The present study examines the synthesis of unique Cu nanostructured model catalysts and their catalytic activity toward CO2 hydrogenation under moderate temperature and pressure reaction conditions. ...Cu-based nanoparticles (NPs) were synthesized by two chemical deposition methods: (1) 5 nm spherical Cu(OH)2 NPs deposited on highly oriented pyrolytic graphite (HOPG) by exposing the HOPG substrate to a colloidal solution of copper, and (2) photocatalytic reduction of Cu(H2O)62+ onto a high density of 15 nm TiO2 NPs grown on HOPG by physical vapor deposition. This photocatalytic reduction results in the deposition of mixed Cu(OH)2 and Cu2O films, while few-nm sized Cu-based NPs are formed on the TiO2 NPs upon subsequent reduction. The chemistry, structure, and morphology of the resulting samples were characterized using X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). The thermocatalytic activity for the CO2 reduction reaction (CO2RR) under H2 was evaluated with synchrotron-based ambient pressure X-ray photoelectron spectroscopy (AP-XPS) and temperature-programmed desorption (TPD) experiments. Several intermediates, including CO2 δ−, HCOO, O–CH3, CO3 2–, CH x , and CO, were observed using AP-XPS. The TiO2 NPs show activity toward the formation of methanol (CH3OH) that occurs mainly through an O–CH3 intermediate. The TiO2 NPs-core–carbon-shell (TiO2@C NPs) shows a clear selectivity toward methane (CH4). The Cu/TiO2 NPs show, however, an activity toward CO, CH4, and CH3OH that depends strongly on the percentage of oxygen present on the Cu NPs surface. This study particularly shows the importance played by the TiO2 NPs for CO2 adsorption and activation and the Cu NPs for H2 and CO2 dissociation. The CO2RR mechanisms are discussed on the basis of the intermediate formation and the surface structure and composition.
The identification of the active sites for the electrochemical reduction of CO2 (CO2RR) to specific chemical products is elusive, owing in part to insufficient data gathered on clean and atomically ...well‐ordered electrode surfaces. Here, ultrahigh vacuum based preparation methods and surface science characterization techniques are used with gas chromatography to demonstrate that subtle changes in the preparation of well‐oriented Cu(100) and Cu(111) single‐crystal surfaces drastically affect their CO2RR selectivity. Copper single crystals with clean, flat, and atomically ordered surfaces are predicted to yield hydrocarbons; however, these were found experimentally to favor the production of H2. Only when roughness and defects are introduced, for example by electrochemical etching or a plasma treatment, are significant amounts of hydrocarbons generated. These results show that structural and morphological effects are the key factors determining the catalytic selectivity of CO2RR.
Subtle changes in the preparation of well‐oriented Cu(100) and Cu(111) single‐crystal surfaces affect their CO2RR selectivity. Clean, flat, atomically ordered surfaces are predicted to yield hydrocarbons; but these actually favor production of H2. Only when roughness and defects are introduced, significant amounts of hydrocarbons are generated. Structural and morphological effects are the key factors determining the catalytic selectivity of CO2RR.
Chemical cross-linking combined with mass spectrometry is a technique used to study protein structures and identify protein complexes. Traditionally, chemical cross-linkers contain two reactive ...groups, allowing them to covalently bond a pair of proximal residues, either within a protein or between two proteins. The output of a cross-linking experiment is a list of interacting site pairs that provide structural constraints for modeling of new structures and complexes. Due to the binary reactive nature of cross-linking reagents, only pairs of interacting sites can be directly observed, and assembly of higher-order structures typically requires prior knowledge of complex composition or iterative docking to produce a putative model. Here, we describe a new tetrameric cross-linker bearing four amine-reactive groups, allowing it to covalently link up to four proteins simultaneously and a real-time instrument method to facilitate the identification of these tetrameric cross-links. We applied this new cross-linker to isolated mitochondria and identified a number of higher-order cross-links in various OXPHOS complexes and ATP synthase, demonstrating its utility in characterizing complex interfaces. We also show that higher-order cross-links can be used to effectively filter models of large protein assemblies generated by using Alphafold. Higher-dimensional cross-linking provides a new avenue for characterizing multiple protein interfaces, even in complex samples such as intact mitochondria.
