Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “active sites”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Diversity in the Common Fold: Structural Insights into Class D β-Lactamases from Gram-Negative Pathogens

Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens Klebsiella and Acinetobacter, particularly regarding loop length and spatial organization. These findings emphasize the B-loop’s critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.

antibiotic resistance↗
DOE OSTI2024

Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease

Abstract RNA ligases of the RTCB-type play an essential role in tRNA splicing, the unfolded protein response and RNA repair. RTCB is the catalytic subunit of the pentameric human tRNA ligase complex. RNA ligation by the tRNA ligase complex requires GTP-dependent activation of RTCB. This active site guanylylation reaction relies on the activation factor Archease. The mechanistic interplay between both proteins has remained unknown. Here, we report a biochemical and structural analysis of the human RTCB-Archease complex in the pre- and post-activation state. Archease reaches into the active site of RTCB and promotes the formation of a covalent RTCB-GMP intermediate through coordination of GTP and metal ions. During the activation reaction, Archease prevents futile RNA substrate binding to RTCB. Moreover, monomer structures of Archease and RTCB reveal additional states within the RNA ligation mechanism. Taken together, we present structural snapshots along the reaction cycle of the human tRNA ligase.

Science & Technology - Other Topics↗
DOE OSTI2021

Transformation of Highly Stable Pt Single Sites on Defect Engineered Ceria into Robust Pt Clusters for Vehicle Emission Control

Engineering surface defects on metal oxide supports could help promote the dispersion of active sites and catalytic performance of supported catalysts. Herein, a strategy of ZrO 2 doping was proposed to create rich surface defects on CeO 2 (CZO) and, with these defects, to improve Pt dispersion and enhance its affinity as single sites to the CZO support (Pt/CZO). The strongly anchored Pt single sites on CZO support were initially not efficient for catalytic oxidation of CO/C 3 H 6 . However, after a simple activation by H 2 reduction, the catalytic oxidation performance over Pt/CZO catalyst was significantly boosted and better than Pt/CeO 2 . Pt/CZO catalyst also exhibited much higher thermal stability. The structural evolution of Pt active sites by H 2 treatment was systematically investigated on aged Pt/CZO and Pt/CeO 2 catalysts. With H 2 reduction, ionic Pt single sites were transformed into active Pt clusters. Much smaller Pt clusters were created on CZO (ca. 1.2 nm) than on CeO 2 (ca. 1.8 nm) due to stronger Pt-CeO 2 interaction on aged Pt/CZO. Consequently, more exposed active Pt sites were obtained on the smaller clusters surrounded by more oxygen defects and Ce 3+ species, which directly translated to the higher catalytic oxidation performance of activated Pt/CZO catalyst in vehicle emission control applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

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

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Impact of microkinetic modeling assumptions on predicted kinetics and mechanisms over undercoordinated sites

Accurate modeling of catalytic reactions on undercoordinated sites requires accounting for the structural and ensemble-specific nature of the active sites. This study examines how common microkinetic modeling (MKM) assumptions affect predicted kinetics and mechanisms on the stepped Pt(211) facet for the ethane dehydrogenation (EDH) and the ethane hydrogenolysis (EH). Six (211) MKMs were developed, differing in (i) the number of active sites represented, (ii) adsorbate site occupancy treatment, and (iii) inclusion of cross-facet interactions. These models are benchmarked against a particle-based microkinetic model (PB-MKM), which best represents step-edge behavior. MKM assumptions caused deviations in turnover frequencies exceeding ten orders of magnitude and led to contrasting mechanistic and selectivity predictions. Multi-site MKMs overestimate activity by inflating free site availability, single-site models underestimate activity, and uniform occupancy models overpredict coverage of multi-dentate intermediates, leading to reaction-specific artifacts. Overall, the Combined Site Edge Model (CSEM), a single-site MKM accounting for site occupancy and cross-facet interactions, most closely approximates PB-MKM predictions. All models predict similar kinetics when surfaces are clean or primarily occupied by monodentate species. This work provides practical guidance for selecting MKM frameworks for undercoordinated catalytic surfaces and highlights the critical role of modeling assumptions in catalytic predictions.

