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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Decoding Active Sites for Highly Efficient Semihydrogenation of Acetylene in Palladium–Copper Nanoalloys

Accurately decoding the three-dimensional atomic structure of surface active sites is essential yet challenging for a rational catalyst design. Here, we used comprehensive techniques combining the pair distribution function and reverse Monte Carlo simulation to reveal the surficial distribution of Pd active sites and adjacent coordination environment in palladium-copper nanoalloys. After the fine-tuning of the atomic arrangement, excellent catalytic performance with 98% ethylene selectivity at complete acetylene conversion was obtained in the Pd 34 Cu 66 nanocatalysts, outperforming most of the reported advanced catalysts. Further, t he quantitative deciphering shows a large number of active sites with a Pd-Pd coordination number of 3 distributed on the surface of Pd 34 Cu 66 nanoalloys, which play a decisive role in highly efficient semihydrogenation. This finding not only opens the way for guiding the precise design of bimetal nanocatalysts from atomic-level insight but also provides a method to resolve the spatial structure of active sites.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Combining ToF‐SIMS and Multivariate Analysis to Resolve Active Sites on Ni‐Based HER Catalysts

Unambiguous identification of active sites in heterogeneous catalysis remains a major challenge, particularly for materials with ultrathin, chemically mixed surface layers. Here, we demonstrate a generalizable approach that combines time-of-flight secondary ion mass spectrometry (ToF-SIMS) with multivariate statistical analysis (principal component analysis [PCA] and multivariate curve resolution [MCR]) to resolve catalytically relevant motifs at the nanoscale. Using Ni electrodes as a model system, PCA distinguished hydroxide-enriched domains from oxide- and metal-rich regions, while MCR decomposed depth profiles and 3D images into hydroxide, oxide, and metallic layers with nanometer resolution. A unique secondary-ion fragment, NiO 3 H 3 − (m/z 108.94), emerged as a marker of hydroxide-rich environments and correlated with hydrogen evolution reaction (HER) activity across a series of Ni electrodes. Complementary density functional theory (DFT) calculations revealed that Ni(OH) 2 clusters adjacent to metallic Ni offer the most favorable water dissociation energetics, establishing the structural origin of the marker. While illustrated here for Ni-based HER, this workflow provides a broadly applicable framework to isolate and rank near-surface patterns that govern catalytic activity, thereby extending ToF-SIMS from a qualitative probe to a predictive tool for active site identification.

HER active sites↗
DOE OSTI2024

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron–oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗
DOE OSTI2021

Computational Investigation of the Role of Active Site Heterogeneity for aSupported Organovanadium(III) Hydrogenation Catalyst

A crucial consideration for supported heterogeneous catalysts is the nonuniformity of the active sites, particularly for supported organometallic catalysts. Standard spectroscopic techniques, such as X-ray absorption spectroscopy, reflect the nature of the most populated sites, which are often intrinsically structurally distinct from the most active catalytic sites. Additionally, with computational models, often, only a few representative structures are used to depict catalytic active sites on a surface, even though there are numerous observable factors of surface heterogeneity that contribute to the kinetically favorable active species. A previously reported study on the mechanism of a surface organovanadium-(III) catalyst [(SiO 2 )V III (Mes)(THF)] for styrene hydrogenation yielded two possible mechanisms: heterolytic cleavage and redox cycling. These two mechanistic scenarios are challenging to differentiate experimentally since the kinetic readouts of the catalyst are identical. To showcase the importance of modeling surface heterogeneity and its effect on catalytic activity, density functional theory (DFT) computational models of a series of potential active sites of [(SiO 2 )V III (Mes)(THF)] for the reaction pathways are applied in combination with kinetic Monte Carlo (kMC) simulations. Computed results were then compared to the previously reported experimental kinetic study: (1) DFT free-energy reaction pathways indicated the likely active site and pathway for styrene hydrogenation, a heterolytic cleavage pathway requiring a bare tripodal vanadium site. (2) From the kMC simulations, a mixture of different bond lengths from the support oxygen to the metal center was required to qualitatively describe the experimentally observed kinetic aspects of a supported organovanadium(III) catalyst for olefin hydrogenation. This work underscores the importance of modeling surface heterogeneity in computational catalysis.

