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At least 685 records · Page 38

Sequence-selective dynamic covalent assembly of information-bearing oligomers

Relatively robust dynamic covalent interactions have been employed extensively to mediate molecular self-assembly reactions; however, these assembly processes often do not converge to a thermodynamic equilibrium, instead yielding mixtures of kinetically-trapped species. Here, we report a dynamic covalent self-assembly process that mitigates kinetic trapping such that multiple unique oligomers bearing covalently coreactive pendant groups are able to undergo simultaneous, sequence-selective hybridization with their complementary strands to afford biomimetic, in-registry molecular ladders with covalent rungs. Analogous to the thermal cycling commonly employed for nucleic acid melting and annealing, this is achieved by raising and lowering the concentration of a multi-role reagent to effect quantitative dissociation and subsequently catalyze covalent bond rearrangement, affording selective assembly of the oligomeric sequences. The hybridization specificity afforded by this process further enabled information encoded in oligomers to be retrieved through selective hybridization with complementary, mass-labeled sequences.

36 MATERIALS SCIENCE↗

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Forces that control self-organization of chemically-propelled Janus tori

Control of the individual and collective behavior of self-propelled synthetic micro-objects has immediate application for nanotechnology, robotics, and precision medicine. Despite significant progress in the synthesis and characterization of self-propelled Janus (two-faced) particles, predictive understanding of their behavior remains challenging, especially if the particles have anisotropic forms. Here, by using molecular simulation, we describe the interactions of chemically-propelled microtori near a wall. The results show that a torus hovers at a certain distance from the wall due to a combination of gravity and hydrodynamic flows generated by the chemical activity. Moreover, electrostatic dipolar interactions between the torus and the wall result in a spontaneous tilt and horizontal translation, in a qualitative agreement with experiment. Simulations of the dynamics of two and four tori near a wall provide evidence for the formation of stable self-propelled bound states. Our results illustrate that self-organization at the microscale occurs due to a combination of multiple factors, including hydrodynamic, chemical, electrostatic and steric interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Bridging the time scale in exascale computing of chemical systems (Final Technical Report)

This report summarizes the work carried out with support of the United States Department of Energy under Award DE-SC0019441. The theme of this project was to develop and apply methods that allowed for the acceleration of atomistic calculations, particularly in challenging areas such as multiphase systems, electrified interfaces, uncertainty estimation, and applications requiring chemical accuracy, which tend to be applications where simulation time is severely bottlenecked by the computational time requirements. Much of the focus was on the application of emerging machine-learning methodologies, although a wide range of methodologies were employed. This report has two major sections. The first focuses on the methodological advances themselves. Within this part, we report a number of major advances, a few examples of which are described here. We report the first machine-learning scheme for the acceleration of electronically grand-canonical calculations (that is, those applicable to electrochemistry). We report new methods of performing transfer learning, in which physics-based priors can be used to provide predictions, often with uncertainty estimates, of images well outside of training sets; we also offer ways to fine-tune these transfer-learning models. We provide a new systematic means to generate and apply minimal training data sets to very large (10,000’s of atoms) systems, with only small training sets appropriate for electronic structure. We developed new methodologies to integrate surface vibrations into surface adsorption calculations. We made advances to the applicability of diffusion Monte Carlo methods to allow (learned) force prediction, finite-size error correction, and force-free means of searching for transition states. We integrated machine-learned atomistic predictions into mechanism generation codes. Additionally, we released new software including AmpTorch, a modernized version of our original atomistic machine-learning code Amp. The second part of this report focuses on the scientific applications that accompanied, and were often enabled by, the methodological advances described earlier. A few examples follow, but full details are in the individual chapters of the report. For example, we developed a general theory of phonon-induced friction on molecular adsorbates. We showed fundamentally how solvent influences the adsorption and desorption process and how it differs from the processes typically involved at the solid–gas interface, making aqueous-phase and electrocatalysis different from traditional thermocatalysis. We examined how metal–insulator and magnetic transitions can be probed, and accelerated exciton dynamics via Frenkel Hamiltonian parameters. We showed that the nearsighted force-training approach, developed within this project, can predict both the stability and reactivity of large nanoparticles, and can also lead to insights on catalyst coverage on binding energies and entropies. These applied studies, which generally integrated with our method development, allowed us to push forward the theoretical understanding of several reaction classes.

