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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 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A combinatory ferroelectric compound bridging simple ABO 3 and A-site-ordered quadruple perovskite

The simple ABO 3 and A-site-ordered AA' 3 B 4 O 12 perovskites represent two types of classical perovskite functional materials. There are well-known simple perovskites with ferroelectric properties, while there is still no report of ferroelectricity due to symmetry breaking transition in A-site-ordered quadruple perovskites. Here we report the high pressure synthesis of an A-site-ordered perovskite PbHg 3 Ti 4 O 12 , the only known quadruple perovskite that transforms from high-temperature centrosymmetric paraelectric phase to low-temperature non-centrosymmetric ferroelectric phase. The coordination chemistry of Hg 2+ is changed from square planar as in typical A-site-ordered quadruple perovskite to a rare stereo type with 8 ligands in PbHg 3 Ti 4 O 12 . Thus PbHg 3 Ti 4 O 12 appears to be a combinatory link from simple ABO 3 perovskites to A-site-ordered AA' 3 Ti 4 O 12 perovskites, sharing both displacive ferroelectricity with former and structure coordination with latter. This is the only example so far showing ferroelectricity due to symmetry breaking phase transition in AA' 3 B 4 O 12 -type A-site-ordered perovskites, and opens a direction to search for ferroelectric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow

Abstract Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of explicit DFT calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NO x adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NO x capture that were not previously studied.

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

Modulating coordinate site occupancy in high-entropy spinel electrocatalysts

High entropy spinel oxides provide a versatile platform for electrocatalysis because multiple metal cations can be incorporated into a single crystalline lattice, enabling tunable electronic structures. However, controlling how these cations distribute between tetrahedral and octahedral coordination sites remains a major challenge, limiting rational catalyst design. Here, we modulate cation coordination site occupancy between tetrahedral and octahedral sites in a Co–Fe–Cr–Mn–Ni framework by introducing a sixth cation (Zn, Ga, Mg, or Al) with distinct site preference energies. Using density functional theory, synchrotron X-ray absorption spectroscopy, and magnetic circular dichroism, we demonstrate that Zn preferentially occupies tetrahedral sites, driving increased octahedral occupancy of cobalt. This redistribution increases the population of octahedrally coordinated cobalt in mixed oxidation states, enhances electrical conductivity, and improves oxygen evolution reaction activity. Our findings establish coordination site occupancy as a critical design parameter, providing a strategic pathway for tailoring multicomponent spinel electrocatalysts with optimized performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Carboxyl intermediate formation via an in situ-generated metastable active site during water-gas shift reaction

Definitive experimental proof for catalytic pathways and active sites during the low-temperature water-gas shift reaction remains elusive. Herein, we combine spectroscopic, kinetic, and computational analyses to address the decades-long mechanistic controversy by studying the reverse water-gas shift over Pd/Al2O3. Isotopic transient kinetic analysis clearly established the minor role of the formate (HCOO) intermediate. Moreover, hydrogen titration experiments unambiguously confirmed the intermediacy of carboxyl (COOH) for the first time. The ability to decouple the parallel formate and carboxyl pathways led to the identification of a distinct active site exhibiting regio- and chemoselective H-addition to CO2 to yield carboxyl. The metastable active site is formed in situ, resulting in hydroxylation of the metal-support interface and electronic restructuring of Pd via reduced coordination. Parallel atomistic simulations of the active site electronic structure and mechanistic landscape provided a framework consistent with experimental observations. Our study highlights the dynamic creation of a coordinatively unsaturated metal site caused by substrate adsorption on an adjacent support site.

Nelson, Nicholas C.↗
DOE OSTI2020

Operando identification of site-dependent water oxidation activity on ruthenium dioxide single-crystal surfaces

Understanding the nature of active sites is central to controlling (electro)catalytic activity. Here we employed surface X-ray scattering coupled with density functional theory and surface-enhanced infrared absorption spectroscopy to examine the oxygen evolution reaction on RuO 2 surfaces as a function of voltage. At 1.5 V RHE , our results suggest that there is an –OO group on the coordinatively unsaturated ruthenium (Ru CUS ) site of the (100) surface (and similarly for (110)), but adsorbed oxygen on the Ru CUS site of (101). Density functional theory results indicate that the removal of –OO from the Ru CUS site, which is stabilized by a hydrogen bond to a neighbouring –OH (–OO–H), could be the rate-determining step for (100) (similarly for (110)), where its reduced binding on (100) increased activity. A further reduction in binding energy on the Ru CUS site of (101) resulted in a different rate-determining step (–O + H 2 O – (H + + e - ) → –OO–H) and decreased activity. Our study provides molecular details on the active sites, and the influence of their local coordination environment on activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

