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At least 217 records · Page 12

A Quantum Mechanical Study of Quartz (101) Interfacial Boundaries

Density functional theory (DFT) calculations were performed on periodic and molecular models to explore the energetics of bonding modes at quartz–quartz interfaces, common grain contacts in sandstones. Four interface types were modeled: H 2 O-mediated, silanol H-bond mediated, O–O peroxide bonds, and siloxane bonds. Each type of interface may exist in the subsurface of the Earth, depending upon water activity, temperature, and pressure, as interfacial structures are stable within DFT molecular dynamics simulations up to 473 K. The results predict interfacial energies SiOSi > SiOOSi > SiOH-6H 2 O > 2SiOH, as expected based on similar bond strengths in other systems. The proposed SiOOSi interface is not generally accounted for in chemomechanical models but could be important in sandstones at depth in the Earth. The implications for intergrain fracturing and H2 generation are discussed.

Hydrogen↗

Earth observing satellite: Understanding the Earth as a system

There is now a plan for global studies which include two very large efforts. One is the International Geosphere/Biosphere Program (IGBP) sponsored by the International Council of Scientific Unions. The other initiative is Mission to Planet Earth, an unbrella program for doing three kinds of space missions. The major one is the Earth Observation Satellite (EOS). EOS is large polar orbiting satellites with heavy payloads. Two will be placed in orbit by NASA, one by the Japanese and one or two by ESA. The overall mission measurement objectives of EOS are summarized: (1) the global distribution of energy input to and energy output from the Earth; (2) the structure, state variables, composition, and dynamics of the atmosphere from the ground to the mesopause; (3) the physical and biological structure, state, composition, and dynamics of the land surface, including terrestrial and inland water ecosystems; (4) the rates, important sources and sinks, and key components and processes of the Earth's biogeochemical cycles; (5) the circulation, surface temperature, wind stress, sea state, and the biological activity of the oceans; (6) the extent, type, state, elevation, roughness, and dynamics of glaciers, ice sheets, snow and sea ice, and the liquid equivalent of snow in the global cryosphere; (7) the global rates, amounts, and distribution of precipitation; and (8) the dynamic motions of the Earth (geophysics) as a whole, including both rotational dynamics and the kinematic motions of the tectonic plates.

Soffen, Gerald↗

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

Dissolving salt is not equivalent to applying a pressure on water

Abstract Salt water is ubiquitous, playing crucial roles in geological and physiological processes. Despite centuries of investigations, whether or not water’s structure is drastically changed by dissolved ions is still debated. Based on density functional theory, we employ machine learning based molecular dynamics to model sodium chloride, potassium chloride, and sodium bromide solutions at different concentrations. The resulting reciprocal-space structure factors agree quantitatively with neutron diffraction data. Here we provide clear evidence that the ions in salt water do not distort the structure of water in the same way as neat water responds to elevated pressure. Rather, the computed structural changes are restricted to the ionic first solvation shells intruding into the hydrogen bond network, beyond which the oxygen radial-distribution function does not undergo major change relative to neat water. Our findings suggest that the widely cited pressure-like effect on the solvent in Hofmeister series ionic solutions should be carefully revisited.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nuclear quantum effects on the quasiparticle properties of the chloride anion aqueous solution within the GW approximation

Photoelectron spectroscopy experiments in ionic solutions reveal important electronic structure information, in which the interaction between hydrated ions and water solvent can be inferred. Based on many-body perturbation theory with GW approximation, we theoretically compute the quasiparticle electronic structure of chloride anion solution, which is modeled by path-integral abinitio molecular dynamics simulation by taking account the nuclear quantum effects (NQEs). The electronic levels of hydrated anion as well as water are determined and compared with the recent experimental photoelectron spectra. It is found that NQEs improve the agreement between theoretical prediction and experiment because NQEs effectively weaken the hybridization of the between the Cl – anion and water. Furthermore, our study indicates that NQEs plays a small but non-negligible role in predicting the electronic structure of the aqueous solvation of ions of the Hofmeister series.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

