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Ecosystem Science with NISAR: Final Preparations in The Pre-Launch Period
The NISAR mission which in its most recent round of launch preparations was set to launch in the spring of 2024, and now delayed until later in the fall or early spring of 2025, will serve as an unprecedented resource for the Remote Sensing of Ecosystems Science community. The two frequency, L- and S-band will full-polarimetric capability over a 250 km wide swath using the SweepSAR technique [1] will collect reliable set of observations (60 per year; 30 each for ascending and descending passes) on a continuing basis that will allow for the modeling and observation of time-varying processes that are prevalent in the living environment broadly described as Ecosystems. Among the prime science goals of the NISAR Ecosystems disciplines are in the characterization of agriculture, disturbance, biomass, forest structure and water dynamics seen in the world’s rivers, coasts, and permafrost regions. In this paper we provide an overview of the Ecosystem science that will be enabled by the NISAR mission and give a status of the basic algorithms that are being used to provide a basic set of tools to the community to make use of the data that NISAR will provide.
Quantifying the Extent of Hydration of a Surface-Bound Peptide Using Neutron Reflectometry
Establishing how water, or the absence of water, affects the structure, dynamics, and function of proteins in contact with inorganic surfaces is critical to developing successful protein immobilization strategies. In this work, the quantity of water hydrating a monolayer of helical peptides covalently attached to self-assembled monolayers (SAMs) of alkyl thiols on Au was measured using neutron reflectometry (NR). The peptide sequence was composed of repeating LLKK units in which the leucines were aligned to face the SAM. When immersed in water, NR measured 2.7 ± 0.9 water molecules per thiol in the SAM layer and between 75 ± 13 and 111 ± 13 waters around each peptide. The quantity of water in the SAM was nearly twice that measured prior to peptide functionalization, suggesting that the peptide disrupted the structure of the SAM. To identify the location of water molecules around the peptide, we compared our NR data to previously published molecular dynamics simulations of the same peptide on a hydrophobic SAM in water, revealing that 49 ± 5 of 95 ± 8 total nearby water molecules were directly hydrogen-bound to the peptide. Finally, we show that immersing the peptide in water compressed its structure into the SAM surface. Together, these results demonstrate that there is sufficient water to fully hydrate a surface-bound peptide even at hydrophobic interfaces. Given the critical role that water plays in biomolecular structure and function, these results are expected to be informative for a broad array of applications involving proteins at the bio/abio interface.
Fast product release requires active-site water dynamics in carbonic anhydrase
Water plays an essential role in enzyme structure, stability, and the substantial rate enhancement of enzyme catalysis. However, direct observations linking enzyme catalysis and active-site water dynamics pose a significant challenge due to experimental difficulties. By integrating an ultraviolet (UV) photolysis technique with temperature-controlled X-ray crystallography, we track the catalytic pathway of carbonic anhydrase II (CAII) at 1.2 Å resolution. This approach enables us to construct molecular movies of CAII catalysis, encompassing substrate (CO 2 ) binding, conversion from substrate to product (bicarbonate), and product release. In the catalytic pathway, we identify an unexpected configuration in product binding and correlate it with sub-nanosecond rearrangement of active-site water. Based on these experimental observations, we propose a comprehensive mechanism of CAII and describe the detailed structure and dynamics of active-site water in CAII. Our findings suggest that CAII has evolved to utilize the structure and fast dynamics of the active-site waters for its diffusion-limited catalytic efficiency.
Exemption of lattice collapse in Ni–MnO 2 birnessite regulated by the structural water mobility
Lattice collapse and associated mechanical fracture frequently occur in Li-intercalated metal oxide cathodes at the deep charge state upon Li-ion removal, governed by chemical compositions and the resulting electron density of the oxygen atoms. However, similar lattice collapse for metal oxide electrodes in aqueous storage and its mitigation have not been well studied. In this work, we reported the lattice collapse of MnO 2 layered birnessite during the aqueous de-sodiation process at high voltage due to the structural water motion, as evidenced by in situ XRD. Unlike non-aqueous Li-intercalated electrodes, Ni-dopants mitigated the lattice collapse of birnessite at deep charge states. Moreover, density functional theory (DFT) calculations showed that Ni doping induces charge depletion of lattice oxygen due to its higher electronegativity than Mn. This charge reduction, in turn, yields a significant decrease in electrostatic repulsion between the oxygens belonging to lattice and structural water. Classical molecular dynamics simulations based on atomic charges obtained from DFT elucidate that Ni-doping facilitates immobilization of structural water in (Ni)MnO 2 and prevents lattice collapse upon Na-ion removal. (Ni)MnO 2 exempted from lattice collapse shows an improved storage capacity relative to MnO 2 while maintaining similar cycling stability.
