Adsorbate-Induced Adatom Formation on Lithium, Iron, Cobalt, Ruthenium, and Rhenium Surfaces

Recent experimental and theoretical studies have demonstrated the reaction-driven metal-metal bond breaking in metal catalytic surfaces even under relatively mild conditions. Here, we construct a density functional theory (DFT) database for the adsorbate-induced adatom formation energy on the close-packed facets of three hexagonal close-packed metals (Co, Ru, and Re) and two body-centered cubic metals (Li and Fe), where the source of the ejected metal atom is either a step edge or a close-packed surface. For Co and Ru, we also considered their metastable face-centered cubic structures. We studied 18 different adsorbates relevant to catalytic processes and predicted noticeably easier adatom formation on Li and Fe compared to the other three metals. The NH3- and CO-induced adatom formation on Fe(110) is possible at room temperature, a result relevant to NH3 synthesis and Fischer-Tropsch synthesis, respectively. There also exist other systems with favorable adsorbate effects for adatom formation relevant to catalytic processes at elevated temperatures (500-700 K). Our results offer insight into the reaction-driven formation of metal clusters, which could play the role of active sites in reactions catalyzed by Li, Fe, Co, Ru, and Re catalysts.

In Situ/Operando Characterization Techniques of Electrochemical CO2 Reduction

Electrocatalytic conversion of carbon dioxide to valuable chemicals and fuels driven by renewable energy plays a crucial role in achieving net-zero carbon emissions. Understanding the structure-activity relationship and the reaction mechanism is significant for tuning electrocatalyst selectivity. Therefore, characterizing catalyst dynamic evolution and reaction intermediates under reaction conditions is necessary but still challenging. We first summarize the most recent progress in mechanistic understanding of heterogeneous CO2/CO reduction using in situ/operando techniques, including surface-enhanced vibrational spectroscopies, X-ray- and electron-based techniques, and mass spectroscopy, along with discussing remaining limitations. We then offer insights and perspectives to accelerate the future development of in situ/operando techniques.

Enriching Reaction Intermediates in Multishell Structured Copper Catalysts for Boosted Propanol Electrosynthesis from Carbon Monoxide

Fine-tuned catalysts that alter the diffusion kinetics of reaction intermediates is of great importance for achieving high-performance multicarbon (C₂₊) product generation in carbon monoxide (CO) reduction. Herein, we conduct a structural design based on Cu₂O nanoparticles and present an effective strategy for enhancing propanol electrosynthesis from CO. The electrochemical characterization, operando Raman monitoring, and finite-element method simulations reveal that the multishell structured catalyst can realize the enrichment of C₁ and C₂ intermediates by nanoconfinement space, leading to the possibility of further coupling. Consequently, the multishell copper catalyst realizes a high Faraday efficiency of 22.22 ± 0.38% toward propanol at the current density of 50 mA cm^-2.

Doping of Cr to Regulate the Valence State of Cu and Co Contributes to Efficient Water Splitting

Water electrolysis in alkaline media is the most promising technology for hydrogen production, but efficient electrocatalysts are required to reduce the overpotential in HER and OER processes. In this work, the multicomponent transition metal catalyst Cr-Cu/CoO_x was loaded on copper foam by electrodeposition and annealing, and the catalyst exhibited excellent electrochemical activity. The HER overpotential is 21 mV and the OER overpotential is 252 mV at a current density of 10 mA cm^-2. The overall water splitting voltage is 1.51 V, even better than the Pt/C//RuO₂ two-electrode system (1.61 V). The excellent performance of this catalyst is mainly derived from the close synergistic interaction among Cu, Co, and Cr. The doping of Cr modulates the valence states of Cu and Co at the active sites and improves the adsorption of various reaction intermediates. Density functional theory (DFT) calculations show that the doping of Cr can optimize the adsorption of the reaction intermediate H*. Meanwhile, the high-valent Cr and Co promote hydrolysis through strong adsorption with OH^-. The present work provides a reasonable strategy for designing low-cost transition metals as efficient catalysts for water electrolysis.

Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases

X-rays used to collect crystallographic data can change the redox states of transition metals utilized by many biological systems including metalloproteins. This disadvantage has been harnessed to drive a complex chemical reaction requiring the delivery of an electron to the active site and recording the structural changes accompanying catalysis, providing a real-time structural movie of an enzymatic reaction, which has been a dream of enzymologists for decades. By coupling the multiple-structures from one crystal technique with single-crystal and solution optical spectroscopy, we show that the electron transfer between the electron accepting type-1 Cu and catalytic type-2 Cu redox centers is gated in a recently characterized copper nitrite reductase. This combined structural/spectroscopic approach is applicable to many complex redox biological systems.

Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br^2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.

Ion spectroscopy in methane activation

This review is devoted to ion spectroscopy studies of complexes relevant for the understanding of methane activation with metal ions and clusters. Methane activation starts with the formation of a complex with a metal ion. The degree of the interaction between an intact methane molecule and the ion can be monitored by the perturbations of C-H stretch vibrations in the methane molecule. Binding mediated by the electrostatic interaction results in a η³ type coordination of methane. In contrast, binding governed by orbital interactions results in a η² type coordination of methane. We further review the spectroscopic characterization of activation products of metal-methane reactions, such as the metal-carbene and carbyne products resulting from the interaction of selected 5d metals with methane. The focus of recent research in the field has shifted towards the investigation of interactions between methane and metal clusters. We show examples highlighting that metal clusters can be more reactive in methane activation reactions.

An aggregation inhibitor specific to oligomeric intermediates of Aβ42 derived from phage display libraries of stable, small proteins

Alzheimer’s disease affects a growing number of people, but a cure is lacking. The disease is connected to the formation of plaques in the brain, the first of which appear years before the first symptoms. Current approaches fail to stop or revert the propagation of these plaques, which are also a source of neurotoxic species in the form of oligomers. This work represents two directions toward therapeutic developments: 1) the design and production of protein libraries based on a small and stable scaffold, and 2) the realization of a screening procedure that allows for the identification of oligomer binders. The approach is successful in identifying a candidate protein that binds to oligomers and reduces the rate of plaque proliferation.

The self-assembly of amyloid β peptide (Aβ) to fibrillar and oligomeric aggregates is linked to Alzheimer’s disease. Aβ binders may serve as inhibitors of aggregation to prevent the generation of neurotoxic species and for the detection of Aβ species. A particular challenge involves finding binders to on-pathway oligomers given their transient nature. Here we construct two phage–display libraries built on the highly inert and stable protein scaffold S100G, one containing a six-residue variable surface patch and one harboring a seven-residue variable loop insertion. Monomers and fibrils of Aβ40 and Aβ42 were separately coupled to silica nanoparticles, using a coupling strategy leading to the presence of oligomers on the monomer beads, and they were used in three rounds of affinity selection. Next-generation sequencing revealed sequence clusters and candidate binding proteins (SXkmers). Two SXkmers were expressed as soluble proteins and tested in terms of aggregation inhibition via thioflavin T fluorescence. We identified an SXkmer with loop–insertion YLTIRLM as an inhibitor of the secondary nucleation of Aβ42 and binding analyses using surface plasmon resonance technology, Förster resonance energy transfer, and microfluidics diffusional sizing imply an interaction with intermediate oligomeric species. A linear peptide with the YLTIRLM sequence was found inhibitory but at a lower potency than the more constrained SXkmer loop. We identified an SXkmer with side-patch VI-WI-DD as an inhibitor of Aβ40 aggregation. Remarkably, our data imply that SXkmer-YLTIRLM blocks secondary nucleation through an interaction with oligomeric intermediates in solution or at the fibril surface, which is a unique inhibitory mechanism for a library-derived inhibitor.

Comprehension of the Route for the Synthesis of Co/Fe LDHs via the Method of Coprecipitation with Varying pH

