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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS

The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

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

Influence of Peripheral Substituents on Fe(II) Spin State in Complexes with Tridentate Schiff‐Base Ligands

Abstract Six Fe(II) complexes with substituted 6‐((quinoline‐8‐ylimino)methyl)phenolates (R 2 qsal) were synthesized. X‐ray crystal structure determination for [Fe(R 2 qsal) 2 ], where R=F ( 1 ), Cl ( 2 ), Br ( 3 ), I ( 4 ), CF 3 /H ( 5 ), or CN/H ( 6 ), revealed mononuclear complexes that crystallize either solvent‐free in case of 1 , 5 , and 6 or as CH 2 Cl 2 solvates in the case of 2 , 3 , and 4 . Complexes 1 – 4 , which contain π‐donating substituents, exhibit only high‐spin (HS) state, as shown by crystal structure analysis and magnetic measurements. In contrast, complexes 5 and 6 , which contain electron‐withdrawing substituents, exist in the low‐spin (LS) state at lower temperatures but exhibit crossover to the HS state above 300 K. Electronic structure calculations show a good correlation between the relative energies of the LS and HS states and the experimentally observed behavior.

Gakiya‐Teruya, Miguel↗
DOE OSTI2026

Protonation Dynamics of Confined Ethanol–Water Mixtures in H-ZSM-5 from Machine Learning-Driven Metadynamics

Zeolites are indispensable heterogeneous catalysts in industrial chemical processes, valued for their strong Brønsted acidity, well-defined microporous frameworks, and tunable pore structures. Their catalytic activity arises primarily from Brønsted acid sites (BAS), typically present as bridging hydroxyl groups (Si–OH–Al). Under aqueous reaction conditions, these protons interact dynamically with water and alcohol molecules, leading to complex solvation and protonation behavior within confined pores. In this study, we investigate the protonation equilibrium occurring between ethanol and water at the BAS of acidic zeolites under varying hydration levels, i.e., C2H5OH–(H2O)n, n=1–4. Local structure was analyzed through an adaptive-learning global optimization algorithm, while enhanced sampling molecular dynamics simulations with Well-Tempered Metadynamics (WMetaD) and machine learning interatomic potentials (MLPs) provide free-energy surfaces (FES) at variable hydration levels. The results reveal a strong dependence of proton localization on the degree of hydration. At low hydration (1 water molecule), the proton resides predominantly on ethanol; with 2 water molecules, it shifts toward water, and at higher hydration (3 or more water molecules), it becomes extensively delocalized over the water cluster. These findings underscore the critical role of solvation in modulating acid site behavior and suggest that a minimum of three water molecules is necessary to fully stabilize the proton on water within the zeolite framework. This solvation threshold has significant implications for catalytic processes, particularly in biomass conversion reactions where alcohol protonation is a key step in dehydration mechanisms.

machine learning↗
DOE OSTI2021

Discovery of Energy Storage Molecular Materials Using Quantum Chemistry-Guided Multiobjective Bayesian Optimization

Redox flow batteries (RFBs) are a promising technology for stationary energy storage applications due to their flexible design, scalability, and low cost. In RFBs, energy is carried in flowable redoxactive materials (redoxmers) which are stored externally and pumped to the cell during operation. Further improvements in the energy density of RFBs necessitates redoxmer designs with wider redox potential windows and higher solubility. Additionally, designing redoxmers with a fluorescence-enabled self-reporting functionality allows monitoring of the state of health of RFBs. To accelerate the discovery of redoxmers with desired properties, state-of-the- art machine learning ( ML) methods, such as multiobjective Bayesian optimization (MBO), are useful. Here, we first employed density functional theory calculations to generate a database of reduction potentials, solvation free energies, and absorption wavelengths for 1400 redoxmer molecules based on a 2,1,3-benzothiadiazole (BzNSN) core structure. From the computed properties, we identified 22 Pareto-optimal molecules that represent best trade-off among all of the desired properties. We further utilized these data to develop and benchmark an MBO approach to identify candidates quickly and efficiently with multiple targeted properties. With MBO, optimal candidates from the 1400-molecule data set can be identified at least 15 times more efficiently compared to the brute force or random selection approach. Importantly, we utilized this approach for discovering promising redoxmers from an unseen database of 1 million BzNSN-based molecules, where we discovered 16 new Pareto-optimal molecules with significant improvements in properties over the initial 1400 molecules. Furthermore, we anticipate that this active learning technique is general and can be utilized for the discovery of any class of functional materials that satisfies multiple desired property criteria.