ARM SGP PBLH and MLH datasets from Raman lidar and Doppler lidar

The planetary boundary layer (PBL) plays a critical role in the atmosphere by transferring heat, moisture, and momentum. The warm PBL has a distinct diurnal cycle including the daytime convective mixing layer (ML) and nighttime residual layer developments. Thus, simultaneous determinations of PBL height (PBLH) and ML height (MLH) are necessary for studying PBL characterization and processes. Here, new approaches are developed to provide reliable PBLH and MLH estimates to characterize warm PBL evolution. The approaches use Raman lidar (RL) water vapor mixing ratio (WVMR) and Doppler lidar (DL) vertical velocity measurements at the Southern Great Plains (SGP) atmospheric observatory, which was established by the Atmospheric Radiation Measurement (ARM) User Facility. Compared to widely used lidar aerosol measurements for PBLH, WVMR is a better tracer for PBL vertical mixing. For PBLH, the approach classifies PBL water vapor structures into a few general patterns, then uses a slope method and dynamic threshold method to determine PBLH. For MLH, wavelet analysis is used to reconstruct 2D variance from DL vertical wind velocity measurements according to the turbulence eddy size to minimize the impacts of gravity wave and eddy size on variance calculations; then, a dynamic threshold method is used to determine MLH. Remotely-sensed PBLHs and MLHs are compared with radiosonde measurements based on the Richardson number method. Good agreements between them confirm that the proposed new algorithms are reliable for PBLH and MLH characterization. The algorithms are applied to warm-season RL and ML measurements at the SGP site for five years to study warm-season PBL structure and processes. The weekly composited diurnal evolutions of PBLHs and MLHs in a warm climate were provided to illustrate diurnal and seasonal PBL evolutions. This reliable data set of PBLH and MLH values will be valuable for studying PBL processes, model evolution, and PBL parameterization improvements. The MLH dataset includes the MLH in values of km above ground level. The PBLH dataset includes the PBLH in values of km above ground level, along with a flag ("situation_PBLH") to determine the state of the PBL (1 = Cloudy Condition, 2 = Stable Layer, 3 = Multi-layer WVMR structure, 4 = Well-Mixed PBL, 5 = A de-coupled layer, 6 = Other).

mixing layer height↗

Investigations of water/oxide interfaces by molecular dynamics simulations

Water/oxide interfaces are ubiquitous on earth and show significant influence on many chemical processes. For example, understanding water and solute adsorption as well as catalytic water splitting can help build better fuel cells and solar cells to overcome our looming energy crisis; the interaction between biomolecules and water/oxide interfaces is one hypothesis to explain the origin of life. However, knowledge in this area is still limited due to the difficulty of studying water/solid interfaces. As a result, research using increasingly sophisticated experimental techniques and computational simulations has been carried out in recent years. Although it is difficult for experimental techniques to provide detailed microscopic structural information, molecular dynamics (MD) simulations have satisfactory performance. In this report, we discuss classical and ab initio MD simulations of water/oxide interfaces. Generally, we are interested in the following questions: How do solid surfaces perturb interfacial water structure? How do interfacial water molecules and adsorbed solutes affect solid surfaces and how do interfacial environments affect solvent and solute behavior? Finally, we discuss progress in the application of neural network potential based MD simulations, which offer a promising future because this approach has already enabled ab initio level accuracy for very large systems and long trajectories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Actinium–DOTA coordination in water from hybrid ML/MM: Structure, free energies, and water-exchange pathways

Quantitative simulation of trivalent ƒ-block chelates in water remains challenging because bonded and non-bonded force-field models make different approximations for coordination structure, exchange dynamics, and ion–ligand interactions in highly charged systems. Here, we develop a hybrid machine-learning/molecular-mechanics (ML/MM) framework for Ac 3+ –DOTA in explicit solvent by training an E(3)-equivariant neural network potential (MACELES) on mechanically embedded QM/MM data for Ac aquo and Ac–DOTA species and coupling it to NAMD 2.14 with particle-mesh Ewald electrostatics. Nanosecond ML/MM trajectories remain numerically stable and preserve chelate integrity, yielding a compact DOTA inner shell with an inner-sphere water coordination number of CN Ac,O w ≈ 1.7 arising from a dynamic equilibrium between one- and two-water states (37.5% and 59.9% of frames; three waters 2.5%). A 5 ns potential of mean force shows two low-lying basins at CN Ac,O w ≈ 1 and CN Ac,O w ≈ 2. DFT end-state free energies are consistent with the ML/MM profile, and DFT minimum-energy paths provide a qualitative electronic-structure reference for the observed basin connectivity. State-resolved kinetics reveal picosecond water-exchange pathways that couple hydration changes to transient DOTA arm fluctuations, and training-set comparisons show that temperature-matched Ac–DOTA data optimize energy/force accuracy while more diverse solvated data improve charge prediction. Overall, the present hybrid ML/MM model provides a practical description of Ac 3+ –DOTA hydration thermodynamics and short-time exchange behavior in explicit water at MD-like cost.

