Bio-inspired Macromolecules Containing Atomically Precise Catalytic Active Sites
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09 BIOMASS FUELS↗
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Interfacial Active Sites for CO2 Assisted Selective Cleavage of C-C/C-H Bonds in Ethane
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99 GENERAL AND MISCELLANEOUS↗
Active Sites and Structural Evolution of NiFeO x Catalysts Supported on Au(111) and HOPG Electrodes in the Electrocatalytic Oxygen Evolution Reaction (OER)
ACS Spring Meeting 2021, Virtual, April 5-16, 2021
Deng, Xingyi↗
Active Sites and Structural Transformation of NiFeOx Catalysts during Electrocatalytic Oxygen Evolution Reaction (OER): Effects of Catalyst Loading and Support
The 67th AVS International Symposium and Exhibition, Virtual, October 24-29, 2021.
Deng, Xingyi↗
Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression
Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.
09 BIOMASS FUELS↗
The Overlooked Potential of Sulfated Zirconia: Reexamining Solid Superacidity Toward the Controlled Depolymerization of Polyolefins
Closed-loop recycling via an efficient chemical process can help alleviate the global plastic waste crisis. However, conventional depolymerization methods for polyolefins, which compose more than 50% of plastics, demand high temperatures and pressures, employ precious noble metals, and yield complex mixtures of products limited to single-use fuels or oils. Superacidic sulfated zirconia (SZrO) with Hammet Acidity Functions (H 0 ) = -12 (i.e., stronger than 100% H 2 SO 4 ) is an industrially deployed heterogeneous catalyst capable of activating hydrocarbons under mild conditions and is shown to decompose polyolefins at ambient pressure and temperatures near 200 °C. Additionally, confinement of active sites in porous supports is known to radically increase selectivity, coking and sintering resistance, and acid site activity, presenting a possible approach to low-energy polyolefin depolymerization. However, a critical examination of the literature on SZrO led us to a surprising conclusion: despite 40 years of catalytic study, engineering, and industrial use, the surface chemistry of SZrO is poorly understood. Ostensibly spurred by SZrO's impressive catalytic activity, the application-driven study of SZrO has resulted in deleterious ambiguity in requisite synthetic conditions and insufficient characterization of acidity, porosity, and active site structure. Here, this ambiguity has produced significant knowledge gaps surrounding the synthesis, structure, and mechanisms of hydrocarbon activation for optimized SZrO, stunting the potential of this catalyst in olefin cracking and other industrially relevant reactions, such as isomerization, esterification, and alkylation. Toward mitigating these long extant issues, we herein identify and highlight these current shortcomings and knowledge gaps, propose explicit guidelines for characterization of and reporting on characterization of solid acidity, and discuss the potential of pore-confined superacids in the efficient and selective depolymerization of polyolefins.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Global Optimization of Adsorbate Covered Supported Cluster Catalysts: The Case of Pt 7 H 10 CH 3 on α-Al 2 O 3
Determining structures of supported sub-nanometer catalytic clusters is important for finding binding sites, active sites, and reaction mechanisms. In realistic conditions, the cluster may be covered with adsorbed reactants and intermediates, which strongly affect the structure of the cluster compared to the low coverage regime. The global optimization of supported adsorbate-covered clusters is not possible with existing methods. In this paper, we present a customized Basin Hopping (BH) approach, with a core (metal cluster) – shell (adsorbates) separation scheme, and perform first applications to the search of low-energy isomers of Pt 7 /α-Al 2 O 3 at high hydrogen coverage (10H). The presence of adsorbates significantly alters the low-energy isomers compared to bare Pt 7 /α-Al 2 O 3 . Molecular dynamics simulations additionally show the different time-scales associated with the mobility of H and Pt atoms. The revised BH method with core-shell separation presents key advantages for the structural exploration of adsorbate-covered supported catalysts, relevant to realistic catalytic conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
PNNL-Predictive-Phenomics/ProCaliper
ProCaliper is a Python library that curates, organizes, and computes protein structure features in a way that easily interfaces with user-provided experimental data. It extracts or computes protein binding site, active site, charge, pLDDT (order/disorder), acid dissociation, protonation, solvent accessible surface area, disulfide bond distance, and protein secondary structure data using precomputed protein structures and publicly available databases. It provides a unified API for integrating additional residue-level data and for visualizing residue features in 3D.