Chemical cross-linking with mass spectrometry (XL-MS) has emerged as a useful tool for the large-scale study of protein structures and interactions from complex biological samples including intact ...cells and tissues. Quantitative XL-MS (qXL-MS) provides unique information on protein conformational and interaction changes resulting from perturbations such as drug treatment and disease state. Previous qXL-MS studies relied on the incorporation of stable isotopes into the cross-linker (primarily deuterium) or metabolic labeling with SILAC. Here, we introduce isobaric quantitative protein interaction reporter (iqPIR) technology which utilizes stable isotopes selectively incorporated into the cross-linker design, allowing for isobaric cross-linked peptide pairs originating from different samples to display distinct quantitative isotope signatures in tandem mass spectra. This enables improved quantitation of cross-linked peptide levels from proteome-wide samples because of the reduced complexity of tandem mass spectra relative to MS
spectra. In addition, because of the isotope incorporation in the reporter and the residual components of the cross-linker that remain on released peptides, each fragmentation spectrum can offer multiple independent opportunities and, therefore, improved confidence for quantitative assessment of the cross-linker pair level. Finally, in addition to providing information on solvent accessibility of lysine sites, dead end iqPIR cross-linked products can provide protein abundance and/or lysine site modification level information all from a single in vivo cross-linking experiment.
Tuning the properties of oxide surfaces through the adsorption of designed ligands is highly desirable for several applications, such as catalysis. N-Heterocyclic carbenes (NHCs) have been ...successfully employed as ligands for the modification of metallic surfaces. On the other hand, their potential as modifiers of ubiquitous oxide surfaces still needs to be developed. Here we show that a model NHC binds covalently to a copper oxide surface under UHV conditions. In particular, we report the first example of a covalent bond between NHCs and oxygen atoms from the oxide layer. This study demonstrates that NHC can also act as a strong anchor on oxide surfaces.
This protocol describes a workflow for utilizing large-scale cross-linking with mass spectrometry (XL-MS) to make systems-level structural biology measurements in complex biological samples, ...including cells, isolated organelles, and tissue samples. XL-MS is a structural biology technique that provides information on the molecular structure of proteins and protein complexes using chemical probes that report the proximity of probe-reactive amino acids within proteins, typically lysine residues. Information gained through XL-MS studies is often complementary to more traditional methods, such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy. The use of MS-cleavable cross-linkers, including protein interaction reporter (PIR) technologies, enables XL-MS studies on protein structures and interactions in extremely complex biological samples, including intact living cells. PIR cross-linkers are designed to contain chemical bonds at specific locations within the cross-linker molecule that can be selectively cleaved by collision-induced dissociation or UV light. When broken, these bonds release the intact peptides that were cross-linked, as well as a reporter ion. Conservation of mass dictates that the sum of the two released peptide masses and the reporter mass equals the measured precursor mass. This relationship is used to identify cross-linked peptide pairs. Release of the individual peptides permits accurate measurement of their masses and independent amino acid sequence determination by tandem MS, allowing the use of standard proteomics search engines such as Comet for peptide sequence assignment, greatly simplifying data analysis of cross-linked peptide pairs. Search results are processed with XLinkProphet for validation and can be uploaded into XlinkDB for interaction network and structural analysis.
Liquid jet X-ray photoelectron spectroscopy is used under near ambient pressure conditions to characterize Fe2+ aqueous solutions. Counter ions, such as Cl– and Br– ions, added to the solution lead ...to changes in the first solvation sphere of the Fe-aqua complex in solution. Binding energy shifts of 0.4 eV to lower binding energy are observed in the Cl 2p spectra, 2 eV to higher binding energy in the Fe 2p spectra and no shifts are observed in the Br 3d spectra. Depletion of the Cl– species is observed at the interface, caused by coordination with Fe2+. Depletion of Cl– at the liquid/vapor interface may have significant impacts on oxidative chemistry at the interface of atmospheric aerosols that contain both chloride and iron. The Cl– complexation with the Fe2+ ions will also affect the Fenton chemistry that is dependent on this metal ion.