08 HYDROGEN↗

A spline-based method to obtain spatially dependent viscosity in confined flows

Coupling chemical physics to continuum theories is a critical step to understanding multi-scale phenomena. This paper will connect non-equilibrium molecular dynamics simulations to a continuum-based Navier-Stokes equation that has relaxed the assumption of spatial uniformity in viscosity. Using a form for viscosity based on spline interpolation, viscosity as a function of position is obtained from the least squares fit of the velocity profile measured from molecular simulations of flow in a nanochannel. Viscosity can vary widely, particularly near the channel boundaries, indicating that uniform viscosity is no longer appropriate. Variations of the viscosity near the channel surfaces imply that considering solution and surface chemistry could be necessary to rigorously understand molecular-scale flows in nanochannels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Viscosity of the magnetized strongly coupled one-component plasma

The viscosity tensor of the magnetized one-component plasma, consisting of five independent shear viscosity coefficients, a bulk viscosity coefficient, and a cross coefficient, is computed using equilibrium molecular dynamics simulations and the Green-Kubo relations. A broad range of Coulomb coupling and magnetization strength conditions are studied. Magnetization is found to strongly influence the shear viscosity coefficients when the gyrofrequency exceeds the Coulomb collision frequency. Three regimes are identified as the Coulomb coupling strength and magnetization strength are varied. Here, the Green-Kubo relations are used to separate kinetic and potential energy contributions to each viscosity coefficient, showing how each contribution depends upon the magnetization strength. The shear viscosity coefficient associated with the component of the pressure tensor parallel to the magnetic field, and the two coefficients associated with the component perpendicular to the magnetic field, are all found to merge to a common value at strong Coulomb coupling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Influence of solution phase environmental heterogeneity and fluctuations on vibronic spectra: Perylene diimide molecular chromophore complexes in solution

Ensembles of ab initio parameterized Frenkel-exciton model Hamiltonians for different perylene diimide dimer systems are used, together with various dissipative quantum dynamics approaches, to study the influence of the solvation environment and fluctuations in chromophore relative orientation and packing on the vibronic spectra of two different dimer systems: a π-stacked dimer in aqueous solution in which the relative chromophore geometry is strongly confined by a phosphate bridge and a side-by-side dimer in dichloromethane involving a more flexible alkyne bridge that allows quasi-free rotation of the chromophores relative to one another. These entirely first-principles calculations are found to accurately reproduce the main features of the experimental absorption spectra, providing a detailed mechanistic understanding of how the structural fluctuations and environmental interactions influence the vibronic dynamics and spectroscopy of solutions of these multi-chromophore complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometric Phase in Anisotropic Kepler Problem: Perspective for Realization in Rydberg Atoms

We predict a gyroscopic effect that can be demonstrated with Rydberg atoms following the dynamics of a Kepler Hamiltonian with an additional uniaxial anisotropy induced by optical ponderomotive force. This effect is analogous to the rotation of the Foucault pendulum in response to the Earth’s rotation. Furthermore, we argue that in Rydberg states with a large principal quantum number a similar geometric angle can be generated by mechanical rotations of an atomic-optical setup on timescales between 1 μ⁢s and 1 ms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SANE: strategic autonomous non-smooth exploration for multiple optima discovery in multi-modal and non-differentiable black-box functions

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and multimodal parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, material structure image spaces, and molecular embedding spaces. Often these systems are black-boxes and time-consuming to evaluate, which resulted in strong interest towards active learning methods such as Bayesian optimization (BO). However, these systems are often noisy which make the black box function severely multi-modal and non-differentiable, where a vanilla BO can get overly focused near a single or faux optimum, deviating from the broader goal of scientific discovery. To address these limitations, here we developed Strategic Autonomous Non-Smooth Exploration (SANE) to facilitate an intelligent Bayesian optimized navigation with a proposed cost-driven probabilistic acquisition function to find multiple global and local optimal regions, avoiding the tendency to becoming trapped in a single optimum. To distinguish between a true and false optimal region due to noisy experimental measurements, a human (domain) knowledge driven dynamic surrogate gate is integrated with SANE. We implemented the gate-SANE into pre-acquired piezoresponse spectroscopy data of a ferroelectric combinatorial library with high noise levels in specific regions, and piezoresponse force microscopy (PFM) hyperspectral data. SANE demonstrated better performance than classical BO to facilitate the exploration of multiple optimal regions and thereby prioritized learning with higher coverage of scientific values in autonomous experiments. Our work showcases the potential application of this method to real-world experiments, where such combined strategic and human intervening approaches can be critical to unlocking new discoveries in autonomous research.

