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

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Proton-Responsive Ligands Promote CO 2 Capture and Accelerate Catalytic CO 2 /HCO 2 – Interconversion

The synthesis and investigation of [Rh(DHMPE) 2 ][BF 4 ] (1) are reported. 1 features proton-responsive 1,2-bis[(dihydroxymethyl)phosphino]ethane (DHMPE) ligands, which readily capture CO 2 from atmospheric sources upon deprotonation. The protonation state of the DHMPE ligand was observed to have a significant impact on the catalytic reactivity of 1 with CO 2 . Deprotonation and CO 2 binding to 1 result in a ∼10-fold rate enhancement in catalytic degenerate CO 2 reduction with formate, monitored by 12 C/ 13 C isotope exchange between H 12 CO 2 – and 13 CO 2 . Studies performed using a similar complex lacking the hydroxyl ligand functionality ([Rh(DEPE) 2 ][BF 4 ] where DEPE = 1,2-bis(diethylphosphino)ethane) do not show the same rate enhancements when base is added. Based upon the cation-dependent activity of the catalyst, Eyring analysis, and cation sequestration experiments, CO 2 binding to 1 is proposed to facilitate preorganization of formate/CO 2 in the transition state via ligand-based encapsulation of Na + or K + cations to lower the activation energy and increase the observed catalytic rate. Incorporation of proton-responsive DHMPE ligands provides a unique approach to accelerate the kinetics of catalytic CO 2 reduction to formate.

Anions↗
DOE OSTI2023

Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature

Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes which cleave polysaccharides oxidatively and are important in pathogen biology, carbon cycling and biotechnology. The Lentinus similis family AA9 isoform A (LsAA9_A) has been extensively studied as a model system because its activity towards smaller soluble saccharide substrates has allowed detailed structural characterization of its interaction with a variety of substrates by X-ray crystallography at high resolution. Here, the joint X-ray/neutron room-temperature crystallographic structure of carbohydrate-free LsAA9_A in the copper(II) resting state refined against X-ray and neutron data at 2.1 and 2.8 Å resolution, respectively, is presented. The results provide an experimental determination of the protonation states of the copper(II)-coordinating residues and second-shell residues in LsAA9_A, paving the way for future neutron crystallographic studies of LPMO–carbohydrate complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Local electronic structure of histidine in aqueous solution

Here, the local electronic structure of aqueous histidine, an amino acid important in nature and biology, is revealed by aerosol X-ray photoemission spectroscopy. A detailed picture of the photoionization dynamics emerges by tuning the pH of the aqueous solution from which the aerosols are generated, allowing us to report the X-ray photoelectron spectroscopy (XPS) of histidine. Assignment of the experimental photoelectron spectra of the C1s and N1s levels allows the determination of the protonation state of histidine in these aqueous aerosols and is confirmed by density functional calculations. XPS spectra show that at pH = 1, both imidazole and amine group nitrogens are protonated, at pH = 7, the amine group nitrogen is protonated and the carboxyl group carbon is deprotonated resulting in a zwitterionic structure, and at pH = 13, only the carboxyl group remains deprotonated. Comparison of these results with previous experimental and theoretical results suggests that X-ray spectroscopy on aqueous aerosols can provide a convenient and simple way of probing their electronic structure in aqueous solutions.

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

pH-Driven Restructuring of Hydration Layers and Cation Adsorption at the Alumina–Water Interface

Oxide−water interfaces underpin ion separations, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. However, the molecular-scale links between pHdependent surface protonation, hydration-layer structure, and counterion adsorption remain 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. Each water layer shifts toward the substrate at transition pHs near 6.5 and 10.6, respectively, 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 counterion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., the potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥ 3.5. The 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.

Adsorption↗
DOE OSTI2025

Accelerating Instanton Theory with the Line Integral Nudged Elastic Band Method and Gaussian Process Regression

Quantum tunneling plays a fundamental role in many chemical reactions, particularly proton transfer processes. Ring polymer instanton theory offers a practical framework for computing tunneling rates in complex molecular systems. However, applying the ring polymer instanton method with a potential energy surface generated on-the-fly using electronic structure calculations can be computationally demanding. Here, in this work, we present a new efficient implementation of the ring polymer instanton method by combining the Line Integral Nudged Elastic Band (LI-NEB) approach with Gaussian Process Regression (GPR). We benchmarked this method on prototypical ground-state proton transfer systems, including the benchmark gas-phase hydrogen abstraction reaction H + CH 4 → H 2 + CH 3 , malonaldehyde, and Z-3-amino-propenal (aminopropenal). Our results show that this approach is an order of magnitude faster than traditional instanton algorithms while maintaining excellent agreement with their tunneling rates. This development opens the door to studying proton transfer in larger systems with improved efficiency.

chemical physics↗
DOE OSTI2026

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↗
DOE OSTI2024

Unexpected Photodriven Linker-to-Node Hole Transfer in a Zirconium-Based Metal–Organic Framework

Zr 6 (μ 3 -O) 4 (μ 3 -OH) 4 node cores are indispensable building blocks for almost all zirconium-based metal–organic frameworks. Consistent with the insulating nature of zirconia, they are generally considered electronically inert. Contrasting this viewpoint, we present spectral measurements and calculations indicating that emission from photoexcited NU-601, a six-connected Zr-based MOF, comes from both linker-centric locally excited and linker-to-node charge-transfer (CT) states. The CT state originates from a hole transfer process enabled by favorable energy alignment of the HOMOs of the node and linker. This alignment can be manipulated by changing the pH of the medium, which alters the protonation state of multiple oxy groups on the Zr-node. Thus, the acid–base chemistry of the node has a direct effect on the photophysics of the MOF following linker-localized electronic excitation. In conclusion, these new findings open opportunities to understand and exploit, for energy conversion, unconventional mechanisms of exciton formation and transport in MOFs.