Liquid jet X-ray photoelectron spectroscopy was used to investigate changes in the local electronic structure of acetic acid in the bulk of aqueous solutions induced by solvation effects. These ...effects manifest themselves as shifts in the difference in the carbon 1s binding energy (ΔBE) between the methyl and carboxyl carbons of acetic acid. Furthermore, molecular dynamics simulations, coupled with correlated electronic structure calculations of the first solvation sphere, provide insight into the number of water molecules directly interacting with the carboxyl group that are required to match the ΔBE from the photoelectron spectroscopy experiments. This comparison shows that a single water molecule in the first solvation shell describes the photoelectron ΔBE of acetic acid while at least 20 water molecules are required for the conjugate base, acetate, in aqueous solutions.
Rationale
Hybrid mass spectrometers combine multiple mass analyzers to achieve optimal performance in terms of tandem mass spectrometry, high mass resolving power, and mass measurement accuracy for ...studying highly complex samples. As a result, the need for transport, trapping, and control of ion kinetic energies is critical for the successful integration of multiple mass analyzers and hybrid instrument operation. In addition, transportation of ion populations between two physically distinct locations can result in time‐of‐flight (TOF) discrimination against ions with widely disparate m/z values, compromising full mass spectral performance. In this work, we demonstrated a new ion guide, referred to as a planar quadrupole (PQ) ion guide, composed of two parallel printed circuit boards (PCB) that allow radiofrequency (RF) and direct current (DC) voltages to be combined to enable both axial transport and trapping of ion populations in the ultrahigh vacuum region of the mass spectrometer. As compared with a conventional multipole ion guide, the PQ ion guide showed comparable performance in ion m/z values, signal‐to‐noise, and intensity and effectively reduced mass discrimination caused by TOF effects.
Methods
A PQ device was developed with two PCBs and simulated with SIMION 8.1. Electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry instrumentation were used for the testing of PQ performance.
Results
.In this work, we demonstrated a planar quadrupole (PQ) ion guide composed of two parallel PCB plates. The PQ enables both axial ion transport and trapping of ion populations throughout the ion transfer process from a LTQ to an ICR cell. As compared with a conventional multipole ion guide, the PQ showed comparable ion transmission efficiency and effectively reduced mass discrimination caused by TOF effects.
Conclusions
The PQ is a simple design that can be implemented for ion transmission and trapping on virtually any mass spectrometer.
Chemical cross-linking with mass spectrometry (XL-MS) has emerged as a useful technique for interrogating protein structures and interactions. When combined with quantitative proteomics strategies, ...protein conformational and interaction dynamics can be probed. Quantitative XL-MS has been demonstrated with the use of stable isotopes incorporated metabolically or into the cross-linker molecules. Isotope-labeled cross-linkers have primarily utilized deuterium and rely on MS1-based quantitation of precursor ion extracted ion chromatograms. Recently the development and application of isobaric quantitative protein interaction reporter (iqPIR) cross-linkers were reported, which utilize 13C and 15N isotope labels. Quantitation is accomplished using relative fragment ion isotope abundances in tandem mass spectra. Here we describe the synthesis and initial evaluation of a multiplexed set of iqPIR molecules, allowing for up to six cross-linked samples to be quantified simultaneously. To analyze data for such cross-linkers, the two-channel mode of iqPIR quantitative analysis was adapted to accommodate any number of channels with defined ion isotope peak mass offsets. The summed ion peak intensities in the overlapping channel isotope envelopes are apportioned among the channels to minimize the difference with respect to the predicted ion isotope envelopes. The result is accurate and reproducible relative quantitation enabling direct comparison among six differentially labeled cross-linked samples. The approach described here is generally extensible for the iqPIR strategy, accommodating future iqPIR reagent design, and enables large-scale in vivo quantitative XL-MS investigation of the interactome.
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