Co/Fe-based layered double hydroxides (LDHs) are among the most promising materials for electrochemical applications, particularly in the development of energy storage devices, such as electrochemical capacitors. They have also been demonstrated to function as energy conversion catalysts in photoelectrochemical applications for CO2 conversion into valuable chemicals. Understanding the formation mechanisms of such compounds is therefore of prime interest for further controlling the chemical composition, structure, morphology, and/or reactivity of synthesized materials. In this study, a combination of X-ray diffraction, vibrational and absorption spectroscopies, as well as physical and chemical analyses were used to provide deep insight into the coprecipitation formation mechanisms of Co/Fe-based LDHs under high supersaturation conditions. This procedure consists of adding an alkaline aqueous solution (2.80 M NaOH and 0.78 M Na2CO3) into a cationic solution (0.15 M CoII and 0.05 M FeIII) and varying the pH until the desired pH value is reached. Beginning at pH 2, pH increases induce precipitation of FeIII as ferrihydrite, which is the pristine reactional intermediate. From pH > 2, CoII sorption on ferrihydrite promotes a redox reaction between FeIII of ferrihydrite and the sorbed CoII. The crystallinity of the poorly crystalized ferrihydrite progressively decreases with increasing pH. The combination of such a phenomenon with the hydrolysis of both the sorbed CoIII and free CoII generates pristine hydroxylated FeII/CoIII LDHs at pH 7. Above pH 7, free CoII hydrolysis proceeds, which is responsible for the local dissolution of pristine LDHs and their reprecipitation and then 3D organization into CoII4FeII2CoIII2 LDHs. The progressive incorporation of CoII into the LDH structure is accountable for two phenomena: decreased coulombic attraction between the positive surface-charge sites and the interlayer anions and, concomitantly, the relative redox potential evolution of the redox species, such as when FeII is re-oxidized to FeIII, while CoIII is re-reduced to CoII, returning to a CoII6FeIII2 LDH. The nature of the interlamellar species (OH−, HCO3−, CO32− and NO3−) depends on their mobility and the speciation of anions in response to changing pH.

Metalloenzymes for Fatty Acid-Derived Hydrocarbon Biosynthesis: Nature's Cryptic Catalysts

Waning resources, massive energy consumption, everdeepening global warming crisis, and climate change have raised grave concerns regarding continued dependence on fossil fuels as the predominant source of energy and generated tremendous interest for developing biofuels, which are renewable. Hydrocarbon-based 'drop-in' biofuels can be a proper substitute for fossil fuels such as gasoline or jet fuel. In Nature, hydrocarbons are produced by diverse organisms such as insects, plants, bacteria, and cyanobacteria. Metalloenzymes play a crucial role in hydrocarbons biosynthesis, and the past decade has witnessed discoveries of a number of metalloenzymes catalyzing hydrocarbon biosynthesis from fatty acids and their derivatives employing unprecedented mechanisms. These discoveries elucidated the enigma related to the divergent chemistries involved in the catalytic mechanisms of these metalloenzymes. There is substantial diversity in the structure, mode of action, cofactor requirement, and substrate scope among these metalloenzymes. Detailed structural analysis along with mutational studies of some of these enzymes have contributed significantly to identifying the key amino acid residues that dictate substrate specificity and catalytic intricacy. In this Review, we discuss the metalloenzymes that catalyze fatty acid-derived hydrocarbon biosynthesis in various organisms, emphasizing the active site architecture, catalytic mechanism, cofactor requirements, and substrate specificity of these enzymes. Understanding such details is essential for successfully implementing these enzymes in emergent biofuel research through protein engineering and synthetic biology approaches.

Basicity as a Thermodynamic Descriptor of Carbanions Reactivity with Carbon Dioxide: Application to the Carboxylation of α,β-Unsaturated Ketones

The utilization of carbon dioxide as a raw material represents nowadays an appealing strategy in the renewable energy, organic synthesis, and green chemistry fields. Besides reduction strategies, carbon dioxide can be exploited as a single-carbon-atom building block through its fixation into organic scaffolds with the formation of new C-C bonds (carboxylation processes). In this case, activation of the organic substrate is commonly required, upon formation of a carbanion C^-, being sufficiently reactive toward the addition of CO₂. However, the prediction of the reactivity of C^- with CO₂ is often problematic with the process being possibly associated with unfavorable thermodynamics. In this contribution, we present a thermodynamic analysis combined with density functional theory calculations on 50 organic molecules enabling the achievement of a linear correlation of the standard free energy (ΔG⁰) of the carboxylation reaction with the basicity of the carbanion C^-, expressed as the pK_a of the CH/C^- couple. The analysis identifies a threshold pK_a of ca 36 (in CH₃CN) for the CH/C^- couple, above which the ΔG⁰ of the carboxylation reaction is negative and indicative of a favorable process. We then apply the model to a real case involving electrochemical carboxylation of flavone and chalcone as model compounds of α,β-unsaturated ketones. Carboxylation occurs in the β-position from the doubly reduced dianion intermediates of flavone and chalcone (calculated ΔG⁰ of carboxylation in β = -12.8 and -20.0 Kcalmol^-1 for flavone and chalcone, respectively, associated with pK_a values for the conjugate acids of 50.6 and 51.8, respectively). Conversely, the one-electron reduced radical anions are not reactive toward carboxylation (ΔG⁰ > +20 Kcalmol^-1 for both substrates, in either α or β position, consistent with pK_a of the conjugate acids < 18.5). For all the possible intermediates, the plot of calculated ΔG⁰ of carboxylation vs. pK_a is consistent with the linear correlation model developed. The application of the ΔG⁰ vs. pK_a correlation is finally discussed for alternative reaction mechanisms and for carboxylation of other C=C and C=O double bonds. These results offer a new mechanistic tool for the interpretation of the reactivity of CO₂ with organic intermediates.