Actinium↗

pH-Driven Restructuring of Hydration Layers and Cation Ad-sorption at the Alumina-Water Interface

Oxide-water interfaces underpin ion separation, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. Yet, the molecular-scale link between pH-dependent surface protonation, hydration-layer structure, and counter-ion adsorption remains poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)-water interface in 10 mM Rb+ over pH 3-12. CTR measurements reveal two distinct adsorbed water layers at ~2.2 and ~3.5 Å above the surface that each shift toward the substrate at transition pHs near 6.5 and 10.6, respectively, directly reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb+ coverage and a decrease in mean adsorption height from ~3.5 to ~2.7 Å with increasing pH, indicating enhanced counter-ion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥3.5. This negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb+ coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid-base chemistry to ion binding distances at an oxide-water interface.

Electrical double layer (EDL), Surface protonation↗

Oceanographic mapping of structure and dynamics of the northern Gulf of California by the use of spectral modeling and ERTS-1

Distribution and flow of water masses at four depth intervals were determined by analyzing ERTS imagery through the use of optical models of classes of vertical oceanographic profiles. Data used for these models was obtained from shipboard measurements including surface spectral radiance, and optical and more conventional oceanographic depth profiles. The spectral models obtained were applied to radiance-contoured ERTS imagery in band 4, 5, 6, and 7. Features mapped by direct photointerpretation of ERTS imagery include submerged shoals, current streamlines, and location of possible upwellings, downwellings and submarine springs.

Lepley, L. K.↗

Localization of Zn 2+ ions affects the structural folding and mechanics of Nereis virens Nvjp-1

Several biological organisms utilize metal-coordination bonds to produce remarkable materials, such as the jaw of the marine worm Nereis virens, where metal-coordination bonds yield remarkable hardness without mineralization. Though the structure of a major component of the jaw, the Nvjp-1 protein, has recently been resolved, a detailed nanostructural understanding of the role of metal ions on the structural and mechanical properties of the protein is missing, especially with respect to the localization of metal ions. In this work, atomistic replica exchange molecular dynamics with explicit water and Zn 2+ ions and steered molecular dynamics simulations were used to explore how the initial localization of the Zn 2+ ions impacts the structural folding and mechanical properties of Nvjp-1. We found that the initial distribution of metal ions for Nvjp-1, and likely for other proteins with high amounts of metal-coordination, has important effects on the resulting structure, with larger metal ion quantity resulting in a more compact structure. These structural compactness trends, however, are independent from the mechanical tensile strength of the protein, which increases with greater hydrogen bond content and uniform distribution of metal ions. Our results indicate that different physical principles underlie the structure or mechanics of Nvjp-1, with broader implications in the development optimized hardened bioinspired materials and the modeling of proteins with significant metal ion content.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL . Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterizing warm atmospheric boundary layer over land by combining Raman and Doppler lidar measurements