(211) facet↗
DOE OSTI2022

Conserved conformational dynamics determine enzyme activity

Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Tuning the Coordination Environment of Rh Single Atoms on Highly Dispersed Reducible Oxides for Enhanced Reverse Water-Gas Shift Performance

Controlling the dynamic mobility of catalyst surface active sites and their interactions with the surrounding environment is critical in generating active surfaces that directly influence the catalytic activity and selectivity. Here, we report a strategy for tailoring the dispersion and electronic environment of single atom Rh catalysts by decorating the alumina support with highly dispersed (HD) cerium and molybdenum oxides. The resulting catalysts exhibit markedly different behavior in the Reverse Water Gas Shift (RWGS) reaction. In particular, Rh/MoOx(HD)/Al2O3 maintains atomically dispersed Rh even at elevated temperatures (up to 400 °C), achieving CO selectivity of up to 100% and resists sintering via the formation of a newly developed structure featuring Rh single atoms embedded in MoOx clusters. In situ spectroscopy and microscopy analyses confirm the stabilization of Rh and the dynamic evolution of Rh–Mo coordination under reaction conditions. Our findings highlight the power of support modification in steering active site structure and activity, offering a pathway toward enhanced and tunable single atom catalysts for CO2 valorization.

CO selectivity↗
DOE OSTI2024

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Solvent Effects on Catalytic Reactions and Related Phenomena at Liquid-Solid Interfaces

Catalytic reactions involve the direct interaction of reactants, intermediates and products with the catalyst surface. We not only need to control the atomic structure and electronic properties of the active site, but also explore the multiple molecular interactions that occur beyond the active site; they play an essential role in altering the binding and reactivity of surface species. In liquid-phase catalysis, solvents provide additional degrees of freedom in the design of the catalytic process for desirable activity and selectivity. Here, the multi-faceted effects of solvents have a profound impact on the catalyst performance by restricting the mass transfer to the site, tuning the chemical potential of the surface species, competing for active sites, stabilizing the initial and transition states, and causing mechanistic changes by participating in the kinetically relevant elementary steps. This review addresses the different aspects of solvent effects, using a few prototype solid-liquid interfaces to illustrate these fundamental features. Recent experimental and computational studies that provide new insight at the molecular level are examined. Solvent structures in the proximity of the catalyst surface are discussed along with their influence in molecular binding and reaction at the solid-liquid interfaces. Furthermore, opportunities to alter such a solid-liquid interaction by tuning the wettability of the catalyst surfaces are explored.

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

Cage effects control the mechanism of methane hydroxylation in zeolites

Catalytic conversion of methane to methanol remains an economically tantalizing but fundamentally challenging goal. Current technologies based on zeolites deactivate too rapidly for practical application. Here, we found that similar active sites hosted in different zeolite lattices can exhibit markedly different reactivity with methane, depending on the size of the zeolite pore apertures. Whereas zeolite with large pore apertures deactivates completely after a single turnover, 40% of active sites in zeolite with small pore apertures are regenerated, enabling a catalytic cycle. Detailed spectroscopic characterization of reaction intermediates and density functional theory calculations show that hindered diffusion through small pore apertures disfavors premature release of CH 3 radicals from the active site after C-H activation, thereby promoting radical recombination to form methanol rather than deactivated Fe-OCH 3 centers elsewhere in the lattice.

