Toward Phase and Catalysis Control: Tracking the Formation of Intermetallic Nanoparticles at Atomic Scale
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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A biohybrid strategy for enabling photoredox catalysis with low-energy light
Natural systems drive the high-energy reactions of photosynthesis with efficient and broadband energy capture. Transition-metal photocatalysts similarly convert light into chemical reactivity, and yet suffer from light-limited operation and require blue-to-UV excitation. In photosynthesis, both light capture and reactivity have been optimized by separation into distinct sites. In this work, inspired by this modular architecture, we synthesized a biohybrid photocatalyst by covalent attachment of the photosynthetic light-harvesting protein R-phycoerythrin (RPE) to the transition-metal photocatalyst tris(2,2'-bipyridine)ruthenium(II) ([Ru(bpy) 3 ] 2+ ). Spectroscopic investigation found that absorbed photoenergy was efficiently funneled from RPE to [Ru(bpy) 3 ] 2+ . The utility of the biohybrid photocatalyst was demonstrated via an increase in yields for a thiol-ene coupling reaction and a cysteinyl-desulfurization reaction, including recovered reactivity at red wavelengths where [Ru(bpy) 3 ] 2+ alone does not absorb.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Synthesis, Characterization, and Oxidation Catalysis Studies of a Monofunctionalized Copper Pyridine-Aza Macrocycle
For this study, a copper-containing pyridine-aza macrocycle (PyMACs) with a propionic acid functionality was synthesized and characterized using X-ray crystallography and various spectroscopic techniques. The complex was then screened for peroxidase , olefin epoxidation, and phenol oxidation properties, using an ABTS assay, GC-MS, and UV-Vis spectrophotometry, respectively. The control copper (II) perchlorate salts were superior oxidation catalysts to the pentadentate carboxylic acid complex, CuLCOOH, and the unfunctionalized amine PyMAC, CuCRH. This might indicate that free copper ions facilitate the one-electron oxidations necessary for the reactions better than complexed copper. It also indicates that the copper PyMACs are far less effective than the analogous nickel and iron systems. We did, however, obtain valuable insights on the chemistry governing this family of PyMACs by probing the CuLCOOH’s solution and solid-phase protonation equilibria, which will be useful for isolating and studying the analogous iron complex, FeLCOOH.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mutagenesis and structural analysis reveal the CTX-M β-lactamase active site is optimized for cephalosporin catalysis and drug resistance
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59 BASIC BIOLOGICAL SCIENCES↗
Properties of the iron-sulfur cluster electron transfer relay in an [FeFe]-hydrogenase that is tuned for H2 oxidation catalysis
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Hydrodechlorination Catalysis of Pd-on-Au Nanoparticles Varies with Particle Size
The dependence of bimetallic PdAu catalytic activity on the relative ratios of Pd and Au has been theoretically predicted and experimentally observed for a number of reactions. Trichloroethene (TCE), a common carcinogenic solvent that is difficult to remove from contaminated groundwater in many industrialized nations, can be chemically degraded especially rapidly with Au nanoparticles partially coated with Pd ("Pd-on-Au NPs"). These NPs catalyze the room-temperature water-phase TCE hydrodechlorination (HDC) reaction with activities that follow a volcano-shape dependence on Pd surface coverage. The effect of particle size is not known, though. Pd-on-Au NPs synthesized with 3, 7, and 10 nm Au NPs and Pd surface coverages between 0 and 150% were studied in detail. Volcano-shape dependence on Au particle size and Pd surface coverage was observed, with 7 nm Au NPs with a Pd coverage of 60-70% having the highest TCE HDC activity. Extended x-ray absorption fine-structure spectroscopy (EXAFS) revealed the correlation was strongest between catalytic activity and the presence of non-oxidized Pd ensembles of ~2-3 atoms in contact with ~8-10 Au atoms. Isolated Pd atoms and Pd ensembles were visualized for the first time through aberration-corrected scanning transmission electron microscopy (STEM). This study provides the most direct evidence yet for Pd-on-Au NPs containing 2-dimensional Pd ensembles as the active sites for TCE HDC and likely for other chemical reactions. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. This research was supported by the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
catalysis↗
A microreactor array for spatially resolved measurement of catalytic activity for high-throughput catalysis science