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

Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP

YiiP from Shewanella oneidensis is a prokaryotic Zn 2+ /H + antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn 2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn 2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn 2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn 2+ to 2–3 H + depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn 2+ .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Improving MicroBooNE's Inclusive Single-Photon Search with Low-Energy Hadronic Identification

This analysis aims to further investigate MicroBooNE’s inclusive single-photon search results, which reported a 2.2$\sigma$ excess below 600 MeV in shower energy for events with no reconstructed protons using roughly half of MicroBooNE's dataset. Taken together with MiniBooNE’s long-standing low-energy excess and MicroBooNE’s recent electron-like search results showing no observable excess with respect to Standard Model predictions, this result provides strong impetus for expanded exploration of the single-photon channel in Fermilab’s short-baseline liquid-argon time projection chamber (LArTPC) experiments. By identifying and classifying isolated MeV-scale energy depositions, or blips, in the vicinity of single-photon events selected by the Wire-Cell reconstruction framework, we establish a more comprehensive labeling scheme for nearby hadronic content. In particular, blips found backwards along the shower axis indicate the presence of previously-unidentified final-state protons, while elevated blip counts at wide angles signal the presence of final-state neutrons. By applying this new technique to its full dataset, MicroBooNE will perform a purer and higher-statistics test of the truly isolated nature of its modest photon-like excess, furthering its hunt for the presence of unexpected new physics beyond the Standard Model.

Andrade Aldana, Diego [Los Alamos; IIT, Chicago (m↗
DOE OSTI2025

Evaluation of Density-Functional Tight-Binding Methods for Simulation of Protic Molecular Ion Pairs

In this work, we benchmark the accuracy of the density-functional tight-binding (DFTB) method, namely the long-range corrected second-order (LC-DFTB2) and third-order (DFTB3) models, for predicting energetics of imidazolium-based ionic liquid (IL) ion pairs. We compare the DFTB models against popular density functionals such as LC-ωPBE and B3LYP, using ab initio domain-based local pair-natural orbital coupled cluster (DLPNO-CC) energies as reference. Calculations were carried out in the gas phase, as well as in aqueous solution using implicit solvent methods. We find that the LC-DFTB2 model shows excellent performance in the gas phase and agrees well with reference energies in implicit solvent, often outperforming DFTB3 predictions for complexation energetics. Our study identifies a range of opportunities for use of the LC-DFTB method and quantifies its sensitivity to protonation states and the types of chemical interactions between ion pairs.

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

Ten-Fold Solvent Kinetic Isotope Effect for the Nonradiative Relaxation of the Aqueous Ferrate(VI) Ion

Hypervalent iron intermediates have been invoked in the catalytic cycles of many metalloproteins, and thus, it is crucial to understand how the coupling between such species and their environment can impact their chemical and physical properties in such contexts. In this work, we take advantage of the solvent kinetic isotope effect (SKIE) to gain insight into the nonradiative deactivation of electronic excited states of the aqueous ferrate-(VI) ion. Here we observe an exceptionally large SKIE of 9.7 for the nanosecond-scale relaxation of the lowest energy triplet ligand field state to the ground state. Proton inventory studies demonstrate that a single solvent O-H bond is coupled to the ion during deactivation, likely due to the sparse vibrational structure of ferrate-(VI). Such a mechanism is consistent with that reported for the deactivation of f-f excited states of aqueous trivalent lanthanides, which exhibit comparably large SKIE values. This phenomenon is ascribed entirely to dissipation of energy into a higher overtone of a solvent acceptor mode, as any impact on the apparent relaxation rate due to a change in solvent viscosity is negligible.

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

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

cytochrome c oxidase↗
DOE OSTI2022

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose–bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease

Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure–activity relationship (SAR) study of noncovalent compounds that bind in the enzyme’s substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor’s P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

One Electron Multiple Proton Transfer in Model Organic Donor–Acceptor Systems: Implications for High-Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. In this work, we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analog, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g X -components of the electronicg-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g X -value of up to 0.003, but are not sensitive to the second proton transfer (E2PT). In the latter case, the change of the g X -value is much smaller (ca. 0.0001), which is too small to be distinguished even by high-frequency EPR. The 14 N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (> 0.001) in the g X -values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N 1 and N 2 positions of the imidazole.

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

Charge Dependence of Local Hydration Dynamics in Poly(Acrylic Acid) Solutions

Localized measurements of hydration dynamics surrounding poly(acrylic acid) (pAA) chains are executed using Overhauser dynamic nuclear polarization relaxometry to determine the role of polymer protonation state on the polymer solvation environment. Alterations in polymer concentration and solution pH uncovered three different regimes of local water dynamics ranging from bulk-water-like to subdued water diffusivity. These experiments, combined with molecular dynamics simulations, reveal that the presence of deprotonated carboxylic acid groups promotes a hydrophilic local environment and extended polymer chain configurations that together incentivize the incorporation of bulk-like water near the polymer. This results in a stretched polymer conformation that leads to faster observed hydration dynamics in the local hydration environment. Meanwhile, protonated carboxylic acid groups are expected to engage in intrapolymer hydrogen bonding between monomer groups, resulting in a more collapsed conformation and slower observed hydration dynamics. The importance of the carboxylic acid groups on mediating hydration behavior is further illustrated by their role in dictating the solvation environment around poly(acrylic acid-stat-(poly(ethylene glycol) methyl ether acrylate) (p(AA-stat-PEGMEA)) copolymers with varying monomer ratios. Furthermore, these local hydration measurements establish a connection between local water dynamics and polymer chain conformation and may provide additional molecular perspective into poly(acrylic acid)’s classification as a superabsorbent polymer.

Conformation↗