Biswas, Arpan [University of Tennessee, Knoxville,↗

Reduced Order Model to Predict Dispersion of Flammable Refrigerant into a Space

As the HVAC&R industry mobilizes to deploy more low-GWP refrigerants, relevant standards are being continually reviewed and updated. Those include the general safety standards ISO 5149 and ASHRAE 15, and the equipment standards IEC and UL. The standards systematically set the allowable maximum amount of refrigerant that should be used in different equipment types and different applications. To do so, they rely on predictions of how a leaked refrigerant mass will disperse into a space. Dispersion characteristics, such as total flammable volume and its residence time, determine the risk associated with the presence of the flammable refrigerant. The standards have included provisions for the use of flammable refrigerants for approximately two decades. They relied on limited analytical analyses and test cases in their development. Dispersion of a refrigerant into a space is complex. Computational fluid dynamics (CFD) are the most accurate in predicting a given problem. However, CFD is computationally expensive and requires specialized expertise and resources and is not suitable for use by standards development working group as prediction tool. This paper presents the development of a reduced order model (ROM) that predicts the key dispersion characteristics relevant to the dispersion of a leaked refrigerant into a space for any combination of input variables. The inputs are the refrigerant release height, the total released refrigerant mass and its release flow rate, the refrigerant molecular weight, the ventilation flow rate, the floor area and height of the space, recirculation air flow rate, and the tightness of the space. The outputs are histograms of volume fraction of the room in prescribed concentration bins and the total mass of the refrigerant in each bin normalized by the total refrigerant charge at 13 prescribed simulation time stamps between 1 and 900 seconds. The ROM is constructed from a set of CFD simulations with carefully chosen combinations of input parameters. The selection if done using a multidimensional sparse grid which is a generalization of the classical tensor approach but offers additional flexibility and thus can be more carefully tuned towards a specific model. The tuning is done to improve the accuracy, measured in the difference between the output values of the ROM and the CFD model, while minimizing the computational cost, measured in number of CFD simulations which is orders of magnitude more expensive than the processing the training data.

Edwards, Dean↗

Quantum spin ice response to a magnetic field in the dipole-octupole pyrochlore Ce 2 Zr 2 O 7

The pyrochlore magnet Ce 2 Zr 2 O 7 has attracted much attention as a quantum spin ice candidate whose novelty derives in part from the dipolar-octupolar nature of the Ce 3+ pseudospin-1/2 degrees of freedom it possesses. We report heat capacity measurements on single crystal samples of Ce 2 Zr 2 O 7 down to T~0.1K in a magnetic field along the [$1,\bar{1},0$] direction. These measurements show that the broad hump in the zero-field heat capacity moves higher in temperature with increasing field strength and is split into two separate humps by the [$1,\bar{1},0$] magnetic field at ~2T. These separate features are due to the decomposition of the pyrochlore lattice into effectively decoupled chains for fields in this direction: One set of chains (α chains) is polarized by the field while the other (β chains) remains free. This situation is similar to that observed in the classical spin ices Ho 2 Ti 2 O 7 and Dy 2 Ti 2 O 7 , but with the twist that here the strong transverse exchange interactions produce substantial quantum effects. Our theoretical modeling suggests that the β chains are close to a critical state, with nearly-gapless excitations. We also report elastic and inelastic neutron scattering measurements on single crystal Ce 2 Zr 2 O 7 in [$1,\bar{1},0$] and [0,0,1] magnetic fields at temperatures down to T=0.03K. The elastic scattering behaves consistently with the formation of independent chains for a [$1,\bar{1},0$] field, while the [0,0,1] field produces a single field-induced elastic magnetic Bragg peak at (0,2,0) and equivalent wavevectors, indicating a polarized spin ice state for fields above ~3T. For both [$1,\bar{1},0$] and [0,0,1] magnetic fields, our inelastic neutron scattering results show an approximately dispersionless continuum of scattering that increases in both energy and intensity with increasing field strength. By modeling the complete set of experimental data using numerical linked cluster and semiclassical molecular dynamics calculations, we demonstrate the dominantly multipolar nature of the exchange interactions in Ce 2 Zr 2 O 7 and the smallness of the parameter θ, which controls the mixing between dipolar and octupolar degrees of freedom. Finally, these results support previous estimates of the microscopic exchange parameters and place strong constraints on the theoretical description of this prominent spin ice candidate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Singlet fission in core-linked terrylenediimide dimers

We have studied two regioisomeric terrylenediimide (TDI) dimers in which the 1-positions of two TDIs are linked via 1,3- or 1,4-phenylene spacers, mTDI 2 and pTDI, respectively. The nature and the dynamics of the multiexciton state are tuned by altering the through-bond electronic couplings in the ground and excited states and by changing the solvent environment. Our results show that controlling the electronic coupling between the two chromophores by an appropriate choice of linker can result in independent triplet state formation, even though the initial correlated triplet pair state is confined to a dimer. Moreover, even in polar solvents, if the electronic coupling is strong, the correlated triplet pair state is observed prior to symmetry-breaking charge separation. These results point out the close relationship between the singlet, correlated triplet pair, and charge transfer states in molecular dimers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of machine learning in the determination of impact parameter in the 132 Sn+ 124 Sn system