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

Importance of nuclear quantum effects on the hydration of chloride ion

Path-integral ab initio molecular dynamics (PI-AIMD) calculations have been employed to probe the nature of chloride ion solvation in aqueous solution. Nuclear quantum effects (NQEs) are shown to weaken hydrogen bonding between the chloride anion and the solvation shell of water molecules. As a consequence, the disruptive effect of the anion on the solvent water structure is significantly reduced compared to what is found in the absence of NQEs. Additionally, the chloride hydration structure obtained from PI-AIMD agrees well with information extracted from neutron scattering data. In particular, the observed satellite peak in the hydrogen-chloride-hydrogen triple angular distribution serves as a clear signature of NQEs. The present results suggest that NQEs are likely to play a crucial role in determining the structure of saline solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Dicarbonyl Electrolyte for High-Voltage Lithium Metal Batteries: Importance of the Entropy of Solvation in Bidentate Solvent

An electrolyte system based on dicarbonyl solvents has been proposed and implemented in lithium metal batteries (LMBs). Among several dicarbonyl solvents explored, dimethyl dicarbonate (DMDC) emerged as the most promising electrolyte candidate. Interestingly, despite the structural similarities between DMDC and its monocarbonyl counterpart DMC, the DMDC electrolyte exhibits higher solvent coordination, even at the same lithium-to-carbonyl ratio. Further, this leads to the formation of a more robust solid-electrolyte interphase and enhances the anodic stability of the electrolyte. Notably, in various electrolyte systems, the solvation energy is typically enthalpy-driven. However, the bidentate nature of DMDC introduces a significant role for the entropy of solvation because the Li + -DMDC complexes release fewer free molecules. With the addition of non-solvating co-solvent 1,1,2,2-tetrafluoro-ethyl 2,2,3,3-tetrafluoro-propyl ether (TTE), which reduces the viscosity of the electrolyte, the DMDC-TTE system enables remarkably stable cycling of the lithium anode by manipulating the entropy of solvation. This introduces a new strategy for tailoring functional electrolyte systems.

25 ENERGY STORAGE↗
DOE OSTI2024

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin’s isoalloxazine ring in the diagnostic 1450–1750 cm−1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

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

G 0 W 0 Ionization Potentials of First-Row Transition Metal Aqua Ions

Here, we report computations of the vertical ionization potentials within the GW approximation of the near-complete series of first-row transition metal (V–Cu) aqua ions in their most common oxidation states, i.e., V 3+ , Cr 3+ , Cr 2+ , Mn 2+ , Fe 3+ , Fe 2+ , Co 2+ , Ni 2+ , and Cu 2+ . The d-orbital occupancy of these systems spans a broad range from d 2 to d 9 . All of the structures were first optimized at the density functional theory level using a large cluster of explicit water molecules that are embedded in a continuum solvation model. Vertical ionization potentials were computed with the one-shot G 0 W 0 approach on a range of transition metal ion clusters (6, 18, 40, and 60 explicit water molecules), wherein the convergence with respect to the basis set size was evaluated using the systems with 40 water molecules. We assess the results using three different density functional approximations as starting points for the vertical ionization potential calculations, namely, G 0 W 0 @PBE, G 0 W 0 @PBE0, and G 0 W 0 @r 2 SCAN. While the predicted ground-state structures are similar to all three exchange-correlation functionals, the vertical ionization potentials were in closer agreement with experiment when using the G 0 W 0 @PBE0 and G 0 W 0 @r 2 SCAN approaches, with the r 2 SCAN-based calculations being significantly less expensive. Computed bond distances and vertical ionization potentials for all structures are in good agreement with available experimental data.