On the active site for electrocatalytic water splitting on late transition metals embedded in graphene

Transition-metal atoms embedded in nitrogen-doped graphene can be used for electrocatalytic water splitting, but there are open questions regarding the identity of the active site. We study the formation of hydrogen and oxygen as well as the reduction of oxygen on 14 transition metals embedded in nitrogen-doped graphene using density functional theory and find that the stability and the catalytic properties of the metals depend on the nitrogen content of the support. While previous studies focus on metal atoms inside nitrogen-free and fully substituted vacancies, we find that partially nitrogen-substituted single sites are significantly more active for later transition metals (groups 10–11). These sites are also more stable than previously suggested active-site models. Our findings suggest that stability and catalytic activity of late transition metals embedded in graphene could be increased by controlling the nitrogen content of the support to obtain partially substituted vacancy sites. For early transition metals, fully substituted vacancies represent the most active site.

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

Methanol tolerance of atomically dispersed single metal site catalysts: mechanistic understanding and high-performance direct methanol fuel cells

Proton-exchange membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs) are promising power sources from portable electronic devices to vehicles. The high-cost issue of these low-temperature fuel cells can be primarily addressed by using platinum-group metal (PGM)-free oxygen reduction reaction (ORR) catalysts, in particular atomically dispersed metal–nitrogen–carbon (M–N–C, M = Fe, Co, Mn). Furthermore, a significant advantage of M–N–C catalysts is their superior methanol tolerance over Pt, which can mitigate the methanol cross-over effect and offer great potential of using a higher concentration of methanol in DMFCs. In this work, we investigated the ORR catalytic properties of M–N–C catalysts in methanol-containing acidic electrolytes via experiments and density functional theory (DFT) calculations. FeN 4 sites demonstrated the highest methanol tolerance ability when compared to metal-free pyridinic N, CoN 4 , and MnN 4 active sites. The methanol adsorption on MN 4 sites is even strengthened when electrode potentials are applied during the ORR. The negative influence of methanol adsorption becomes significant for methanol concentrations higher than 2.0 M. However, the methanol adsorption does not affect the 4e - ORR pathway or chemically destroy the FeN 4 sites. The understanding of the methanol-induced ORR activity loss guides the design of promising M–N–C cathode catalyst in DMFCs. Accordingly, we developed a dual-metal site Fe/Co–N–C catalyst through a combined chemical-doping and adsorption strategy. Instead of generating a possible synergistic effect, the introduced Co atoms in the first doping step act as “scissors” for Zn removal in metal–organic frameworks (MOFs), which is crucial for modifying the porosity of the catalyst and providing more defects for stabilizing the active FeN 4 sites generated in the second adsorption step. The Fe/Co–N–C catalyst significantly improved the ORR catalytic activity and delivered remarkably enhanced peak power densities (i.e., 502 and 135 mW cm -2 ) under H 2 –air and methanol–air conditions, respectively, representing the best performance for both types of fuel cells. Notably, the fundamental understanding of methanol tolerance, along with the encouraging DMFC performance, will open an avenue for the potential application of atomically dispersed M–N–C catalysts in other direct alcohol or ammonia fuel cells.