Rozum, Jordan [Pacific Northwest National Lab]↗
Recommendations for improving rigor and reproducibility in site specific characterization
Heterogeneous catalysis is driven by the interaction of reactant molecules and the catalyst surface. The locus of this interaction as well as the surrounding ensemble of atoms is referred to as the catalyst active site. Active site characterization attempts to distinguish active catalytic sites from inactive surface sites, to elucidate the structural and chemical nature of active sites, and to quantify active site concentration. Numerous techniques have been demonstrated to provide compositional and structural information about the active sites within a catalyst. However, each technique has its own limitations and experimental pitfalls that can lead to data misinterpretation or irreproducible results. Further, this work aims to provide an overview of the types of data that can be collected, to outline common experimental challenges and how to avoid them, and to assemble relevant references for the most used active site characterization techniques. More broadly, we aim to outline best practices for researchers to collect, interpret, and report active site characterization data in a way that provides the most benefit to the broader catalysis community. Increasing the rigor and reproducibility of active site characterization offers a strategy to better link properties with catalytic performance and to enable the community to develop consensus concerning these relationships.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Determination of the Evolution of Heterogeneous Single Metal Atoms and Nanoclusters under Reaction Conditions: Which Are the Working Catalytic Sites?
Identification of active sites in heterogeneous metal catalysts is critical for understanding the reaction mechanism at the molecular level and for designing more efficient catalysts. Because of their structural flexibility, subnanometric metal catalysts, including single atoms and clusters with a few atoms, can exhibit dynamic structural evolution when interacting with substrate molecules, making it difficult to determine the catalytically active sites. Here, Pt catalysts containing selected types of Pt entities (from single atoms to clusters and nanoparticles) have been prepared, and their evolution has been followed, while they were reacting in a variety of heterogeneous catalytic reactions, including selective hydrogenation reactions, CO oxidation, dehydrogenation of propane, and photocatalytic H2 evolution reaction. By in situ X-ray absorption spectroscopy, in situ IR spectroscopy, and high-resolution electron microscopy techniques, we will show that some characterization techniques carried out in an inadequate way can introduce confusion on the interpretation of coordination environment of highly dispersed Pt species. Finally, the combination of catalytic reactivity and in situ characterization techniques shows that, depending on the catalyst–reactant interaction and metal–support interaction, singly dispersed metal atoms can rapidly evolve into metal clusters or nanoparticles, being the working active sites for those abovementioned heterogeneous reactions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗
Modulating Operational Conditions to Mitigate Deactivation in Formate Dehydrogenation on Pd Phases
In heterogeneous catalysis, poisoning by surface-bound intermediates poses a major barrier to sustained catalyst performance in (de)hydrogenation reactions. Formate/bicarbonate systems, as liquid organic hydrogen carriers (LOHCs), offer a CO 2 -integrated, low-temperature pathway for hydrogen storage and release, making them attractive for circular energy applications. However, their lower hydrogen density and susceptibility to catalyst deactivation limit their competitiveness compared to conventional LOHCs like methylcyclohexane. Here, this study investigates the mechanistic origins of formate (HCOO – ) dehydrogenation and associated deactivation on Pd interfaces. Using density functional theory (DFT) simulations, we show that under thermocatalytic conditions, strongly bound formate accumulates on the catalyst surface (Pd(111)), blocking active sites, raising activation barriers, and leading to progressive performance loss. Because formate adsorption involves charge transfer, we exploit its sensitivity to electronic structure by modulating the electrochemical potential of the catalyst. Our results reveal that hydrogen transfer from water and formate exhibits opposing potential dependencies, providing insights into the opposing driving forces behind both catalytic activity and poisoning. To further probe this phenomenon, we examine electrochemically induced phase transitions in Pd, focusing on PdO(100) and PdH(110), which are stable under oxidizing and reducing potentials, respectively, and demonstrate enhanced dehydrogenation activity between −0.4 and 0.2 V vs standard hydrogen electrode (SHE). Complementary thermal treatments help decouple kinetic and thermodynamic contributions to intermediate binding. These findings underscore the critical role of the catalyst phase and external stimuli in dictating poison-active site interactions and highlight phase engineering as a promising strategy to mitigate deactivation. This work offers mechanistic insights and design principles for developing more resilient and efficient catalysts for LOHC applications under realistic operating conditions.