Here, 132 Sn + 124 Sn collisions at a beam energy of 270 MeV/nucleon were performed at the Radioactive Isotope Beam Factory (RIBF) in RIKEN to investigate the nuclear equation of state. Reconstructing the impact parameter is one of the important tasks in the experiment as it relates to many observable. In this work, we employ three commonly used algorithms in machine learning, the artificial neural network (ANN), the convolutional neural network (CNN), and the light gradient boosting machine (LightGBM), to determine the impact parameter by analyzing either the charged particle spectra or several features simulated with events from the ultrarelativistic quantum molecular dynamics (UrQMD) model. To closely imitate experimental data and investigate the generalizability of the trained machine learning algorithms, incompressibility of nuclear equation of state and the in-medium nucleon-nucleon cross sections are varied in the UrQMD model to generate the training data. The mean absolute error Δb between the true and the predicted impact parameter is smaller than 0.45 fm if training and testing sets are sampled from the UrQMD model with the same parameter set. However, if training and testing sets are sampled with different parameter sets, Δb would increase to 0.8 fm. The generalizability of the trained machine learning algorithms suggests that these machine learning algorithms can be used reliably to reconstruct the impact parameter in experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Advanced Microscopy and Spectroscopy for Probing and Optimizing Electrode-Electrolyte Interphases in High Energy Lithium Batteries (Final Scientific/Technical Report)

The earliest developed LiCoO 2 layered oxide cathode material sparked the development of other layered cathode materials, dominating the positive electrode materials for lithium ion batteries. Within the practical operating conditions of today, the current generation layered oxide materials do not meet the future energy storage demands of 350 Wh kg -1 at cell level. Li-rich layered oxide (LRLO) materials have the potential to meet the high energy demands. Unlike the classical layered oxides, LRLO materials exhibit capacities that go beyond conventional topotactic mechanistic theoretical values. Despite its high capacities, this material has several challenges (voltage fading, structural instability, sluggish kinetics, cathode electrolyte interphase instability, etc.) that must be overcome in order to reach commercialization. In the past five years, our research group has made great progress on developing advanced characterization techniques coupled with atomic scale modeling to properly characterize the dynamic phenomena that govern the performance limitations of LRLO materials. Furthermore, our efforts have guided the material synthesis and surface modification to improve capacity retention. By carefully controlling the oxygen activities through the creation of uniform oxygen vacancies, we were able to avoid structural decomposition in LRLO. Our materials deliver a discharge capacity as high as 306 mAh g -1 with an initial coulombic efficiency of 90.6%. Furthermore, they do not exhibit obvious capacity decay with a reversible capacity over 300 mAh g -1 after 100 cycles at 0.1 C-rate. Our approach demonstrates the critical needs for advanced diagnosis and characterization. It is through the in-depth understanding of these high voltage cathode materials at atomistic and molecular level and their dynamic changes during the operation of batteries; we can successfully formulate strategies to further optimize this class of cathode materials, especially for the voltage instabilities. The diagnostic tools developed here can also be leveraged to study anode materials such as Li metal anode. The challenge of probing Li metal is the low dose tolerance (high beam sensitivity) of Li metal. We will have to apply cryogenic method (low-temperature) and low-dose electron microscopy and specialized camera to enable the characterization of the lithium metal.

25 ENERGY STORAGE↗

Uranium (VI) Adsorbate Structures on Portlandite [Ca(OH)2] Type Surfaces Determined by Computational Modelling and X-ray Absorption Spectroscopy