25 ENERGY STORAGE↗
DOE OSTI2021

Stabilized open metal sites in bimetallic metal–organic framework catalysts for hydrogen production from alcohols

Liquid organic hydrogen carriers such as alcohols and polyols are a high-capacity means of transporting and reversibly storing hydrogen that demands effective catalysts to drive the (de)hydrogenation reactions under mild conditions. We employed a combined theory/experiment approach to develop MOF-74 catalysts for alcohol dehydrogenation and examine the performance of the open metal sites (OMS), which have properties analogous to the active sites in high-performance single-site catalysts and homogeneous catalysts. Methanol dehydrogenation was used as a model reaction system for assessing the performance of five monometallic M-MOF-74 variants (M = Co, Cu, Mg, Mn, Ni). Co-MOF-74 and Ni-MOF-74 give the highest H 2 productivity. However, Ni-MOF-74 is unstable under reaction conditions and forms metallic nickel particles. To improve catalyst activity and stability, bimetallic (NixMg 1-x )-MOF-74 catalysts were developed that stabilize the Ni OMS and promote the dehydrogenation reaction. An optimal composition exists at (Ni 0.32 Mg 0.68 )-MOF-74 that gives the greatest H2 productivity, up to 203 mL gcat -1 min -1 at 300 °C, and maintains 100% selectivity to CO and H 2 between 225–275 °C. The optimized catalyst is also active for the dehydrogenation of other alcohols. DFT calculations reveal that synergistic interactions between the open metal site and the organic linker lead to lower reaction barriers in the MOF catalysts compared to the open metal site alone. This work expands the suite of hydrogen-related reactions catalyzed by MOF-74 which includes recent work on hydroformulation and our earlier reports of aryl-ether hydrogenolysis. Moreover, it highlights the use of bimetallic frameworks as an effective strategy for stabilizing a high density of catalytically active open metal sites.

08 HYDROGEN↗
DOE OSTI2022

Spiers Memorial Lecture: activating metal sites for biological electron transfer

Metal sites in biology often exhibit unique spectroscopic features that reflect novel geometric and electronic structures imposed by the protein that are key to reactivity. The blue copper active site involved in long range, rapid biological electron transfer is a classic example. This review presents an overview of both traditional and synchrotron based spectroscopic methods and their coupling to electronic structure calculations to understand the unique features of the blue copper active site, their contributions to function and the role of the protein in determining the geometric and electronic structure of the active site (called the “entatic state”). The relation of this active site to other biological electron transfer sites is further developed. Specifically, ultrafast XFEL spectroscopy is used to evaluate the methionine–S–Fe bond in cytochrome c, and its entatic control by the protein in determining function (electron transfer vs. apoptosis).

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

Determination of the vacancy distribution over Al cation sites in γ-Al 2 O 3

Although gamma-alumina (γ-Al 2 O 3 ) is an extensively used material with wide-ranging applications due to its inherently high surface area and acidity, its atomic structure is still not fully understood. γ-Al 2 O 3 is described as having a spinel-like structure, where the O sublattice has a face-centered cubic (FCC) arrangement and Al cations are placed in the spinel tetrahedral and octahedral interstitial sites. Achieving the correct stoichiometry of Al 2 O 3 , however, requires the introduction of Al vacancies into some of the interstitial sites. Despite the importance of accurately describing the structure of γ-Al 2 O 3 , the distribution of vacancies between tetrahedral and octahedral sites remains unclear, in part because of the usually poor crystalline quality of γ-Al 2 O 3 that has often been used in previous studies. To determine the actual cation distribution in γ-Al 2 O 3 , single-crystalline γ-Al 2 O 3 was investigated using a correlative approach of experimental and simulated selected-area electron diffraction (SAED) and high-resolution electron energy-loss spectroscopy (EELS). Comparison of the reflection intensities in single-crystal SAED to simulated SAED from models with varied vacancy distributions revealed that vacancies exist primarily on tetrahedral sites, contrary to the placement of vacancies on octahedral sites proposed in several common models. Comparison of EELS spectra—acquired with the highest energy resolution reported so far for γ-Al 2 O 3 —with ab initio multiple scattering EELS simulations confirmed the distribution of vacancies on tetrahedral sites. These results enable more accurate modeling of γ-Al 2 O 3 to better predict its properties in existing and future applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Cu site differentiation in tetracopper(I) sulfide clusters enables biomimetic N 2 O reduction