PBL plays a critical role in the atmosphere by transferring heat, moisture, and momentum. The warm PBL has a distinct diurnal cycle including daytime convective mixing layer (ML) and nighttime residual layer developments. Thus, for PBL characterization and process study, simultaneous determinations of PBL height (PBLH) and ML height (MLH) are necessary. Here, new approaches are developed to provide reliable PBLH and MLH to characterize warm PBL evolution. The approaches use Raman lidar (RL) water vapor mixing ratio (WVMR) and Doppler lidar (DL) vertical velocity measurements at the Southern Great Plains (SGP) atmospheric observatory, which was established by the Atmospheric Radiation Measurement (ARM) user facility. Compared with widely used lidar aerosol measurements for PBLH, WVMR is a better trace for PBL vertical mixing. For PBLH, the approach classifies PBL water vapor structures into a few general patterns, then uses a slope method and dynamic threshold method to determine PBLH. For MLH, wavelet analysis is used to re-construct 2-D variance from DL vertical wind velocity measurements according to the turbulence eddy size to minimize the impacts of gravity wave and eddy size on variance calculations; then, a dynamic threshold method is used to determine MLH. Remotely-sensed PBLHs and MLHs are compared with radiosonde measurements based on the Richardson number method. Good agreements between them confirm that the proposed new algorithms are reliable for PBLH and MLH characterization. The algorithms are applied to warm seasons’ RL and ML measurements at the SGP site for five years to study warm season PBL structure and processes. The weekly composited diurnal evolutions of PBLHs and MLHs in warm climate were provided to illustrate diurnal and seasonal PBL evolutions. This reliable PBLH and MLH dataset will be valuable for PBL process study, model evolution, and PBL parameterization improvement.

54 ENVIRONMENTAL SCIENCES↗

Annual review of earth observations from space

An overview is given of the present state of satellites making observations of the earth. Satellite systems discussed include the NOAA series of Synchronous Meteorological Satellites (SMS) and sun-synchronous satellites, the two LANDSATS (formerly called ERTS), and the NIMBUS series. Examples are presented of the types of observations being made as well as their purposes. These include observations of synoptic and mesoscale atmospheric processes for daily weather forecasting, global atmospheric processes for long-range weather forecasting, planetary radiation budget and ocean circulation for monitoring climatic trends, earth dynamics and tectonic structure for mineral exploration and assessing earthquake hazards, atmospheric composition and water quality for environment monitoring, and thematic mapping for monitoring land use, managing crops and water resources, and assessing environmental impacts.

Nordberg, W.↗

Cavitation Effects on the Structural Dynamics of Turbomachinery Components

The structural integrity of inducer and impeller blades in rocket engine turbomachinery must be evaluated in the face of complex excitation mechanisms including fluctuating pressures due to cavitation. Cavitation occurs when the local fluid pressure drops below the vapor pressure, causing the formation of vapor-filled bubbles. Cavitation can exist to various extents within the typical operating range of rocket engine turbopumps. Despite recent progress towards reducing uncertainties in structural dynamic models of turbomachinery components, the extent to which pump cavitation affects the structural dynamic properties (i.e., natural frequencies, damping, and mode shapes) of inducer and impeller blades remains largely unknown. To study the structural dynamic effects of cavitating flows, experiments are conducted in a high-speed water tunnel. The test articles mimic a single inducer blade that is unwrapped from the hub, thus resembling a low aspect ratio cantilevered plate. To induce cavitation, the plates are oriented at a non-zero angle of attack and have rough strips near their leading edges. To control the extent of cavitation, the static pressure of the water tunnel is controlled between roughly 0.5 and 1.5 atm. A high-speed camera is used to quantify the coverage of the cavitations heet. The sheet coverage is then correlated to changes in fluid-added mass and hydroelstic damping. In addition, a corresponding two-way coupled CFD/FE model is under development for test/analysis correlation.

Ben Davis↗

Investigating the Adsorption–Desorption Kinetics of a Molecular Water Oxidation Catalyst at an Electrode Interface

Probing the dynamics of molecular catalysts at electrode–electrolyte interfaces is essential for understanding catalytic mechanisms. Structure-specific spectroscopic methods are particularly powerful for examining electrocatalytic interfaces but are mostly used under steady-state conditions. Herein, we combined surface-enhanced infrared absorption spectroscopy (SEIRAS) with phase-sensitive detection (PSD) to investigate the dynamics of a molecular Ir-based water oxidation catalyst at the Au–electrolyte interface. We found that the amplitude of the absorbance of the catalyst is anticorrelated to that of interfacial water. This anticorrelation can be understood by the adsorption of the electrooxidized catalyst on the electrode and concurrent displacement of interfacial water. The infrared signals from the interface exhibit an increasing phase lag with respect to the electrode potential with an increasing scan rate of the potential. Kinetic modeling suggests that the potential-dependent adsorption–desorption kinetics of the molecular catalyst on the electrode gives rise to this phase lag. Furthermore, this study shows that PSD-SEIRAS is a powerful tool for investigating the interfacial dynamics of electrocatalytic systems.