Functionalized Hydroperoxide Formation from the Reaction of Methacrolein-Oxide, an Isoprene-Derived Criegee Intermediate, with Formic Acid: Experiment and Theory

Methacrolein oxide (MACR-oxide) is a four-carbon, resonance-stabilized Criegee intermediate produced from isoprene ozonolysis, yet its reactivity is not well understood. This study identifies the functionalized hydroperoxide species, 1-hydroperoxy-2-methylallyl formate (HPMAF), generated from the reaction of MACR-oxide with formic acid using multiplexed photoionization mass spectrometry (MPIMS, 298 K = 25 °C, 10 torr = 13.3 hPa). Electronic structure calculations indicate the reaction proceeds via an energetically favorable 1,4-addition mechanism. The formation of HPMAF is observed by the rapid appearance of a fragment ion at m/z 99, consistent with the proposed mechanism and characteristic loss of HO2 upon photoionization of functional hydroperoxides. The identification of HPMAF is confirmed by comparison of the appearance energy of the fragment ion with theoretical predictions of its photoionization threshold. The results are compared to analogous studies on the reaction of formic acid with methyl vinyl ketone oxide (MVK-oxide), the other four-carbon Criegee intermediate in isoprene ozonolysis.

Continuous Fluidic Techniques for the Precise Synthesis of Metal-Organic Frameworks

The continuous fluidics-based synthesis of metal-organic frameworks (MOFs) has attracted considerable attention, resulting in advancements in the reaction efficiency, a continuous production of complex structures, and access to products that are difficult or impossible to attain by bulk synthetic routes. This Minireview discusses the continuous fluidics-based synthesis of MOFs in terms of reaction process control, and is divided into three chapters dealing with the efficient synthesis of high-quality MOFs, the confined-space synthesis of MOF composites with diverse morphologies, and the selective synthesis of metastable products. The products of continuous fluidic synthetic process are introduced (e. g., uniform products, composites, fibers, membranes, and metastable products with advantageous properties that cannot be obtained by bulk synthesis), and their usefulness is demonstrated by referencing representative examples.

Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides

Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the product formation by the variation in initial conditions. In the present study, we use Car–Parrinello molecular dynamics to simulate the fastest reaction steps under such circumstances. We investigate the behavior of amino acids and peptides under anodic conditions. Such highly reactive situations lead to chemical reactions within picoseconds, and we can model the reaction mechanisms in full detail. The role of the electric current is to discharge charged species and, hence, to produce radicals from ions. This leads to ultra-fast radical reactions in a bulk environment, which can also be seen as redox reactions as the oxidation states change. In the case of amino acids, the educts can be zwitterionic, so we also observe complex acid–base chemistry. Hence, we obtain the full spectrum of condensed-phase chemistry.

Synthesis of a Gold-Metal Oxide Core-Satellite Nanostructure for In Situ SERS Study of CuO-Catalyzed Photooxidation

This work reports on an assembling-calcining method for preparing gold-metal oxide core-satellite nanostructures, which enable surface-enhanced Raman spectroscopic detection of chemical reactions on metal oxide nanoparticles. By using the nanostructure, we study the photooxidation of Si-H catalyzed by CuO nanoparticles. As evidenced by the in situ spectroscopic results, oxygen vacancies of CuO are found to be very active sites for oxygen activation, and hydroxide radicals (*OH) adsorbed at the catalytic sites are likely to be the reactive intermediates that trigger the conversion from silanes into the corresponding silanols. According to our finding, oxygen vacancy-rich CuO catalysts are confirmed to be of both high activity and selectivity in photooxidation of various silanes.