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

Controlling the Morphology of PEDOT:PSS Blend Films with Pre-Deposition Solution Composition and Deposition Technique

Understanding the relationships between morphology, fabrication processes, and thermoelectric performance in conducting polymers is essential to the development of high- efficiency organic thermoelectrics as an alternative to commonly used rare metals. Altering the film fabrication process of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) with the addition of high boiling solvents to the precast solution improves the electrical conductivity and significantly increases its Seebeck value. Neutron scattering monitors the changes in the atomic, nanoscale, and mesoscale morphologies of PEDOT:PSS thin films with the addition of dimethyl sulfoxide (DMSO) to the aqueous solution prior to film formation and with varying fabrication procedures. The neutron scattering results show a decrease in the deuterated PSS domain size along with systematic variations in PEDOT fibril assemblies in the final blend film with the addition of DMSO to the pre-deposition solution. These structural modifications indicate that the increase in conductivity of PEDOT:PSS blends with addition of DMSO reported in the literature can be ascribed to the disruption of solvated PEDOT assemblies by the DMSO, forming smaller PSS domains in the pre-deposition solution and allowing smoother film formation. These improvements are observed significantly with the addition of just 1% DMSO but continue to modestly improve with the addition of up to 5% DMSO to the PEDOT:PSS blend pre-deposition solution. The fact that the variations in the measured morphology are independent of whether the films were deposited by spin or ultrasonic spray casting methods emphasizes the crucial importance of the structure of the blend in the pre-deposition solution in determining the final thin film blend morphology.

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

Anion Effects on the Interfacial Structure and Bulk Physical Properties in Choline-Based Hydrogen-Bonded Electrolytes

Electrolytes consisting of choline (Ch) salts with acetate (Ac) and oxalate (Ox) anions were studied in mixtures with ethylene glycol (EG), in comparison to chloride (Cl)- and bis(trifluorosulfonyl)imide (TFSI)-containing systems to understand the impact of anion size and charge density on the bulk electrolyte and interfacial properties. These represent hydrogen-bonded concentrated electrolytes where the Ch salts are the H-bond acceptors (HBAs) and EG is the H-bond donor (HBD) in 1:2 and 1:4 HBA:HBD ratios. Increased H-bonding in Ch 2 Ox with EG compacts the liquid compared to ChAc, consistent with the increased dissociation energies of the HBA:HBD clusters with Ox –2 calculated by density functional theory (DFT), thus leading to denser and more viscous liquids. Electrochemical impedance spectroscopy (EIS) and surface-enhanced Raman spectroscopy (SERS) were used to investigate interfacial charge density and the electrode surface species. Differential capacitance curves demonstrate weak dependence on potential except for ChAc:EG, where Ac – is found to adsorb on the Au surface, in particular at +0.055 V vs Ag quasi-reference while no specific adsorption was observed on glassy carbon (GC). In situ SERS measurement confirms the formation of a surface layer in the ChAc:EG systems resulting from a Au–acetate interaction. Despite the structural similarities, Ox –2 did not show specific binding or any dependence of capacitance on potential as a result of strongly solvating EG molecules via H-bonds. Furthermore, this study shows that the charge density of the HBAs impacts both bulk properties and the electrical double-layer formation in concentrated H-bonded electrolytes that is relevant to electrochemical kinetics and morphology in electrodeposition processes and energy storage applications.

