Jinan Spring Basin

The Jinan spring basin is located in the karst area of northern China, where springs serve as important sources of water supply. Several studies on spring protection and water supply have been carried out, and scholars have developed some laws on local groundwater flow dynamic and characteristics of aquifer structures. Unfortunately, there is a lack of detailed research on preferential recharge zones, which are the main recharge pathways of springs. Therefore, this research focuses on identifying preferential recharge zones based on the correlation between the spring level and precipitation. The results show that when precipitation is more intense or lasts longer, there is a stronger correlation between spring level and precipitation. It has been established that the precipitation at Donghongmiao station has the closest relationship with the dynamic of Baotu spring, which is found to be the most significant contribution to spring preservation. Two potential preferential recharge zones in the Jinan spring basin are detected through correlation analysis and geological exploration data. These findings support spring protection and water supply projects in karst regions.

58 GEOSCIENCES↗
DOE OSTI2025

Molecular Dynamics Simulations of Supercritical Carbon Dioxide and Water using TraPPE and SWM4-NDP Force Fields

The increased levels of carbon dioxide (CO 2 ) emissions due to the combustion of fossil fuels and the consequential impact on global climate change have made CO 2 capture, storage, and utilization a significant area of focus for current research. In most electrochemical CO 2 applications, water is used as a proton donor due to its high availability and mobility and use as a polar solvent. Additionally, supercritical CO 2 is a promising avenue for electrochemical applications due to its unique chemical and physical properties. Consequently, understanding the interactions between water and supercritical CO 2 is of great importance for future electrochemical applications. Molecular dynamics (MD) simulation is a powerful tool that enables atomistic-resolution dynamics of molecular systems, which can complement and guide future experimental investigations. This study employed atomistic MD to study the cosolubilities, codiffusivities, and structure of supercritical CO 2 and water systems, with a polarizable water model (SWM4-NDP) and a nonpolarizable CO 2 model (TraPPE). Additionally, ab initio MD simulations were used to better understand how atomistic polarizable/nonpolarizable models compare to explicit modeling of electron densities. The polarizable water model exhibited substantial improvement in water-associated properties. In conclusion, we anticipate the development of a compatible polarizable CO 2 model to yield similar improvement, providing a pathway for realizing novel high-pressure electrochemical systems.

25 ENERGY STORAGE↗