Portlandite [Ca(OH) 2 ] is a potentially dominant solid phase in the high pH fluids expected within the cementitious engineered barriers of Geological Disposal Facilities (GDF). This study combined X-ray Absorption Spectroscopy with computational modelling in order to provide atomic-scale data which improves our understanding of how a critically important radionuclide (U) will be adsorbed onto this phase under conditions relevant to a GDF environment. Such data are fundamental for predicting radionuclide mass transfer. Surface coordination chemistry and speciation of uranium with portlandite [Ca(OH) 2 ] under alkaline groundwater conditions (ca. pH 12) were determined by both in situ and ex situ grazing incidence extended X-ray absorption fine structure analysis (EXAFS) and by computational modelling at the atomic level. Free energies of sorption of aqueous uranyl hydroxides, [UO 2 (OH) n ] 2–n (n = 0–5) with the (001), (100) and (203) or (101) surfaces of portlandite are predicted from the potential of mean force using classical molecular umbrella sampling simulation methods and the structural interactions are further explored using fully periodic density functional theory computations. Although uranyl is predicted to only weakly adsorb to the (001) and (100) clean surfaces, there should be significantly stronger interactions with the (203/101) surface or at hydroxyl vacancies, both prevalent under groundwater conditions. The uranyl surface complex is typically found to include four equatorially coordinated hydroxyl ligands, forming an inner-sphere sorbate by direct interaction of a uranyl oxygen with surface calcium ions in both the (001) and (203/101) cases. In contrast, on the (100) surface, uranyl is sorbed with its axis more parallel to the surface plane. The EXAFS data are largely consistent with a surface structural layer or film similar to calcium uranate, but also show distinct uranyl characteristics, with the uranyl ion exhibiting the classic dioxygenyl oxygens at 1.8 Å and between four and five equatorial oxygen atoms at distances between 2.28 and 2.35 Å from the central U absorber. These experimental data are wholly consistent with the adsorbate configuration predicted by the computational models. These findings suggest that, under the strongly alkaline conditions of a cementitious backfill engineered barrier, there would be significant uptake of uranyl by portlandite to inhibit the mobility of U(VI) from the near field of a geological disposal facility.

36 MATERIALS SCIENCE↗

Para-particle oscillator simulations on a trapped-ion quantum computer

Deformed oscillators allow for a generalization of the standard fermions and bosons, namely, for the description of para-particles. Such particles remain hypothetical and unobserved in nature; yet, they can model physical phenomena, such as topological phases of matter. Here, we report the digital quantum simulation of para-particle oscillators by mapping para-particle states to the state of a qubit register, which allows us to identify the para-particle oscillator Hamiltonian as an XY model and further digitize the system onto a universal set of gates. In both instances, the gate depth grows polynomially with the number of qubits used. To establish the validity of our results, we experimentally simulate the dynamics of para-fermions and para-bosons, demonstrating full control of para-particle oscillators on a quantum computer. Furthermore, we compare the overall performance of the digital simulation of dynamics of the driven para-Fermi oscillator to a recent analog quantum simulation result.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Role of Cation Coordination in the Electrical and Optical Properties of Amorphous Transparent Conducting Oxides

Amorphous oxide semiconductor materials have demonstrated numerous advantages without compromise of electrical properties as compared to their crystalline counterparts, yet understanding of the fundamental principles allowing this has remained elusive. To study the origins of enhanced optoelectronic properties, we apply high-throughput, combinatorial sputtering, structural and spectral mapping, and computationally intensive ab initio molecular dynamics simulations with density functional theory to a ternary, post-transition metal oxide system, namely, zinc tin oxide. The deposited thin films exhibit a high figure of merit, achieving carrier densities in the range of 1019 to 1020 cm–3 and carrier mobilities up to 35 cm2/Vs. These results highlight the role of local distortions and cation coordination in determining the microscopic origins of carrier generation and transport. In particular, we identify the strong likelihood of Sn undercoordination in both Zn-poor and Zn-rich phases leading to the high carrier concentrations observed. This not only diverges from the still widespread historical indictment of oxygen vacancies controlling carrier population in crystalline oxides but also provides a comprehensive framework to describe the unique structure–property relationships using specific structural and electronic descriptors in disordered phase materials.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗

Selectivity of nitrate and chloride ions in microporous carbons: the role of anisotropic hydration and applied potentials

Understanding ion transport in porous carbons is critical for a wide range of technologies, including supercapacitors and capacitive deionization for water desalination, yet many details remain poorly understood. For instance, an atomistic understanding of how ion selectivity is influenced by the molecular shape of ions, morphology of the micropores and applied voltages is largely lacking. In this work, we combined molecular dynamics simulations with enhanced sampling methods to elucidate the mechanism of nitrate and chloride selectivity in subnanometer graphene slit-pores. We demonstrate that nitrate is preferentially adsorbed over chloride in the slit-like micropores. This preferential adsorption was found to stem from the weaker hydration energy and unique anisotropy of the ion solvation of nitrate. Beside the effects of ion dehydration, we found that applied potential plays an important role in determining the ion selectivity, leading to a lower selectivity of nitrate over chloride at a high applied potential. We conclude that the measured ion selectivity results from a complex interplay between voltage, confinement, and specific ion effects-including ion shape and local hydration structure.

36 MATERIALS SCIENCE↗