Molecular Thin Films Enable the Synthesis and Screening of Nanoparticle Megalibraries Containing Millions of Catalysts.

Megalibraries are centimeter-scale chips containing millions of materials synthesized in parallel using scanning probe lithography. As such, they stand to accelerate how materials are discovered for applications spanning catalysis, optics, and more. However, a long-standing challenge is the availability of substrates compatible with megalibrary synthesis, which limits the structural and functional design space that can be explored. To address this challenge, thermally removable polystyrene films were developed as universal substrate coatings that decouple lithography-enabled nanoparticle synthesis from the underlying substrate chemistry, thus providing consistent lithography parameters on diverse substrates. Multi-spray inking of the scanning probe arrays with polymer solutions containing metal salts allows patterning of >56 million nanoreactors designed to vary in composition and size. These are subsequently converted to inorganic nanoparticles via reductive thermal annealing, which also removes the polystyrene to deposit the megalibrary. Megalibraries with mono-, bi-, and trimetallic materials were synthesized, and nanoparticle size was controlled between 5 and 35 nm by modulating the lithography speed. Importantly, the polystyrene coating can be used on conventional substrates like Si/SiOx, as well as substrates typically more difficult to pattern on, such as glassy carbon, diamond, TiO2, BN, W, or SiC. Finally, high-throughput materials discovery is performed in the context of photocatalytic degradation of organic pollutants using Au-Pd-Cu nanoparticle megalibraries on TiO2 substrates with 2,250,000 unique composition/size combinations. The megalibrary was screened within 1 h by developing fluorescent thin-film coatings on top of the megalibrary as proxies for catalytic turnover, revealing Au0.53Pd0.38Cu0.09-TiO2 as the most active photocatalyst composition.

Supramolecular Enhancement of Electrochemical Nitrate Reduction Catalyzed by Cobalt Porphyrin Organic Cages for Ammonia Electrosynthesis in Water.

The electrochemical nitrate (NO3 - ) reduction reaction (NO3 RR) to ammonia (NH3 ) represents a sustainable approach for denitrification to balance global nitrogen cycles and an alternative to traditional thermal Haber-Bosch processes. Here, we present a supramolecular strategy for promoting NH3 production in water from NO3 RR by integrating two-dimensional (2D) molecular cobalt porphyrin (CoTPP) units into a three-dimensional (3D) porous organic cage architecture. The porphyrin box CoPB-C8 enhances electrochemical active site exposure, facilitates substrate-catalyst interactions, and improves catalyst stability, leading to turnover numbers and frequencies for NH3 production exceeding 200,000 and 56 s-1 , respectively. These values represent a 15-fold increase in NO3 RR activity and 200-mV improvement in overpotential for the 3D CoPB-C8 box structure compared to its 2D CoTPP counterpart. Synthetic tuning of peripheral alkyl substituents highlights the importance of supramolecular porosity and cavity size on electrochemical NO3 RR activity. These findings establish the incorporation of 2D molecular units into 3D confined space microenvironments as an effective supramolecular design strategy for enhancing electrocatalysis.

Synergistic Porosity and Charge Effects in a Supramolecular Porphyrin Cage Promote Efficient Photocatalytic CO2 Reduction.

We present a supramolecular approach to catalyzing photochemical CO2 reduction through second-sphere porosity and charge effects. An iron porphyrin box (PB) bearing 24 cationic groups, FePB-2(P), was made via post-synthetic modification of an alkyne-functionalized supramolecular synthon. FePB-2(P) promotes the photochemical CO2 reduction reaction (CO2 RR) with 97 % selectivity for CO product, achieving turnover numbers (TON) exceeding 7000 and initial turnover frequencies (TOFmax ) reaching 1400 min-1 . The cooperativity between porosity and charge results in a 41-fold increase in activity relative to the parent Fe tetraphenylporphyrin (FeTPP) catalyst, which is far greater than analogs that augment catalysis through porosity (FePB-3(N), 4-fold increase) or charge (Fe p-tetramethylanilinium porphyrin (Fe-p-TMA), 6-fold increase) alone. This work establishes that synergistic pendants in the secondary coordination sphere can be leveraged as a design element to augment catalysis at primary active sites within confined spaces.

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.

Hybrid Catalysts for Artificial Photosynthesis: Merging Approaches from Molecular, Materials, and Biological Catalysis.