Catalysts↗

Thermodynamic and Kinetic Transitions of Liquids in Nanoconfinement

Core principles of chemistry are ubiquitously invoked to shed light on the nature of molecular level interactions in nanoconfined fluids, which play a pivotal role in a wide range of processes in geochemistry, biology, and engineering. A detailed understanding of the physicochemical processes involved in the flow, structural transitions, and freezing or melting behavior of fluids confined within nanometer-sized pores of solid materials is thus of enormous importance for both basic research and technological applications. This Account provides a perspective on new insights into the thermodynamic and kinetic transitions of nanoconfined fluids in their stable and metastable forms. After briefly introducing the unique properties of mesoporous silicas from the SBA, MCM, and FDU families that serve as the confinement matrices, combining highly ordered single and bimodal mesopore architectures with tunable pore sizes in the ~2-15 nm range and narrow size distributions, recent studies on melting/freezing behavior of water confined in these host matrices are reviewed. While differential scanning calorimetry (DSC) reveals a linear relationship between melting point depression and pore size (independent of the pore shape), as predicted by the Gibbs-Thomson relation, variable temperature 2 H wide-line nuclear magnetic resonance (NMR) spectroscopy studies confirm the core-shell model of water and give evidence for a layer-by-layer freezing mechanism, which gives rise to an apparent fragile-to-strong transition in the solidification dynamics. In contrast to the freezing/melting behavior of water, the effect of nanoconfinement on the glass transition of supercooled liquids is nonuniversal and the glass transition temperature T g can either increase or decrease with the dimensionality and extent of confinement. This nonuniversal behavior is exemplified by the two glass-forming molecular liquids, glycerol and ortho-terphenyl (OTP). While glycerol shows an increase in T g and a pronounced slowdown of the rotational dynamics of the constituent molecules due to a change in the molecular packing between the bulk and the confined liquid, OTP displays a linear and confining-media-dependent depression of T g with increased confinement that is strongly influenced by the pore-liquid interface characteristics. This Account concludes with a focus on recent experimental evidence of extreme spatial and dynamical heterogeneity in both freezing and glass transition processes. This discovery was enabled by the unique mesoporous structures of SBA-16 and FDU-5, possessing bimodal architectures with two interconnected pore types of different size and shape (spherical and cylindrical). For the very first time, two melting points for water and two glass transitions for supercooled OTP, corresponding to a specific pore type, were observed. Collectively, these observations strongly suggest a close mechanistic connection between the local fluctuations in the structure and dynamics of nanoconfined liquids. Finally, while the findings reviewed in this Account provide new insights into thermodynamic and kinetic transitions of fluids, there remain many unanswered questions regarding the effects of nanoconfinement on the fundamental properties of fluids, which offer exciting future opportunities in chemical research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solution Structure and Hydration Forces between Mica and Hydrophilic Versus Hydrophobic Surfaces

Solid-liquid interfaces are central to a range of interesting phenomena including catalysis, heterogeneous nucleation, water desalination, and biomolecular assembly. While three-dimensional Fast Force Mapping (3D FFM) has emerged as a technique for resolving interfacial solution structure at the molecular scale, key challenges for data interpretation persist, most notably regarding the influence of the probe on the measured structure. Using the mica-water system as a case study, we investigate the effect of hydrophilic and hydrophobic probes on interfacial solution structure measured by 3D FFM. Data from hydrophilic silicon-based probes are in good agreement with molecular dynamics simulations, wherein the innermost water molecules adsorb preferentially at the surface ditrigonal cavity sites followed by two subsequent hydration layers. In contrast, the hydrophobic carbon-based probes detect vertical oscillatory features, but do not show lateral patterning that matches the underlying mica lattice. At high ionic strength, up to six of these oscillatory features are observed extending 2 nm into the solution phase with an average spacing of 0.29 ± (0.04) nm. Further, we also determine that the repulsive hydration force between mica and the hydrophilic probe depends on the nature and concentration of ions in solution. Specifically, solutions with stronger ion-water and ion-ion interactions increase the interfacial viscosity, which results in a stronger repulsive hydration force as the probe approaches the surface. Based on these observations, we present a scheme for controlling the outcomes of particle attachment and aggregation by varying the solution conditions to tune the hydration force.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