Copper clusters feature prominently in both metalloenzymes and synthetic nanoclusters that mediate catalytic redox transformations of gaseous small molecules. Such reactions are critical to biological energy conversion and are expected to be crucial parts of renewable energy economies. However, the precise roles of individual metal atoms within clusters are difficult to elucidate, particularly for cluster systems that are dynamic under operating conditions. Here, we present a metal site-specific analysis of synthetic Cu 4 (μ 4 -S) clusters that mimic the Cu Z active site of the nitrous oxide reductase enzyme. Leveraging the ability to obtain structural snapshots of both inactive and active forms of the synthetic model system, we analyzed both states using resonant X-ray diffraction anomalous fine structure (DAFS), a technique that enables X-ray absorption profiles of individual metal sites within a cluster to be extracted independently. Using DAFS, we found that a change in cluster geometry between the inactive and active states is correlated to Cu site differentiation that is presumably required for efficient activation of N 2 O gas. More precisely, we hypothesize that the Cu δ+ ∙∙∙Cu δ- pairs produced upon site differentiation are poised for N 2 O activation, as supported by computational modeling. These results provide an unprecedented level of detail on the roles of individual metal sites within the synthetic cluster system and how those roles interplay with cluster geometry to impact the reactivity function. We expect this fundamental knowledge to inform understanding of metal clusters in settings ranging from (bio)molecular to nanocluster to extended solid systems involved in energy conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Simultaneous occupancy of Cu C and Cu D in the ammonia monooxygenase active site

Ammonia monooxygenase (AMO), a copper-dependent membrane enzyme, catalyzes the first and rate-limiting step of nitrification: the oxidation of ammonia to hydroxylamine. Despite its central role in the global nitrogen cycle and its biotechnological relevance, structural characterization of AMO has lagged behind that of its homolog, particulate methane monooxygenase (pMMO), due to the slow growth rates of ammonia-oxidizing bacteria and the instability of AMO upon purification. Recent cryoEM studies of Nitrosomonas europaea AMO and Methylococcus capsulatus (Bath) pMMO in native membranes revealed new structural features, including two adjacent copper-binding sites in the transmembrane region, Cu C and Cu D , believed to constitute the active site. Although multiple structures were determined under various conditions, simultaneous occupancy of Cu C and Cu D was never observed, leaving their potential functional interplay unresolved. Here we report the 2.6 Å resolution cryoEM structure of AMO from Nitrosospira briensis C-128 in isolated native membranes. This structure reveals the first instance of simultaneous copper occupancy of the Cu C and Cu D sites, along with occupancy of the periplasmic Cu B site. Electron paramagnetic resonance (EPR) spectroscopic data indicate that the Cu B site is primarily occupied by Cu(II), while Cu C and Cu D are primarily occupied by diamagnetic ions, presumably Cu(I). Notably, a lipid molecule is bound between the Cu C and Cu D sites, separating them by ∼8.0 Å. The results underscore the importance of studying these enzymes in their native environments across species to resolve conserved and divergent molecular features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Influence of n{sup +} and p{sup +} doping on the lattice sites of implanted Fe in Si

We report on the lattice location of implanted {sup 59}Fe in n{sup +}- and p{sup +}-type Si by means of emission channeling. We found clear evidence that the preferred lattice location of Fe changes with the doping of the material. While in n{sup +}-type Si Fe prefers displaced bond-centered (BC) sites for annealing temperatures up to 600 °C, changing to ideal substitutional sites above 700 °C, in p{sup +}-type Si, Fe prefers to be in displaced tetrahedral interstitial positions after all annealing steps. The dominant lattice sites of Fe in n{sup +}-type Si therefore seem to be well characterized for all annealing temperatures by the incorporation of Fe into vacancy-related complexes, either into single vacancies which leads to Fe on ideal substitutional sites, or multiple vacancies, which leads to its incorporation near BC sites. In contrast, in p{sup +}-type Si, the major fraction of Fe is clearly interstitial (near-T or ideal T) for all annealing temperatures. The formation and possible lattice sites of Fe in FeB pairs in p{sup +}-Si are discussed. We also address the relevance of our findings for the understanding of the gettering effects caused by radiation damage or P-diffusion, the latter involving n{sup +}-doped regions.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Validity of the site-averaging approximation for modeling the dissociative chemisorption of H{sub 2} on Cu(111) surface: A quantum dynamics study on two potential energy surfaces