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

Introducing metal–sulfur active sites in metal–organic frameworks via post-synthetic modification for hydrogenation catalysis

Metal–sulfur active sites play a central role in catalytic processes such as hydrogenation and dehydrogenation, yet the majority of active sites in these compounds reside on the surfaces and edges of catalyst particles, limiting overall efficiency. Here we present a strategy to embed metal–sulfur active sites into metal–organic frameworks (MOFs) by converting bridging or terminal chloride ligands into hydroxide and subsequently into sulfide groups through post-synthetic modification. We apply this method to two representative MOF families: one featuring one-dimensional metal–chloride chains and another containing discrete multinuclear metal clusters. Crystallographic and spectroscopic analyses confirm structural integrity and sulfide incorporation, and the transformation is monitored by in situ total scattering methods. The sulfided MOFs display enhanced catalytic activity in the selective hydrogenation of nitroarenes using molecular hydrogen. Density functional theory calculations indicate that sulfur incorporation promotes homolytic metal–ligand bond cleavage and facilitates H 2 activation. This work establishes an approach to construct MOFs featuring accessible metal–sulfide sites.

Catalyst synthesis↗
DOE OSTI2021

Dynamically Unveiling Metal–Nitrogen Coordination during Thermal Activation to Design High‐Efficient Atomically Dispersed CoN 4 Active Sites

Abstract We elucidate the structural evolution of CoN 4 sites during thermal activation by developing a zeolitic imidazolate framework (ZIF)‐8‐derived carbon host as an ideal model for Co 2+ ion adsorption. Subsequent in situ X‐ray absorption spectroscopy analysis can dynamically track the conversion from inactive Co−OH and Co−O species into active CoN 4 sites. The critical transition occurs at 700 °C and becomes optimal at 900 °C, generating the highest intrinsic activity and four‐electron selectivity for the oxygen reduction reaction (ORR). DFT calculations elucidate that the ORR is kinetically favored by the thermal‐induced compressive strain of Co−N bonds in CoN 4 active sites formed at 900 °C. Further, we developed a two‐step (i.e., Co ion doping and adsorption) Co‐N‐C catalyst with increased CoN 4 site density and optimized porosity for mass transport, and demonstrated its outstanding fuel cell performance and durability.

He, Yanghua↗
DOE OSTI2021

Dynamically Unveiling Metal–Nitrogen Coordination during Thermal Activation to Design High-Efficient Atomically Dispersed CoN 4 Active Sites

We elucidate the structural evolution of CoN 4 sites during thermal activation by developing a zeolitic imidazolate framework (ZIF)-8-derived carbon host as an ideal model for Co 2+ ion adsorption. Subsequent in situ X-ray absorption spectroscopy analysis can dynamically track the conversion from inactive Co-OH and Co-O species into active CoN 4 sites. The critical transition occurs at 700 °C and becomes optimal at 900 °C, generating the highest intrinsic activity and four-electron selectivity for the oxygen reduction reaction (ORR). DFT calculations elucidate that the ORR is kinetically favored by the thermal-induced compressive strain of Co-N bonds in CoN 4 active sites formed at 900 °C. Further, we developed a two-step (i.e., Co ion doping and adsorption) Co-N-C catalyst with increased CoN 4 site density and optimized porosity for mass transport, and demonstrated its outstanding fuel cell performance and durability.