36 MATERIALS SCIENCE↗
DOE OSTI2024

N and OH-Immobilized Cu 3 Clusters In Situ Reconstructed from Single-Metal Sites for Efficient CO 2 Electromethanation in Bicontinuous Mesochannels

Cu-based catalysts hold promise for electrifying CO 2 to produce methane, an extensively used fuel. However, the activity and selectivity remain insufficient due to the lack of catalyst design principles to steer complex CO 2 reduction pathways. Herein, we develop a concept to design carbon-supported Cu catalysts by regulating Cu active sites’ atomic-scale structures and engineering the carbon support’s mesoscale architecture. This aims to provide a favorable local reaction microenvironment for a selective CO 2 reduction pathway to methane. In situ X-ray absorption and Raman spectroscopy analyses reveal the dynamic reconstruction of nitrogen and hydroxyl-immobilized Cu 3 (N,OH-Cu 3 ) clusters derived from atomically dispersed Cu–N 3 sites under realistic CO 2 reduction conditions. The N,OH-Cu 3 sites possess moderate *CO adsorption affinity and a low barrier for *CO hydrogenation, enabling intrinsically selective CO 2 -to-CH 4 reduction compared to the C–C coupling with a high energy barrier. Importantly, a block copolymer-derived carbon fiber support with interconnected mesopores is constructed. The unique long-range mesochannels offer an H 2 O-deficient microenvironment and prolong the transport path for the CO intermediate, which could suppress the hydrogen evolution reaction and favor deep CO 2 reduction toward methane formation. Thus, the newly developed catalyst consisting of in situ constructed N,OH-Cu 3 active sites embedded into bicontinuous carbon mesochannels achieved an unprecedented Faradaic efficiency of 74.2% for the CO 2 reduction to methane at an industry-level current density of 300 mA cm –2 . In conclusion, this work explores effective concepts for steering desirable reaction pathways in complex interfacial catalytic systems via modulating active site structures at the atomic level and engineering pore architectures of supports on the mesoscale to create favorable microenvironments.

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

Structural and mechanistic basis for protein glutamylation by the kinase fold

The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here, in this work, we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Highly Oxidized Oxide Surface toward Optimum Oxygen Evolution Reaction by Termination Engineering

The oxygen evolution reaction (OER) is a critical step for sustainable fuel production through electrochemistry process. Maximizing active sites of nanocatalyst with enhanced intrinsic activity, especially the activation of lattice oxygen, is gradually recognized as the primary incentive. Since the surface reconfiguration to oxyhydroxide is unavoidable for oxygen-activated transition metal oxides, developing a surface termination like oxyhydroxide in oxides is highly desirable. In this work, we demonstrate an unusual surface termination of (111)-facet Co 3 O 4 nanosheet that is exclusively containing edge-sharing octahedral Co 3+ similar to CoOOH that can perform at approximately 40 times higher current density at 1.63 V (vs RHE) than commercial RuO 2 . It is found that this surface termination has an oxidized oxygen state in contrast to standard Co-O systems, which can serve as active site independently, breaking the scaling relationship limit. Finally, this work forwards the applications of oxide electrocatalysts in the energy conversion field by surface termination engineering.

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

Nature of Zirconia on a Copper Inverse Catalyst Under CO 2 Hydrogenation Conditions

The growing concern over the escalating levels of anthropogenic CO 2 emissions necessitates effective strategies for its conversion to valuable chemicals and fuels. In this research, we embark on a comprehensive investigation of the nature of zirconia on a copper inverse catalyst under the conditions of CO 2 hydrogenation to methanol. We employ density functional theory calculations in combination with the Grand Canonical Basin Hopping method, enabling an exploration of the free energy surface including a variable amount of adsorbates within the relevant reaction conditions. Our focus centers on a model three-atom Zr cluster on a Cu(111) surface decorated with various OH, O, and formate ligands, noted Zr 3 O x (OH) y (HCOO) z /Cu(111), revealing major changes in the active site induced by various reaction parameters such as the gas pressure, temperature, conversion levels, and CO 2 /H 2 feed ratios. Further, through our analysis, we have unveiled insights into the dynamic behavior of the catalyst. Specifically, under reaction conditions, we observe a large number of composition and structures with similar free energy for the catalyst, with respect to changing the type, number, and binding sites of adsorbates, suggesting that the active site should be regarded as a statistical ensemble of diverse structures that interconvert.