A new finding of the site-averaging approximation was recently reported on the dissociative chemisorption of the HCl/DCl+Au(111) surface reaction [T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 139, 184705 (2013); T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 140, 144701 (2014)]. Here, in order to investigate the dependence of new site-averaging approximation on the initial vibrational state of H{sub 2} as well as the PES for the dissociative chemisorption of H{sub 2} on Cu(111) surface at normal incidence, we carried out six-dimensional quantum dynamics calculations using the initial state-selected time-dependent wave packet approach, with H{sub 2} initially in its ground vibrational state and the first vibrational excited state. The corresponding four-dimensional site-specific dissociation probabilities are also calculated with H{sub 2} fixed at bridge, center, and top sites. These calculations are all performed based on two different potential energy surfaces (PESs). It is found that the site-averaging dissociation probability over 15 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability for H{sub 2} (v = 0) and (v = 1) on the two PESs.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Benzene derivatives adsorbed to the Ag(111) surface: Binding sites and electronic structure

Dispersion corrected Density Functional Theory calculations were employed to study the adsorption of benzenes derivatized with functional groups encompassing a large region of the activated/deactivated spectrum to the Ag(111) surface. Benzenes substituted with weak activating or deactivating groups, such as methyl and fluoro, do not have a strong preference for adsorbing to a particular site on the substrate, with the corrugations in the potential energy surface being similar to those of benzene. Strong activating (N(CH{sub 3}){sub 2}) and deactivating (NO{sub 2}) groups, on the other hand, possess a distinct site preference. The nitrogen in the former prefers to lie above a silver atom (top site), but in the latter a hollow hexagonal-closed-packed (H{sub hcp}) site of the Ag(111) surface is favored instead. Benzenes derivatized with classic activating groups donate electron density from their highest occupied molecular orbital to the surface, and those functionalized with deactivating groups withdraw electron density from the surface into orbitals that are unoccupied in the gas phase. For benzenes functionalized with two substituents, the groups that are strongly activating or deactivating control the site preference and the other groups assume sites that are, to a large degree, dictated by their positions on the benzene ring. The relative stabilities of the ortho, meta, and para positional isomers of disubstituted benzenes can, in some cases, be modified by adsorption to the surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites

Selective ion conduction across ion channel pores is central to cellular physiology. To understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores based on the nonselective NaK channel and determined their structures to high resolution. These structures showcase an ensemble of selectivity filters with a various number of contiguous ion binding sites ranging from 2 to 4, with each individual site maintaining a geometry and ligand environment virtually identical to that of equivalent sites in K{sup +} channel selectivity filters. Combined with single channel electrophysiology, we show that only the channel with four ion binding sites is K{sup +} selective, whereas those with two or three are nonselective and permeate Na{sup +} and K{sup +} equally well. These observations strongly suggest that the number of contiguous ion binding sites in a single file is the key determinant of the channel's selectivity properties and the presence of four sites in K{sup +} channels is essential for highly selective and efficient permeation of K{sup +} ions.

Derebe, Mehabaw G.↗
DOE OSTI2023

A first principles analysis of potential-dependent structural evolution of active sites in Fe-N-C catalysts

Fe-N-C (iron–nitrogen–carbon) electrocatalysts have emerged as potential alternatives to precious metal-based materials for the oxygen reduction reaction (ORR). However, the structure of these materials under electrochemical conditions is not well understood, and their poor stability in acidic environments poses a formidable challenge for successful adoption in commercial fuel cells. To provide molecular-level insights into these complex phenomena, we combine periodic density functional theory (DFT) calculations, exhaustive treatment of coadsorption effects for ORR reaction intermediates, including O and OH, and comprehensive analysis of solvation stabilization effects to construct voltage-dependent ab initio thermodynamic phase diagrams that describe the in situ structure of the active sites. These structures are further linked to activity and stability descriptors that can be compared with experimental parameters such as the half-wave potential for ORR and the onset potential for carbon corrosion and CO 2 evolution. The results indicate that pyridinic Fe sites at zigzag carbon edges, as well as other edge sites, exhibit high activity for ORR compared to sites in the bulk. However, edges neighboring the active sites are prone to instability via overoxidation and consequent site loss. The results suggest that it could be beneficial to synthesize Fe-N-C catalysts with small sizes and large perimeter edge lengths to enhance ORR activity, while voltage fluctuations should be limited during fuel cell operation to prevent carbon corrosion of overoxidized edges.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