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

Atomic-Scale Structural Mapping of Active Sites in Monolayer PGM-Free Catalysts by Low-Voltage 4D-STEM

Two-dimensional (2D) materials have attracted a large amount of attention in both basic and applied fields, and scanning transmission electron microscopy (STEM) is often uniquely well-suited for characterizing the atomic-scale structure of these materials [1-4]. As a result, STEM is poised to significantly impact progress on platinum group metal (PGM)-free catalysts, which are currently under intense development to enable low-cost, commercially viable hydrogen fuel cells [5]. While recent advancements have resulted in fuel cell performance comparable to Pt catalysts by some measures [6], cell durability remains a significant challenge, limiting practical applications [7]. Catalytically active sites in PGM-free materials are proposed to be FeN4 complexes embedded in a graphene lattice (Fig. 1b) within layered or other larger materials, but this is still under debate largely due to the range of potential actives sites predicted by computational methods and lack of methods for directly validating these models [5]. Fundamental insights into the atomic structure and resulting degradation pathways of proposed active sites are therefore needed to fully understand and control cell performance and durability [6].2D materials typically make ideal samples for STEM, but those within PGM-free catalysts present additional challenges since these materials are often defect-rich, with a high density of edges, dopant atoms, etc., which significantly increase susceptibility to beam damage at standard operating voltages. This makes analysis of potential FeN4 active sites particularly challenging, since a large proportion of Fe exists at edge sites where beam-induced atomic displacements can prohibit high-resolution structural characterization [6]. Conventional dark-field imaging compounds this problem by producing less signal for a given dose and being less sensitive to light elements than dose-efficient phase contrast imaging techniques such as those enabled by four-dimensional (4D)-STEM [8-10] (Fig. 1a). Consequently, active site structural analysis is often left to methods such as low-resolution imaging combined with quantum chemical calculations [6], which hinders accurate determination of reaction and degradation mechanisms.Here, we demonstrate direct atomic-scale structural mapping of FeN4 sites by performing low-voltage 4D-STEM on a model PGM-free catalyst system with many exposed monolayer regions. To accomplish this, we pair a 30 keV aberration-corrected probe with a fast pixelated detector that has optimal performance at low beam voltages [11]. This enables us to simultaneously image light and heavy elements with high signal-to-noise by center-of-mass analysis (Fig. 1c) while minimizing beam-induced atomic displacements at sensitive sites. The monolayer nature of these materials additionally allows for experimental validation by direct comparison with multislice simulations [12] of model structures (Fig. 1d-e). This work demonstrates how low-voltage 4D-STEM will provide new insights into the atomic-scale structure and degradation mechanisms of active sites in PGM-free catalysts, facilitating the development of low-cost hydrogen fuel cells and other energy conversion technologies in the future [13].

Zachman, Michael↗
NASA NTRSDate not supplied

Implementation of active sites to capture pitting of oxidizing carbon materials in DSMC.

In this work we demonstrate a newly developed capability to capture pitting of carbon fibers in DSMC simulations, specifically using the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code [1]. State-of-the-art reactive surface models in DSMC compute collision dependent carbon consumption rates (usually through desorption of CO) based on a set of surface reactions that has been derived from molecular beam experiments [2]. The reactivity on each carbon surface element is constant in those models, such that the carbon surface recedes uniformly as a result of ablation. However, it is well known that in reality the carbon surface has locally different reaction rates due to the presence of defects at the atomic scale [3]. These defective sites have a much higher reactivity than the average sites (2-3 orders of magnitude) and are first to react during ablation leading to its removal. This causes all the neighboring atoms to be defective and increase their reactivity, thus leading to the localized carbon removal around these ”active” sites (as shown in Fig. 1). In this manner, these highly reactive defective sites serve as nucleation sites for the formation and growth of etch pits with potentially detrimental effects on the structural integrity. Recently a detailed surface chemistry framework was developed in SPARTA, capable of incorporating various reaction mechanisms such as adsorption, desorption, Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms [4]. Within this framework, we have implemented the capability of a single surface having multiple site sets with different reactivities. Using this feature, we can simulate the presence of active sites on carbon surfaces, whose reactivity is much greater than an average site as a result of defects. We have implemented the active site fraction as a property of surface elements within SPARTA, which is directly proportional to the local reactivity of each surface element. By introducing an initial distribution of the active site fraction across the carbon surface, and propagating it in a manner that mimics the evolution of real reacting carbon surfaces, we are able to capture the formation and growth of etch pits as a result of surface consumption reactions such as oxidation.