We describe a 100 channel microreactor array capable of spatially resolved measurement of catalytic activity across the surface of a flat substrate. When used in conjunction with a composition spread alloy film (CSAF, e.g. Pd{sub x}Cu{sub y}Au{sub 1-x-y}) across which component concentrations vary smoothly, such measurements permit high-throughput analysis of catalytic activity and selectivity as a function of catalyst composition. In the reported implementation, the system achieves spatial resolution of 1 mm{sup 2} over a 10×10 mm{sup 2} area. During operation, the reactant gases are delivered at constant flow rate to 100 points of differing composition on the CSAF surface by means of a 100-channel microfluidic device. After coming into contact with the CSAF catalyst surface, the product gas mixture from each of the 100 points is withdrawn separately through a set of 100 isolated channels for analysis using a mass spectrometer. We demonstrate the operation of the device on a Pd{sub x}Cu{sub y}Au{sub 1-x-y} CSAF catalyzing the H{sub 2}-D{sub 2} exchange reaction at 333 K. In essentially a single experiment, we measured the catalytic activity over a broad swathe of concentrations from the ternary composition space of the Pd{sub x}Cu{sub y}Au{sub 1-x-y} alloy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Scalable production of Cu@C composites for cross-coupling catalysis
Highlights: • Cu@C core–shell composite was prepared by reduction of [Cu(NH{sub 3}){sub 4}]{sup 2+} with glucose. • The carbon shell in Cu@C can be tuned to the different degree of carbonization. • The Cu@C composites were utilized to catalyze the C−N cross coupling reaction. • The catalytic ability of Cu@C depends on the degree of shell-carbonization. - Abstract: A novel Cu@C core–shell microstructure was prepared by reduction of [Cu(NH{sub 3}){sub 4}]{sup 2+} with glucose using a mild hydrothermal process. The carbon shell of such Cu@C composite can be tuned to different carbonization degrees just through varying the calcination conditions. The structural properties of as-prepared Cu@C were investigated in detail by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), transmission electron micrographs (TEM) and Raman spectra. In addition, these Cu@C composites were firstly used to catalyze the C−N cross coupling of amines with iodobenzene. Among them, the catalytic ability of Cu@C composites increased as their surface carbon’s carburization degree improved.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Facile synthesis of various α-Fe2O3 micro/nanostructures: Highlighting on the enhanced catalysis activities by formation of bowl-like α-Fe2O3/Au composites
Highlights: • Various α-Fe{sub 2}O{sub 3} micro/nanostructures are fabricated by a hydrothermal method. • The morphologies are tunable by changing the content of NaHCO{sub 3} and reaction time. • Bowl-like α-Fe{sub 2}O{sub 3} has the highest Fenton catalytic efficiency in dark condition. • Fast photo-Fenton reaction of α-Fe{sub 2}O{sub 3}/Au can be tuned by multiphase structures. • Bowl-like α-Fe{sub 2}O{sub 3}/Au is an excellent photo-Fenton catalyst for water treatment. - Abstract: Various α-Fe{sub 2}O{sub 3} micro/nanostructures referring to spherical-like, bowl-like, cubic, and discoid shapes have been fabricated by a facile hydrothermal method using sodium bicarbonate as surfactant and alkaline reagents, displaying superior Fenton catalytic performances for degradation of Rhodamine 6G. Because of abundant exposed crystal surfaces such as (110) and (104) on the surfaces of bowl-like α-Fe{sub 2}O{sub 3}, the rapid degradation rate of 90.0% in 5 min is observed under the dark condition as the adding amount of H{sub 2}O{sub 2} limiting to 300 μL. Significantly, the enhanced catalytic performances of bowl-like α-Fe{sub 2}O{sub 3}/Au catalysts under natural light condition have been investigated and carried out by in situ reduction of well-distributed Au nanoparticles with average sizes of 3–6 nm. Due to the appropriate phase structures and heterogenous interface properties, the highest photo-Fenton catalytic activity with the degradation rate of 90.0% in 2 min can be obtained for α-Fe{sub 2}O{sub 3}/Au{sub 0.01} composites.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Heterogeneous catalysis: Optimal performance at a phase boundary?
Most of the industrially used heterogeneous catalysts have been discovered by trial and error, and despite decades of experience, the discovery of new catalysts continues to be extremely challenging. The drive to uncover guiding principles in catalyst design is more present than ever. We share a series of observations indicating that optimal catalysts typically function at characteristic phase boundaries (e.g., abrupt changes in adsorbate coverage, catalyst structure, etc.) accessed in the reaction conditions. The catalyst exploits the associated instability—the desire to exist in multiple states simultaneously—as a driving force for chemical transformations. In other words, phase boundaries are good places to start the catalyst search, and indeed, we should focus on at least two phases at once rather than just one. Here, we substantiate this claim with several studies that combine statistical operando modeling and experiments. Transpiring from these observations is a hitherto unrecognized vector in catalyst discovery.