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

Adsorbate-induced adatom formation on Au-Cu bimetallic alloys and its possible consequences for CO 2 electroreduction

The adsorbate-induced formation of sub-nanometer clusters on transition-metal single crystals observed in previous high-pressure microscopic studies hinted at the in-situ formation of unique active sites even on large nanoparticle catalysts. We propose that the adatom formation energy can be used as an energetic descriptor for the initial step toward the adsorbate-induced metal-cluster formation process. This descriptor can be efficiently computed using density functional theory (DFT) calculations and applied for screening and identification of metal catalysts where this phenomenon may play an important role in generating active sites in-situ. As a proof of concept, here, we construct an adatom formation energy database for three Au x Cu y alloys (x:y = 3:1, 1:1, or 1:3) and eighteen adsorbates (H, C, N, O, F, S, Cl, Br, I, CH x , NH x (x = 1 – 3), CO, NO, and OH) commonly involved in catalytic reactions. The energetics of adatom formation were examined in all cases where the (111) terrace, (211) step-edge, and (874) kink were the sources of the adatom. We demonstrate that the presence of an adsorbate could alter not only the energetics for adatom formation but also the elemental nature of the preferred adatom being formed. Using our database, we identified promising systems which favor adsorbate-induced adatom formation under near-ambient conditions. Specifically, CO-induced adatom formation on all three Au-Cu alloy surfaces could occur under CO 2 electroreduction (CO 2 RR) conditions. This phenomenon offers a qualitative explanation for the experimentally observed CO 2 RR activity on Au-Cu alloy catalysts. As a result, our methodology offers an easily expandable and efficient approach for large-scale catalyst screening with regards to adatom/cluster formation under reaction conditions and provides insight into the possible nature of active sites on alloy catalysts from a novel perspective.

Active site↗
DOE OSTI2022

Role of Molecular Simulations in the Design of Metal–Organic Frameworks for Gas-Phase Thermocatalysis: A Perspective

Here, metal organic frameworks (MOFs) are highly tunable porous crystalline solids with spatially and electronically isolated catalytically active sites that have been demonstrated for a variety of thermo-, redox-, and photocatalytic reactions. Their tunable natures and relatively well-defined active sites make them advantageous for catalyst design, and molecular simulations have proven highly valuable in this endeavor. However, complexities in the MOF structure require advanced simulation strategies that accurately capture quantum chemistry at the strongly correlated transition metal cation active sites, compositional and structural changes caused by finite temperature and pressure reaction conditions, and transport effects in variously sized pore environments. Luckily, several groups have started using such simulation strategies, paving the way for rich opportunities to design MOF catalysts. Herein, we highlight such examples and provide a perspective on the needs for molecular simulations in the design of MOF catalysts moving forward.

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

Mechanistic Studies of Continuous Partial Methane Oxidation on Cu−Zeolites Using Kinetic and Spectroscopic Methods

Abstract Over the past few decades, a significant amount of research effort has focused on investigating the active site requirements and reaction mechanisms for partial methane oxidation (PMO) to methanol over copper–exchanged zeolites during stoichiometric and stepwise chemical looping routes. More recently, research efforts have expanded to include investigating the PMO reaction in a continuous catalytic regime, primarily focusing on determining the influence of catalyst composition on Cu speciation and structure and, in turn, on PMO rate and selectivity. The structures of candidate Cu active sites are commonly studied using a combination of ex situ and in situ spectroscopic approaches. In this perspective, we critically examine the prior literature on catalytic PMO over Cu–zeolites to identify key knowledge gaps that remain in our understanding as motivation for future research efforts. We identify opportunities for future research to address these gaps by adapting analogous interrogation techniques that have been successfully used to elucidate the active site requirements and mechanistic details of another catalytic redox reaction cycle on Cu–zeolites, the selective catalytic reduction (SCR) of nitrogen oxides (NO x ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