Pd phase↗
Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor
Abstract Fungal tRNA ligase (Trl1) rectifies RNA breaks with 2′,3′-cyclic-PO4 and 5′-OH termini. Trl1 consists of three catalytic modules: an N-terminal ligase (LIG) domain; a central polynucleotide kinase (KIN) domain; and a C-terminal cyclic phosphodiesterase (CPD) domain. Trl1 enzymes found in all human fungal pathogens are untapped targets for antifungal drug discovery. Here we report a 1.9 Å crystal structure of Trl1 KIN-CPD from the pathogenic fungus Candida albicans, which adopts an extended conformation in which separate KIN and CPD domains are connected by an unstructured linker. CPD belongs to the 2H phosphotransferase superfamily by dint of its conserved central concave β sheet and interactions of its dual HxT motif histidines and threonines with phosphate in the active site. Additional active site motifs conserved among the fungal CPD clade of 2H enzymes are identified. We present structures of the Candida Trl1 KIN domain at 1.5 to 2.0 Å resolution—as apoenzyme and in complexes with GTP•Mg2+, IDP•PO4, and dGDP•PO4—that highlight conformational switches in the G-loop (which recognizes the guanine base) and lid-loop (poised over the nucleotide phosphates) that accompany nucleotide binding.
59 BASIC BIOLOGICAL SCIENCES↗
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↗
Controlling Heterogeneous Catalysis with Organic Monolayers on Metal Oxides
A key theme of heterogeneous catalysis research is achieving control of the environment surrounding the active site to precisely steer the reactivity toward desired reaction products. One method toward this goal has been the use of organic ligands or self-assembled monolayers (SAMs) on metal nanoparticles. Metal-bound SAMs are typically employed to improve catalyst selectivity but often decrease the reaction rate as a result of site blocking from the ligands. Recently, the use of metal oxide-bound organic modifiers such as organophosphonic acid (PA) SAMs has shown promise as an additional method for tuning reactions on metal oxide surfaces as well as modifying oxide-supported metal catalysts. In this Account, we summarize recent approaches to enhance catalyst performance with oxide-bound monolayers. These approaches include (1) modification of metal oxide catalysts to tune surface reactions, (2) formation of SAMs on the oxide component of supported metal catalysts to modify sites at the metal–support interface, and (3) enhancement of catalyst performance (e.g., stability) through modification of sites remote from the active sites. Further, both the headgroups and organic tail groups of PA SAMs or other ligands can influence reactions on metal oxide surfaces. Binding of the headgroup can selectively poison certain active sites, altering the selectivity in a manner analogous to metal-bound ligands (at the expense of active site quantity). Moreover, tail groups can be functionalized to interact favorably with reactants and intermediates, for instance through dipole–dipole interactions. On supported metal catalysts like Pt/Al 2 O 3 , PA SAMs can selectively form on the oxide support. This selective deposition allows for modification of the metal–support interface with minimal blockage of metal sites. PA headgroups were shown to provide tunable acid sites at the interface, dramatically improving hydrodeoxygenation rates of various alcohols. Additionally, organic tail functionality was used to activate or stabilize specific reactants at the interface, such as with the use of amine-functionalized PAs to stabilize chemisorption of CO 2 during the reverse water gas shift reaction. PAs have also been found to affect the electronic properties of bulk metal sites through long-range electron withdrawal via the oxide, providing an additional avenue to tune catalytic behavior. Finally, organic modifiers were shown to enhance catalytic performance without directly modifying the active site. For instance, in biphasic liquid environments the modification of catalyst particles with hydrophobic or hydrophilic SAMs shifts the selectivity of multipath reactions on the basis of the hydrophobicities of different intermediates and products. As another “long-range” effect, the deposition of ligands on oxide supports improved catalyst stability through both improved resistance to sintering and suppression of active site poisoning. The recent contributions discussed in this Account demonstrate the versatility and significant potential for the approach of modifying catalysts with oxide-bound organic monolayers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Direct Observation of Ammonia Storage in UiO-66 Incorporating Cu(II) Binding Sites