Increasing demand for sustainable energy sources continues to motivate the development of new catalytic processes that store intermittent energy in the form of chemical bonds. In this context, photosynthetic organisms harvest light to drive dark reactions reducing carbon dioxide, an abundant and accessible carbon source, to store solar energy in the form of glucose and other biomass feedstocks. Inspired by this biological process, the field of artificial photosynthesis aims to store renewable energy in chemical bonds spanning fuels, foods, medicines, and materials using light, water, and CO2 as the primary chemical feedstocks, with the added benefit of mitigating the accumulation of CO2 as a greenhouse gas in the atmosphere. As such, devising new catalyst platforms for transforming CO2 into value-added chemical products is of importance. Historically, catalyst design for artificial photosynthesis has been approached from the three traditional fields of catalysis: molecular, materials, and biological. In this Account, we show progress from our laboratory in constructing new hybrid catalysts for artificial photosynthesis that draw upon design concepts from all three of these traditional fields of catalysis and blur the boundaries between them. Starting with molecular catalysis, we incorporated biological design elements that are prevalent in enzymes into synthetic systems. Specifically, we demonstrated that proper positioning of intramolecular hydrogen bond donors or addition of intermolecular multipoint hydrogen bond donors with classic iron porphyrin and nickel cyclam platforms can substantially increase rates of CO2 reduction and break electronic scaling relationships. In parallel, we incorporated a key materials design element, namely, high surface area and porosity for maximizing active site exposure, into molecular systems. A supramolecular porous organic cage molecule was synthesized with iron porphyrin building blocks, and the porosity was observed to facilitate substrate and charge transport through the catalyst film. In turn, molecular design elements can be incorporated into materials catalysts for CO2 reduction. First, we utilized molecular synthons in a bottom-up reticular approach to drive polymerization/assembly into a bulk framework material. Second, we established an organometallic approach in which molecular ligands, including chelating ones, are adsorbed onto a bulk inorganic solid to create and tune new active sites on surfaces. Finally, we describe two examples in which molecular, materials, and biological design elements are all integrated to catalyze the reduction of CO2 into CH4 using a hybrid biological-materials interface with sustainably generated H2 as the reductant or to reduce CO into value-added C2 products acetate and ethanol using a hybrid molecular-materials interface to construct a biomimetic, bimetallic active site. Taken together, our program in catalysis for energy and sustainability has revealed that combining more conventional design strategies in synergistic ways can lead to advances in artificial photosynthesis.

Metal-Ligand Cooperativity via Exchange Coupling Promotes Iron- Catalyzed Electrochemical CO2 Reduction at Low Overpotentials.

Biological and heterogeneous catalysts for the electrochemical CO2 reduction reaction (CO2RR) often exhibit a high degree of electronic delocalization that serves to minimize overpotential and maximize selectivity over the hydrogen evolution reaction (HER). Here, we report a molecular iron(II) system that captures this design concept in a homogeneous setting through the use of a redox non-innocent terpyridine-based pentapyridine ligand (tpyPY2Me). As a result of strong metal-ligand exchange coupling between the Fe(II) center and ligand, [Fe(tpyPY2Me)]2+ exhibits redox behavior at potentials 640 mV more positive than the isostructural [Zn(tpyPY2Me)]2+ analog containing the redox-inactive Zn(II) ion. This shift in redox potential is attributed to the requirement for both an open-shell metal ion and a redox non-innocent ligand. The metal-ligand cooperativity in [Fe(tpyPY2Me)]2+ drives the electrochemical reduction of CO2 to CO at low overpotentials with high selectivity for CO2RR (>90%) and turnover frequencies of 100 000 s-1 with no degradation over 20 h. The decrease in the thermodynamic barrier engendered by this coupling also enables homogeneous CO2 reduction catalysis in water without compromising selectivity or rates. Synthesis of the two-electron reduction product, [Fe(tpyPY2Me)]0, and characterization by X-ray crystallography, Mössbauer spectroscopy, X-ray absorption spectroscopy (XAS), variable temperature NMR, and density functional theory (DFT) calculations, support assignment of an open-shell singlet electronic structure that maintains a formal Fe(II) oxidation state with a doubly reduced ligand system. This work provides a starting point for the design of systems that exploit metal-ligand cooperativity for electrocatalysis where the electrochemical potential of redox non-innocent ligands can be tuned through secondary metal-dependent interactions.

An NADH-Inspired Redox Mediator Strategy to Promote Second-Sphere Electron and Proton Transfer for Cooperative Electrochemical CO2 Reduction Catalyzed by Iron Porphyrin.