Surface Hydroxyls of Imogolite Nanotubes Drive Distinct Structures and Mobility Differentiation of Nanoconfined Water
Abstract Nanoconfined fluids, particularly water, govern subsurface geochemistry, yet the molecular-level mechanisms by which mineral surfaces dictate confined water structure and mobility remain poorly resolved. Here, we combine solution- and solid-state proton (1H) NMR spectroscopy, NMR relaxometry, modulated-gradient spin–echo (MGSE) NMR diffusometry, infrared spectroscopy, and molecular dynamics simulations to demonstrate that surface hydroxyls drive the structural and dynamic differentiation of water in imogolite nanotubes. In saturated suspensions, we observe the coexistence of distinct water 1H environments, each exhibiting significantly reduced mobility, which we attribute to strong interactions with the imogolite surfaces. As more mobile water is removed, long-range water diffusivity in the fibrous solid samples slows to 1.6 × 10–10 m2·s–1 while local fluctuations increase to 3.4 × 10–8 m2·s–1, indicating a significant increase in molecular restriction through surface interactions. Together, our experiments reveal three coexisting populations with varied structures and mobilities, all distinct from liquid bulk water. We resolve a persistent solid-like interfacial layer strongly bound to surface hydroxyls, characterized by an unusually short T2 (<1 ms), and a very close effective 1H–1H distance of ∼1.55 Å between water and the inner-surface silanol group. An inner-core population occupying the inner cavity exhibits an intermediate dynamic regime with restricted axial diffusion, while outer-surface water associated with aluminum hydroxyls retains relatively higher mobility. These results experimentally substantiate a hierarchy of water populations in imogolite and show how surface chemistry dictates the structures and dynamics of confined water.
Coarse-Grained Water Model Development for Accurate Dynamics and Structure Prediction
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Mixed Molecular and Dissociative Water Adsorption on Hydroxylated TiO 2 (110): An Infrared Spectroscopy and Ab Initio Molecular Dynamics Study
For this work, we have investigated the structure and dynamics of water (D 2 O) adsorbed on TiO 2 (110) for coverages between 0 and 1 monolayer with infrared reflection absorption spectroscopy (IRAS) and ab initio molecular dynamics (AIMD) simulations. For D 2 O coverages as low as 0.4 monolayers (ML) on a hydroxylated surface, IR spectra typical of hydrogen-bonded chains of water molecules are observed. However, for D 2 O coverages ≥ 0.3 ML, a sharp, high frequency peak is also observed in the p-polarized spectra that is red-shifted relative to the bridging hydroxyl peak. This new peak is not observed for water adsorbed on an oxidized surface. Based on the AIMD simulations and comparisons with previous IR spectra for TiO 2 nanoparticles, the new peak is assigned to terminal hydroxyl groups produced by dissociative adsorption of some of the water on TiO 2 (110). The simulations indicate that water dissociation is related to the presence of defect electrons in the system, but not due to direct interactions between adsorbed water and bridging hydroxyls.
Structural modeling and dynamic analysis of condensate storage tanks in nuclear power plants
Condensate storage tanks (CSTs) in nuclear power plants (NPPs) are classified as critical equipment capable of surviving strong shaking in a design basis earthquake to assure the ability to subsequently provide cooling water. Structural modeling and dynamic analysis of CSTs are complicated due to fluid-structure interaction (FSI) and coupling issues, which could have significant effects on seismic response. The capability of a number of approximate models to capture seismic response is investigated using dynamic analysis results from detailed finite element models. Modal analyses and time history analyses are carried out using both 2D and 3D models to predict the dynamic behavior of CSTs as a function of ground motion intensity. Although 2D simplified models can be used to quickly evaluate the dynamic response of CSTs when there is substantial margin to failure, a detailed 3D model is required when it is necessary to examine a limit state associated with the failure mode of the tank. The findings show good agreement between the natural frequencies of convective modes determined from the 2D and 3D CST models. The difference between the frequencies of impulsive modes were found to be equal to or less than 25%.
Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature
It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the overstructuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. Here, we find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.
Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of EDS to ab initio molecular dynamics (AIMD) simulation based on electronic density functional theory (DFT), the AIMD simulations of water were biased to reproduce its experimentally derived solvation structure. In particular, by solely biasing the O-O pair correlation functions, other structural and dynamical properties that were not biased were improved. In this work, the hypothesis is tested that directly biasing the OH pair correlation (and hence the H-O∙∙∙H hydrogen bonding), will provide an even better improvement of DFT-based water properties in AIMD simulations. The logic behind this hypothesis is that for most electronic DFT descriptions of water the hydrogen bonding is known to be deficient due to anomalous charge transfer and over polarization in the DFT. Using recent advances to the EDS learning algorithm, we thus train a minimal bias on AIMD water that reproduces the O-H radial distribution function derived from the highly accurate MB-pol model of water. Finally, it is then confirmed that biasing the O-H pair correlation alone can lead to improved AIMD water properties, with structural and dynamical properties in even closer to experiment than the previous EDS-AIMD model.