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Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis
We have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF{sub 3}{sup -}. Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg{sup 2+} ion in the active site. Coupled with a strong [Mg{sup 2+}] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg{sup 2+} ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg{sup 2+} concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg{sup 2+} ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated {gamma}-phosphate from solvent.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis
Poxviruses encode decapping enzymes that remove the protective 5' cap from both host and viral mRNAs to commit transcripts for decay by the cellular exonuclease Xrn1. Decapping by these enzymes is critical for poxvirus pathogenicity by means of simultaneously suppressing host protein synthesis and limiting the accumulation of viral double-stranded RNA (dsRNA), a trigger for antiviral responses. Here we present a high-resolution structural view of the vaccinia virus decapping enzyme D9. This Nudix enzyme contains a domain organization different from other decapping enzymes in which a three-helix bundle is inserted into the catalytic Nudix domain. The 5' mRNA cap is positioned in a bipartite active site at the interface of the two domains. Specificity for the methylated guanosine cap is achieved by stacking between conserved aromatic residues in a manner similar to that observed in canonical cap-binding proteins VP39, eIF4E, and CBP20, and distinct from eukaryotic decapping enzyme Dcp2.
59 BASIC BIOLOGICAL SCIENCES↗
Involvement of histone methyltransferase GLP in HIV-1 latency through catalysis of H3K9 dimethylation
Understanding the mechanism of HIV-1 latency is crucial to eradication of the viral reservoir in HIV-1-infected individuals. However, the role of histone methyltransferase (HMT) G9a-like protein (GLP) in HIV-1 latency is still unclear. In the present work, we established four clonal cell lines containing HIV-1 vector. We found that the integration sites of most clonal cell lines favored active gene regions. However, we also observed hypomethylation of CpG of HIV 5′LTR in all four clonal cell lines. Additionally, 5′-deoxy-5′-methylthioadenosine (MTA), a broad-spectrum histone methyltransferase inhibitor, was used to examine the role of histone methylation in HIV-1 latency. MTA was found to decrease the level of H3K9 dimethylation, causing reactivation of latent HIV-1 in C11 cells. GLP knockdown by small interfering RNA clearly induced HIV-1 LTR expression. Results suggest that GLP may play a significant role in the maintenance of HIV-1 latency by catalyzing dimethylation of H3K9. - Highlights: ► We have established an in vitro model of HIV-1 latency. ► The integration sites of most clonal cell lines favor in active gene regions. ► Hypomethylation occurs in CpG islands of HIV 5′LTR in all four clonal cell lines. ► MTA can reactivate latent HIV-1 by decreasing the level of H3K9 me2 in C11 cells. ► HMT GLP may play a significant role in the maintenance of HIV-1 latency.
60 APPLIED LIFE SCIENCES↗
Imaging a Haber-Bosch catalysis precursor at the atomic scale
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure-guided utilization of lignocellulose for catalysis, energy, and biomaterials
As a complex composite of cellulose, hemicellulose, and lignin, plant lignocellulose has long served as a major resource for biomass conversion, materials engineering, and bio-based product development. High-resolution structural insights enabled by solid-state nuclear magnetic resonance (ssNMR) now allow the mapping of polymer interfaces, identification of functional group accessibility, and tracking of molecular organization during processing, all of which are critical factors for optimizing catalytic strategies. These insights could drive transformative progress in lignocellulose-based applications, including selective depolymerization, improved pretreatment design, and efficient upcycling of lignin into resins, plastics, and biomedical materials. In industry-relevant contexts, such as biofuel generation and renewable material manufacturing, understanding the hydration dynamics, cross-linking patterns, and structural heterogeneity is also essential. The ability to visualize these features in native biomass presents a unique opportunity to develop new strategies for sustainability and performance. As the structural toolbox continues to expand, it is becoming a central enabler for innovations in renewable energy, green chemistry, and advanced bioproducts.
bioproduct↗
Heterogeneous Catalysis: A Central Science for a Sustainable Future
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catalysis (heterogeneous), mesostructured material↗
Bridging Scales in Bioenergy and Catalysis: A Review of Mesoscale Modeling Applications, Methods, and Future Directions
Between the molecular and reactor scales, which are familiar to the chemical engineering community, lies an intermediate regime, here termed the “mesoscale,” where transport phenomena and reaction kinetics compete on similar time scales. Bioenergy and catalytic processes offer particularly important examples of mesoscale phenomena owing to their multiphase nature and the complex, highly variable porosity characteristic of biomass and many structured catalysts. In this review, we overview applications and methods central to mesoscale modeling as they apply to reaction engineering of biomass conversion and catalytic processing. A brief historical perspective is offered to put recent advances in context. Applications of mesoscale modeling are described, and several specific examples from biomass pyrolysis and catalytic upgrading of bioderived intermediates are highlighted. Methods including reduced order modeling, finite element and finite volume approaches, geometry construction and import, and visualization of simulation results are described; in each category, recent advances, current limitations, and areas for future development are presented. Owing to improved access to high-performance computational resources, advances in algorithm development, and sustained interest in reaction engineering to sustainably meet societal needs, we conclude that a significant upsurge in mesoscale modeling capabilities is on the horizon that will accelerate design, deployment, and optimization of new bioenergy and catalytic technologies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Selective Metal–Organic Framework Catalysis of Glucose to 5-Hydroxymethylfurfural Using Phosphate-Modified NU-1000
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catalysis (heterogeneous), materials and chemistry↗