We present a bioinspired strategy for enhancing electrochemical carbon dioxide reduction catalysis by cooperative use of base-metal molecular catalysts with intermolecular second-sphere redox mediators that facilitate both electron and proton transfer. Functional synthetic mimics of the biological redox cofactor NADH, which are electrochemically stable and are capable of mediating both electron and proton transfer, can enhance the activity of an iron porphyrin catalyst for electrochemical reduction of CO2 to CO, achieving a 13-fold rate improvement without altering the intrinsic high selectivity of this catalyst platform for CO2 versus proton reduction. Evaluation of a systematic series of NADH analogues and redox-inactive control additives with varying proton and electron reservoir properties reveals that both electron and proton transfer contribute to the observed catalytic enhancements. This work establishes that second-sphere dual control of electron and proton inventories is a viable design strategy for developing more effective electrocatalysts for CO2 reduction, providing a starting point for broader applications of this approach to other multielectron, multiproton transformations.

Supramolecular Tuning Enables Selective Oxygen Reduction Catalyzed by Cobalt Porphyrins for Direct Electrosynthesis of Hydrogen Peroxide.

We report a supramolecular strategy for promoting the selective reduction of O2 for direct electrosynthesis of H2 O2 . We utilized cobalt tetraphenylporphyrin (Co-TPP), an oxygen reduction reaction (ORR) catalyst with highly variable product selectivity, as a building block to assemble the permanently porous supramolecular cage Co-PB-1(6) bearing six Co-TPP subunits connected through twenty-four imine bonds. Reduction of these imine linkers to amines yields the more flexible cage Co-rPB-1(6). Both Co-PB-1(6) and Co-rPB-1(6) cages produce 90-100 % H2 O2 from electrochemical ORR catalysis in neutral pH water, whereas the Co-TPP monomer gives a 50 % mixture of H2 O2 and H2 O. Bimolecular pathways have been implicated in facilitating H2 O formation, therefore, we attribute this high H2 O2 selectivity to site isolation of the discrete molecular units in each supramolecule. The ability to control reaction selectivity in supramolecular structures beyond traditional host-guest interactions offers new opportunities for designing such architectures for a broader range of catalytic applications.

Iron Porphyrins Embedded into a Supramolecular Porous Organic Cage for Electrochemical CO2 Reduction in Water.

A porous organic cage composed of six iron tetraphenylporphyrins was used as a supramolecular catalyst for electrochemical CO2 -to-CO conversion. This strategy enhances active site exposure and substrate diffusion relative to the monomeric catalyst, resulting in CO generation with near-quantitative Faradaic efficiency in pH 7.3 water, with activities reaching 55 250 turnovers. These results provide a starting point for the design of supramolecular catalysts that can exploit the properties of the surrounding matrix yet retain the tunability of the original molecular unit.

Chelating N-Heterocyclic Carbene Ligands Enable Tuning of Electrocatalytic CO2 Reduction to Formate and Carbon Monoxide: Surface Organometallic Chemistry.

Reported here is the chelate effect as a design principle for tuning heterogeneous catalysts for electrochemical CO2 reduction. Palladium functionalized with a chelating tris-N-heterocyclic carbene (NHC) ligand (Pd-timtmbMe ) exhibits a 32-fold increase in activity for electrochemical reduction of CO2 to C1 products with high Faradaic efficiency (FEC1 =86 %) compared to the parent unfunctionalized Pd foil (FE=23 %), and with sustained activity relative to a monodentate NHC-ligated Pd electrode (Pd-mimtmbMe ). The results highlight the contributions of the chelate effect for tailoring and maintaining reactivity at molecular-materials interfaces enabled by surface organometallic chemistry.

Osmoprotective polymer additives attenuate the membrane pore-forming activity of antimicrobial peptoids.

Antimicrobial peptides (AMPs) are critical components of the innate immune system and exhibit bactericidal activity against a broad spectrum of bacteria. We investigated the use of N-substituted glycine peptoid oligomers as AMP mimics with potent antimicrobial activity. The antimicrobial mechanism of action varies among different AMPs, but many of these peptides can penetrate bacterial cell membranes, causing cell lysis. We previously hypothesized that amphiphilic cyclic peptoids may act through a similar pore formation mechanism against methicillin-resistant Staphylococcus aureus (MRSA). Peptoid-induced membrane disruption is observed by scanning electron microscopy and results in a loss of membrane integrity. We demonstrate that the antimicrobial activity of the peptoids is attenuated with the addition of polyethylene glycol osmoprotectants, signifying protection from a loss of osmotic balance. This decrease in antimicrobial activity is more significant with larger osmoprotectants, indicating that peptoids form pores with initial diameters of ∼2.0-3.8 nm. The initial membrane pores formed by cyclic peptoid hexamers are comparable in diameter to those formed by larger and structurally distinct AMPs. After 24 h, the membrane pores expand to >200 nm in diameter. Together, these results indicate that cyclic peptoids exhibit a mechanism of action that includes effects manifested at the cell membrane of MRSA.