The presence of active sites in metal–organic framework (MOF) materials can control and affect their performance significantly in adsorption and catalysis. However, revealing the interactions between the substrate and active sites in MOFs at atomic precision remains a challenging task. Here, we report the direct observation of binding of NH 3 in a series of UiO-66 materials containing atomically dispersed defects and open Cu(I) and Cu(II) sites. While all MOFs in this series exhibit similar surface areas (1111–1135 m 2 g –1 ), decoration of the -OH site in UiO-66-defect with Cu(II) results in a 43% enhancement of the isothermal uptake of NH 3 at 273 K and 1.0 bar from 11.8 in UiO-66-defect to 16.9 mmol g –1 in UiO-66-Cu II . A 100% enhancement of dynamic adsorption of NH 3 at a concentration level of 630 ppm from 2.07 mmol g –1 in UiO-66-defect to 4.15 mmol g –1 in UiO-66-Cu II at 298 K is observed. In situ neutron powder diffraction, inelastic neutron scattering, and electron paramagnetic resonance, solid-state nuclear magnetic resonance, and infrared spectroscopies, coupled with modeling reveal that the enhanced NH 3 uptake in UiO-66-Cu II originates from a {Cu(II)···NH 3 } interaction, with a reversible change in geometry at Cu(II) from near-linear to trigonal coordination. This work represents the first example of structural elucidation of NH 3 binding in MOFs containing open metal sites and will inform the design of new efficient MOF sorbents by targeted control of active sites for NH 3 capture and storage.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree
Hydroxynitrile lyase fromHevea brasiliensis(HbHNL) and the esterase SABP2 fromNicotiana tabacumshare the α/β-hydrolase fold, a Ser–His–Asp catalytic triad and 44% sequence identity, yet catalyze different reactions. Prior studies showed that three active-site substitutions inHbHNL conferred weak esterase activity. To investigate how regions beyond the active site influence catalytic efficiency and active-site geometry, we engineeredHbHNL variants with increasing numbers of substitutions to match SABP2. Variant HNL16 has all amino acids within 6.5 Å of the active site identical to SABP2, HNL40 those within 10 Å and HNL71 those within 14 Å. HNL16 exhibited poor esterase activity, whereas both HNL40 and HNL71 showed efficient esterase catalysis, demonstrating that residues beyond the immediate active site are critical for functional conversion. X-ray structures of HNL40 and HNL71 reveal a progressive shift in backbone positions toward those of SABP2, with r.m.s.d. values of 0.51 Å (HNL40) and 0.41 Å (HNL71) over the C α atoms, and even smaller r.m.s.d.s within the active-site region. Both HNL40 and HNL71 show a restored oxyanion hole and an additional tunnel connecting the active site to the protein surface. This work demonstrates the essential role of distant, indirectly acting residues to catalysis in α/β-hydrolase enzymes.
Biochemistry & Molecular Biology↗
Prediction of Feasibility of Polaronic OER on (110) Surface of Rutile TiO 2
The polaronic effects at the atomic level hold paramount significance for advancing the efficacy of transition metal oxides in applications pertinent to renewable energy. The lattice–distortion mediated localization of photoexcited carriers in the form of polarons plays a pivotal role in the photocatalysis. This investigation focuses on rutile TiO 2 , an important material extensively explored for solar energy conversion in artificial photosynthesis, specifically targeting the generation of green H 2 through photoelectrochemical (PEC) H 2 O splitting. By employing Hubbard-U corrected and hybrid density functional theory (DFT) methods, we systematically probe the polaronic effects in the catalysis of oxygen evolution reaction (OER) on the (110) surface of rutile TiO 2 . Theoretical understanding of polarons within the surface, coupled with simulations of OER at distinct titanium (Ti) and oxygen (O) active sites, reveals diverse polaron formation energies within the lattice sites with strong preference for bulk and surface bridge (O b ) oxygen sites. Moreover, we provide the evidence for the facilitative role of polarons in OER. Here, we find that hole polarons situated at the equatorial oxygen sites near the Ti–active site, along with bridge site hole polarons distal from the O b active site yield a small reduction in OER overpotential by ~0.06 eV and ~0.12 eV, respectively. However, subsurface, equatorial, and bridge site hole polarons significantly reduce the Ti-active site OER overpotential by ~0.4 eV through the peroxo–type oxygen pathway. We also observe that the presence of hole polarons stabilizes the *OH, *O, and *OOH intermediate species compared to the scenario without hole polarons. Overall, this study provides a detailed mechanistic insight into polaron–mediated OER, offering a promising avenue for improving the catalytic activity of transition metal oxide-based photocatalysts catering to renewable energy requisites.
14 SOLAR ENERGY↗