25 ENERGY STORAGE↗
DOE OSTI2025

Assessing the Effect of Explicit Polarizability on Models of Carbon Dioxide Solvation in Ionic Liquids

Ionic liquids are an important possible carbon capture material because of their anomalously high sorption selectivity for carbon dioxide over other gases common in air. Many research groups have investigated the molecular origins of this property and provided important insights, including using 1D and 2D-IR spectroscopy. Molecular dynamics simulations have been indispensable to the interpretation of these experiments. In prior molecular dynamics simulation work, charge-scaled force fields have typically been used to provide a mean-field treatment of effects vital to ionic liquid systems such as charge transfer and polarization. Here, we compare models of carbon dioxide solvated in ionic liquids with explicit polarization to models of the same with implicit polarizability through charge-scaling. We calculate structural, dynamical, and spectroscopic properties, and make comparisons to the same items measured in experiment. In this study, we focus on two ionic liquids: 1-butyl-3- methylimidazolium (BMIM + ) paired with bis(trifluoromethane sulfonyl imide) (Tf 2 N − ) and 1-butyl-3-methylimidazolium (BMIM+) paired with hexafluorophosphate (PF 6 − ). We find that many structural, dynamical, and spectroscopic properties are changed when polarization is modeled explicitly. We also find that explicit polarizability softens local ion cages around the carbon dioxide and that the long-time diffusion of the carbon dioxide is gated by the reorganization of the ionic liquid molecules. Comparisons to experiment show modest improvement of many observables compared with experiment for the explicitly polarizable model over the charge-scaled model. Overall, our results show that charge-scaled force fields are likely sufficient to compute spectroscopic properties of carbon dioxide in ionic liquids and suggest some interpretive rules for understanding their structural and dynamical properties. Those using charge-scaled force fields should generally assume that the ion cages around solutes such as carbon dioxide are too stiff and cation-rich in their models and adjust their interpretations and predictions accordingly.

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

Aqueous solvation of the chloride ion revisited with density functional theory: impact of correlation and exchange approximations

The specificity of aqueous halide solvation is fundamental to a wide range of bulk and interfacial phenomena spanning from biology to materials science. Halide polarizability is thought to drive the ion specificity, and if so, it is essential to have an accurate description of the electronic properties of halide ions in water. To this end, the solvation of the chloride anion, Cl - has been reinvestigated with state-of-the-art density functional theory. Specifically, the PBE-D3, PBE0-D3, and SCAN functionals have been employed to probe the impact of correlation and exchange approximations. Anticipating the findings, adding exact exchange improves the electronic structure, but simultaneously significantly reduces the Cl - polarizability, resulting in an over-structured Cl–O radial distribution function (RDF) and longer water H-bond lifetimes to Cl - . SCAN does not yield as much improvement in the energetics of Cl - relative to bulk water, but does result in a smaller reduction of the polarizability and thus a less structured Cl–O RDF, which agrees better with experiment. Special consideration is therefore warranted in assessing the impact of exchange on the energy, charge density, and the charge density response when designing and testing hybrid functionals for aqueous halide solvation.

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

Molecular polarizabilities as fingerprints of perturbations to water by ions and confinement

Perturbations to water, both by ions and confining media, have been the focus of numerous experimental and theoretical studies. Yet, several open questions remain, including the extent to which such perturbations modify the structural and dielectric properties of the liquid. Here, we present a first-principles molecular dynamics study of alkali cations in water (Li + , Na + , and K + ) as well as of water and LiCl and KCl solutions under confinement within carbon nanotubes (CNTs) of small diameter (1.1-1.5 nm). Our simulations support the view that the water structure is only modified locally in the presence of cations. We found that molecular polarizabilities are fingerprints of hydrogen bonding modifications, which occur at most up to the second solvation shell for all cations in bulk water. Under confinement, we found that the overall value of the molecular polarizability of water molecules near the surface is determined by the balance of two effects, which are quantitatively different in CNTs of different radii: the presence of broken hydrogen bonds at the surface leads to a decrease in the polarizabilities of water molecules, while the interaction with the CNT enhances polarizabilities. Interestingly, the reduction in dipole moments of interfacial water molecules under confinement is instead driven only by changes in the water structure and not by interfacial interactions. As expected, confinement effects on water molecular polarizabilities and dipole moments are more pronounced in the case of the 1.1 nm CNT.