Positional effects of second-sphere amide pendants on electrochemical CO2 reduction catalyzed by iron porphyrins.

The development of catalysts for electrochemical reduction of carbon dioxide offers an attractive approach to transforming this greenhouse gas into value-added carbon products with sustainable energy input. Inspired by natural bioinorganic systems that feature precisely positioned hydrogen-bond donors in the secondary coordination sphere to direct chemical transformations occurring at redox-active metal centers, we now report the design, synthesis, and characterization of a series of iron tetraphenylporphyrin (Fe-TPP) derivatives bearing amide pendants at various positions at the periphery of the metal core. Proper positioning of the amide pendants greatly affects the electrocatalytic activity for carbon dioxide reduction to carbon monoxide. In particular, derivatives bearing proximal and distal amide pendants on the ortho position of the phenyl ring exhibit significantly larger turnover frequencies (TOF) compared to the analogous para-functionalized amide isomers or unfunctionalized Fe-TPP. Analysis of TOF as a function of catalyst standard reduction potential enables first-sphere electronic effects to be disentangled from second-sphere through-space interactions, suggesting that the ortho-functionalized porphyrins can utilize the latter second-sphere property to promote CO2 reduction. Indeed, the distally-functionalized ortho-amide isomer shows a significantly larger through-space interaction than its proximal ortho-amide analogue. These data establish that proper positioning of secondary coordination sphere groups is an effective design element for breaking electronic scaling relationships that are often observed in electrochemical CO2 reduction.

Supramolecular Porphyrin Cages Assembled at Molecular-Materials Interfaces for Electrocatalytic CO Reduction.

Conversion of carbon monoxide (CO), a major one-carbon product of carbon dioxide (CO2) reduction, into value-added multicarbon species is a challenge to addressing global energy demands and climate change. Here we report a modular synthetic approach for aqueous electrochemical CO reduction to carbon-carbon coupled products via self-assembly of supramolecular cages at molecular-materials interfaces. Heterobimetallic cavities formed by face-to-face coordination of thiol-terminated metalloporphyrins to copper electrodes through varying organic struts convert CO to C2 products with high faradaic efficiency (FE = 83% total with 57% to ethanol) and current density (1.34 mA/cm2) at a potential of -0.40 V vs RHE. The cage-functionalized electrodes offer an order of magnitude improvement in both selectivity and activity for electrocatalytic carbon fixation compared to parent copper surfaces or copper functionalized with porphyrins in an edge-on orientation.

BONLAC: A combinatorial proteomic technique to measure stimulus-induced translational profiles in brain slices.

Stimulus-triggered protein synthesis is critical for brain health and function. However, due to technical hurdles, de novo neuronal translation is predominantly studied in cultured cells, whereas electrophysiological and circuit analyses often are performed in brain slices. The different properties of these two experimental systems create an information gap about stimulus-induced alterations in the expression of new proteins in mature circuits. To address this, we adapted two existing techniques, BONCAT and SILAC, to a combined proteomic technique, BONLAC, for use in acute adult hippocampal slices. Using BDNF-induced protein synthesis as a proof of concept, we found alterations in expression of proteins involved in neurotransmission, trafficking, and cation binding that differed from those found in a similar screen in cultured neurons. Our results indicate important differences between cultured neurons and slices, and suggest that BONLAC could be used to dissect proteomic changes underlying synaptic events in adult circuits. This article is part of the Special Issue entitled 'Synaptopathy--from Biology to Therapy'.

Endogenous antibodies for tumor detection.

The study of cancer immunology has provided diagnostic and therapeutic instruments through serum autoantibody biomarkers and exogenous monoclonal antibodies. While some endogenous antibodies are found within or surrounding transformed tissue, the extent to which this exists has not been entirely characterized. We find that in transgenic and xenograft mouse models of cancer, endogenous gamma immunoglobulin (IgG) is present at higher concentration in malignantly transformed organs compared to non-transformed organs in the same mouse or organs of cognate wild-type mice. The enrichment of endogenous antibodies within the malignant tissue provides a potential means of identifying and tracking malignant cells in vivo as they mutate and diversify. Exploiting these antibodies for diagnostic and therapeutic purposes is possible through the use of agents that bind endogenous antibodies.