DSMC↗
NASA NTRSDate not supplied

Implementation of Active Sites in DSMC to Capture Pitting of Oxidizing Carbon Materials

In this work we demonstrate a newly developed capability to capture pitting of carbon fibers in DSMC simulations, specifically using the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code. State-of-the-art reactive surface models in DSMC compute collision dependent carbon consumption rates (usually through desorption of CO) based on a set of surface reactions that has been derived from molecular beam experiments. The reactivity on each carbon surface element is constant in those models, such that the carbon surface recedes uniformly as a result of ablation. However, it is well known that in reality the carbon surface has locally different reaction rates due to the presence of defects at the atomic scale. These defective sites have a much higher reactivity than the average sites (2-3 orders of magnitude) and are first to react during ablation leading to its removal. This causes all the neighboring atoms to be defective and increase their reactivity, thus leading to the localized carbon removal around these ”active” sites. In this manner, these highly reactive defective sites serve as nucleation sites for the formation and growth of etch pits with potentially detrimental effects on the structural integrity. Recently a detailed surface chemistry framework was developed in SPARTA, capable of incorporating various reaction mechanisms such as adsorption, desorption, Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms. Within this framework, we have implemented the capability of a single surface having multiple site sets with different reactivities. Using this feature, we can simulate the presence of active sites on carbon surfaces, whose reactivity is much greater than an average site as a result of defects. We have implemented the active site fraction as a property of surface elements within SPARTA, which is directly proportional to the local reactivity of each surface element. By introducing an initial distribution of the active site fraction across the carbon surface, and propagating it in a manner that mimics the evolution of real reacting carbon surfaces, we are able to capture the formation and growth of etch pits as a result of surface consumption reactions such as oxidation.

DSMC↗
DOE OSTI2024

Atomic-scale identification of active sites of oxygen reduction nanocatalysts

Heterogeneous nanocatalysts play a crucial role in both the chemical and energy industries. Despite substantial advancements in theoretical, computational and experimental studies, identifying their active sites remains a major challenge. Here we utilize atomic electron tomography to determine the three-dimensional atomic structure of PtNi and Mo-doped PtNi nanocatalysts for the electrochemical oxygen reduction reaction. We then employ the experimental atomic structures as input to first-principles-trained machine learning to identify the active sites of the nanocatalysts. Through the analysis of the structure–activity relationships, we formulate an equation termed the local environment descriptor, which balances the strain and ligand effects to provide physical and chemical insights into active sites in the oxygen reduction reaction. The ability to determine the three-dimensional atomic structure and chemical composition of realistic nanoparticles, combined with machine learning, could transform our fundamental understanding of the active sites of catalysts and guide the rational design of optimal nanocatalysts.

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

Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning

Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation

Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO 4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl–AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl•ATP•(Mn 2+ ) 2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn 2+ . The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Active Sites of Cobalt Phthalocyanine in Electrocatalytic CO 2 Reduction to Methanol

Many metal coordination compounds catalyze CO 2 electroreduction to CO, but cobalt phthalocyanine hybridized with conductive carbon such as carbon nanotubes is currently the only one that can generate methanol. The underlying structure–reactivity correlation and reaction mechanism desperately demand elucidation. Here, in this study, we report the first in situ X-ray absorption spectroscopy characterization, combined with ex situ spectroscopic and electrocatalytic measurements, to study CoPc-catalyzed CO 2 reduction to methanol. Molecular dispersion of CoPc on CNT surfaces, as evidenced by the observed electronic interaction between the two, is crucial to fast electron transfer to the active sites and multi-electron CO 2 reduction. CO, the key intermediate in the CO 2 -to-methanol pathway, is found to be labile on the active site, which necessitates a high local concentration in the microenvironment to compete with CO 2 for active sites and promote methanol production. A comparison of the electrocatalytic performance of structurally related porphyrins indicates that the bridging aza-N atoms of the Pc macrocycle are critical components of the CoPc active site that produces methanol. In situ X-ray absorption spectroscopy identifies the active site as Co(I) and supports an increasingly non-centrosymmetric Co coordination environment at negative applied potential, likely due to the formation of a Co−CO adduct during the catalysis.