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

Reorganization Energy of Electron Transfer in Ionic Liquids

We report bandshape analysis of charge-transfer optical bands in room-temperature ionic liquids (ILs) is performed to extract reorganization energy of electron transfer. Remarkably, the reorganization energies in ILs are close to those in cyclohexane. This result runs against common wisdom in the field since conducting ILs, characterized by an infinite static dielectric constant, and nonpolar cyclohexane fall to the opposite ends of the polarity scale based on their dielectric constants. Theoretical calculations employing structure factors of ILs from molecular dynamics simulations support low values of the reorganization energy. Standard dielectric arguments do not apply to solvation in ILs and nonergodic reorganization energies are required for a quantitative analysis.

14 SOLAR ENERGY↗
DOE OSTI2025

Molecular Insights Into the Ionic Assembly of Poly-Galacturonic Acid Oligomers - Impact of Charge, Ionic Radius, and Polymer Functionalization

Pectin, a major class of matrix polysaccharides present in plant cell walls (PCW), contains widespread anionic saccharides that cross-link in the presence of cations. It modulates important functions such as cell-cell adhesion and determines the PCW's biomechanical properties. It is known that mono-, di-, and tri-valent cations facilitate cross-linking; however, significant knowledge gaps remain in understanding the structure and mechanism of pectin cross-linking. In this study, replica-exchange molecular dynamics (REMD) simulations were employed to elucidate the role of ionic charge, ionic radii, and functional groups on the cross-linking of homogalacturonan (HG), the most abundant pectin molecule. Our enhanced sampling approach in fully solvated environments suggests more effective cross-linking with higher-valent and smaller ions, and that the "zipper" conformation is more favorable than the prevalent "egg-box" conformation. These findings advance our fundamental understanding of pectin matrix structure in PCWs and provide a solid foundation to probe structure-property relationships in pectic polysaccharides.

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

Striking stability of a mixed-valence thallium(III)-thallium(I) complex in some solvents

At the dissolution of solid anhydrous thallium(III) trifluoromethanesulfonate, Tl(CF 3 SO 3 ) 3 , or thallium(III) trifluoroacetate, Tl(CF 3 COO) 3 , in dimethylsulfoxide (dmso) or N,N,N’,N’-tetramethylurea (tmu), intensely red-colored complexes are formed. This red thallium complex is stable for years in dmso, while it is reduced fairly rapidly to thallium(I) in tmu with a half-life time of an hour. At the dissolution of Tl(CF 3 SO 3 ) 3 in N,N-dimethylpropyleneurea (dmpu) an immediate reduction to thallium(I) takes place. A stable colorless aqueous thallium(III) solution is obtained at the dissolution in acidic water. Stable dmso solutions and solid dmso solvates of thallium(III) perchlorate, nitrate and trifluormethanesulfonate can be prepared by adding dmso to concentrated acidic aqueous thallium(III) solutions. These experimental observations conclude that the pure solids Tl(CF 3 SO 3 ) 3 and Tl(CF 3 COO) 3 play an essential role in the formation of the red-colored thallium complexes. 205 Tl NMR data show that the red thallium complex contains equal amounts of thallium(III) and thallium(I). The structure of the red thallium complex in dmso, as determined by EXAFS, has Tl–O bond distances of 2.216(3) and 2.80(2) Å, which are in very close agreement with the bond distances obtained in the pure dmso solvates of the thallium(III) and thallium(I) ions, respectively, and a Tl···Tl distance of 3.49(1) Å bridged by oxygen atoms. From the EXAFS data it is impossible to distinguish if dmso molecules and/or trifluoromethanesulfonate ions act as bridges. DFT calculations could eliminate some structures due to the irrelevant structural parameters or the energetics of the proposed reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