Insights into the rapid two-phase transport dynamics in different structured porous transport layers of water electrolyzers through high-speed visualization
In proton exchange membrane electrolyzer cells (PEMECs), maintaining efficient two-phase transport is one of the most important functions of porous transport layers (PTLs). To enhance the two-phase transport in PTLs, thin/titanium liquid/gas diffusion layers (TT-LGDLs) are introduced in PEMECs, and their difference from the conventional Ti felt PTLs are analyzed in-situ through high-speed and microscale visualization and electrochemical characterizations. The visualization results show that unfavorable large slugs can be greatly reduced in the PEMEC with a TT-LGDL compared to the PEMEC with a Ti felt PTL. More importantly, the recovery capability of water starvation with different PTLs is studied. After water starvation, the PEMEC with the TT-LGDL can recover the water starvation much more rapidly than the Ti felt cell, benefiting from its short and straight-through flow paths. Furthermore, the TT-LGDL tends to generate oxygen bubbles that are almost six times smaller and 236 times more frequently than the Ti felt PTL, indicating significantly boosted removal efficiency of produced oxygen and PEMEC performance. Finally, this study offers new insights into the dynamic processes of two-phase transport and the recovery capability of water starvation for different PTLs, which will provide valuable guidance for further optimization of PTLs and performance enhancement of PEMECs.
Hydration of NH 4 + in Water: Bifurcated Hydrogen Bonding Structures and Fast Rotational Dynamics
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Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments
Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO 3 ·nH 2 O systems, where M 2+ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Finally, water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.
Dynamic entity formed by protein and its hydration water
The interaction between protein and water plays a pivotal role in shaping the structure, dynamics, and function of biomacromolecules. A comprehensive understanding of this intricate interplay necessitates a systematic evaluation of interaction strength and its consequential impact on the dynamics of proteins and water across diverse protein systems. Despite numerous works on understanding the dynamics of water and proteins and the coupling between them, there are still unanswered questions. Here, we combine neutron scattering and isotope labeling to probe the dynamics of proteins and their hydration water in a variety of protein systems. We consider proteins of different structures and varying thermostability as well as proteins within living cells with distinct growth temperatures. Simultaneous characterization of protein and hydration water dynamics across diverse systems was achieved. Moreover, we performed water sorption isothermal measurements on three representative proteins to correlate the observed dynamics with the strength of the interaction energies governing each system. The experimental results underscore that proteins manifesting stronger attractive interactions with water display diffusionlike dynamics with higher flexibility upon hydration, concomitant with a reduced mobility in hydration water. Significantly, our findings suggest that, in fact, it is the interaction between protein and its hydration water that facilitates the transfer of mobility from water to protein, with stronger interactions correlating to greater protein flexibility and slower hydration water diffusion. Published by the American Physical Society 2024
Structure of Water Adsorbed on Nanocrystalline Calcium Silicate Hydrate Determined from Neutron Scattering and Molecular Dynamics Simulations
Calcium silicate hydrate (C-S-H) is a disordered, nanocrystalline material that acts as a primary binding phase in Portland cement. Thin films of water are present on the surfaces and in nanopores of C-S-H, impacting many of its chemical and mechanical properties, such as ion transport, creep, or thermal behavior. Despite decades of research, a full understanding of the structural details of adsorbed, confined, and bulk water in C-S-H remains elusive. In this work, we applied a multitechnique study involving molecular dynamics (MD) simulations validated by neutron diffraction with isotopic substitution (NDIS) and X-ray scattering methods to investigate the structure of water in C-S-H and C-A-S-H (an Al-bearing, low-CO 2 C-S-H substitute). Direct comparison of NDIS data with the MD results reveals that the structure of confined and interfacial water differs significantly from the bulk water and exhibits a larger degree of mesoscale ordering for more hydrated C-S-H structures. As a result, this observation suggests an important role of water as a stabilizer of the atomistic-level structure of C-S-H.
Modeling Liquid Water by Climbing up Jacob’s Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials
Within the framework of Kohn–Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob’s ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric–isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.
Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement
Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules attain the configuration of a “brush”: these PE brushes, due to their ability to form hydrogen bonds (HBs) with water via the PE functional groups, act as a source of soft and active nanoconfinement for the brush-trapped water molecules. In this paper, we study the effects of PE brush-induced confinement on the structure, dynamics and energetics of the water-water and water-PE HBs. Our results indicate a significant weakening of the HBs from bulk to sparsely grafted to densely grafted brushes. i.e., by increasing the degree of brush-induced nanoconfinement. We explain that this weakening of water-water HBs is caused by the disruption of the extended network of water molecules within the brush-induced nanoconfinement. This is confirmed by performing a ring structure analysis of the water molecules, which yields a reduction in the average ring size at higher degrees of brush-induced nanoconfinement (i.e., at higher brush grafting densities). Furthermore, we investigate the role of HB on the orientational dynamics of the water molecules. Here, we observe that the rotational motion of the water molecules becomes sluggish inside the PE brushes. Recent findings have indicated that the water and counterions trapped in brush-induced nanoconfinement demonstrate structures (in combination with the PE functional group) analogous to that in “water-in-salt” electrolytes that have seen extensive recent uses for Li-ion battery applications. However, the rotational dynamics of water molecules inside the brush-induced nanoconfinement is found to be distinctly different from that of conventional “water-in-salt” electrolytes in absence of any confinement; therefore, the present study will provide the necessary platform towards conceptualizing polymer-based nanoconfinement for battery applications.