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

Creation of discrete active site domains via mesoporous silica poly(styrene) composite materials for incompatible acid–base cascade reactions

This work highlights the design and synthesis of bifunctional mesoporous silicate – polymer composite dual acid–base supported cascade catalysts. Compartmentalization of the two incompatible active sites is sought by segregating acid sites on the silica surface, and base sites within polymer chains and/or polymer domains. The ability to isolate and segregate active sites via control of the mesoporous silica pore size and polymer molecular weight is probed with silica samples functionalized by a grafting-to process. Supplemental activator and reducing agent (SARA) atom transfer radical polymerization is used to synthesize random copolymers containing protected primary amines. Thiol–ene ‘click’ chemistry facilitates silica functionalization via a convergent approach, with the ene-functionalized polymer end group and silica-grafted thiols forming SBA/MCM-SH-poly(styrene-co-2-(4-vinylbenzyl)isoindoline-1,3-dione). Polymer deprotection and thiol oxidation produces primary amine/sulfonic acid containing composite catalysts. With the polymer supported Lewis base and silica grafted Brønsted acid, the two-step deacetalization – Knoevenagel condensation cascade is explored to assess the ability of these polymer/silica hybrids to segregate active sites, allowing both acid and base site accessibility. Six composite catalysts are synthesized and tested in individual and cascade reactions with kinetic results demonstrating that lower molecular weight SBA-15-P1 and MCM-41-P1 catalysts outperform (higher turnover frequencies and initial rates) their higher molecular weight analogues, as well as a polymer-free system containing molecular active sites dispersed on the silica surface. Higher molecular weight composite catalysts perform more poorly due to limited chain solubility, mass transfer limitations, and poor catalyst accessibility. In many cases, the polymer chains effectively thread into the mesopores, with higher molecular weight polymers leading to pore blockage and inhibited mass transfer.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Active-Site Environmental Factors Customize the Photophysics of Photoenzymatic Old Yellow Enzymes

The development of non-natural photoenzymatic systems has reinvigorated the study of photoinduced electron transfer (ET) within protein active sites, providing new and unique platforms for understanding how biological environments affect photochemical processes. Here, we use ultrafast spectroscopy to compare the photoinduced electron transfer in known photoenzymes. 12-Oxophytodienoate reductase 1 (OPR1) is compared to Old Yellow Enzyme 1 (OYE1) and morphinone reductase (MR). The latter enzymes are structurally homologous to OPR1. We find that slight differences in the amino acid composition of the active sites of these proteins determine their distinct electron-transfer dynamics. Our work suggests that the inside of a protein active site is a complex/heterogeneous dielectric network where genetically programmed heterogeneity near the site of biological ET can significantly affect the presence and lifetime of various intermediate states. Our work motivates additional tunability of Old Yellow Enzyme active-site reorganization energy and electron-transfer energetics that could be leveraged for photoenzymatic redox approaches.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Fast product release requires active-site water dynamics in carbonic anhydrase

Water plays an essential role in enzyme structure, stability, and the substantial rate enhancement of enzyme catalysis. However, direct observations linking enzyme catalysis and active-site water dynamics pose a significant challenge due to experimental difficulties. By integrating an ultraviolet (UV) photolysis technique with temperature-controlled X-ray crystallography, we track the catalytic pathway of carbonic anhydrase II (CAII) at 1.2 Å resolution. This approach enables us to construct molecular movies of CAII catalysis, encompassing substrate (CO 2 ) binding, conversion from substrate to product (bicarbonate), and product release. In the catalytic pathway, we identify an unexpected configuration in product binding and correlate it with sub-nanosecond rearrangement of active-site water. Based on these experimental observations, we propose a comprehensive mechanism of CAII and describe the detailed structure and dynamics of active-site water in CAII. Our findings suggest that CAII has evolved to utilize the structure and fast dynamics of the active-site waters for its diffusion-limited catalytic efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