Enhancing Tris(pyrazolyl)borate-Based Models of Cysteine/Cysteamine Dioxygenases through Steric Effects: Increased Reactivities, Full Product Characterization and Hints to Initial Superoxide Formation

The design of biomimetic model complexes for the cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO) is reported, where the 3-His coordination of the iron ion is simulated by three pyrazole donors of a trispyrazolyl borate ligand (Tp) and protected cysteine and cysteamine represent substrate ligands. It is found that the replacement of phenyl groups-attached at the 3-positions of the pyrazole units in a previous model-by mesityl residues has massive consequences, as the latter arrange to a more spacious reaction pocket. Thus, the reaction with O₂ proceeds much faster and afterwards the first structural characterization of an iron(II) η² -O,O-sulfinate product became possible. If one of the three Tp-mesityl groups is placed in the 5-position, an even larger reaction pocket results, which leads to yet faster rates and accumulation of a reaction intermediate at low temperatures, as shown by UV/Vis and Mössbauer spectroscopy. After comparison with the results of investigations on the cobalt analogues this intermediate is tentatively assigned to an iron(III) superoxide species.

Esterification of Tertiary Amides: Remarkable Additive Effects of Potassium Alkoxides for Generating Hetero Manganese-Potassium Dinuclear Active Species

A catalyst system of mononuclear manganese precursor 3 combined with potassium alkoxide served as a superior catalyst compared with our previously reported manganese homodinuclear catalyst 2 a for esterification of not only tertiary aryl amides, but also tertiary aliphatic amides. On the basis of stoichiometric reactions of 3 and potassium alkoxide salt, kinetic studies, and density functional theory (DFT) calculations, we clarified a plausible reaction mechanism in which in situ generated manganese-potassium heterodinuclear species cooperatively activates the carbonyl moiety of the amide and the OH moiety of the alcohols. We also revealed details of the reaction mechanism of our previous manganese homodinuclear system 2 a, and we found that the activation free energy (ΔG≠ ) for the manganese-potassium heterodinuclear complex catalyzed esterification of amides is lower than that for the manganese homodinuclear system, which was consistent with the experimental results. We further applied our catalyst system to deprotect the acetyl moiety of primary and secondary amines.

Photocatalytic Oxidation of Propane Using Hydrothermally Prepared Anatase-Brookite-Rutile TiO2 Samples. An In Situ DRIFTS Study

Photocatalytic oxidation of propane using hydrothermally synthesized TiO₂ samples with similar primary crystal size containing different ratios of anatase, brookite and rutile phases has been studied by measuring light-induced propane conversion and in situ DRIFTS (diffuse reflectance Fourier transform infrared spectroscopy). Propane was found to adsorb on the photocatalysts, both in the absence and presence of light. The extent of adsorption depends on the phase composition of synthesized titania powders and, in general, it decreases with increasing rutile and brookite content. Still, the intrinsic activity for photocatalytic decomposition of propane is higher for photocatalysts with lower ability for propane adsorption, suggesting this is not the rate-limiting step. In situ DRIFTS analysis shows that bands related to adsorbed acetone, formate and bicarbonate species appear on the surface of the photocatalysts during illumination. Correlation of propane conversion and infrared (IR) data shows that the presence of formate and bicarbonate species, in excess with respect to acetone, is composition dependent, and results in relatively low activity of the respective TiO₂. This study highlights the need for precise control of the phase composition to optimize rates in the photocatalytic oxidation of propane and a high rutile content seems to be favorable.

Gas-Phase Synthesis of 3-Vinylcyclopropene via the Crossed Beam Reaction of the Methylidyne Radical (CH; X2 Π) with 1,3-Butadiene (CH2 CHCHCH2 ; X1 Ag )

The crossed molecular beam reactions of the methylidyne radical (CH; X² Π) with 1,3-butadiene (CH₂ CHCHCH₂ ; X¹ A_g ) along with their (partially) deuterated counterparts were performed at collision energies of 20.8 kJ mol^-1 under single collision conditions. Combining our laboratory data with ab initio calculations, we reveal that the methylidyne radical may add barrierlessly to the terminal carbon atom and/or carbon-carbon double bond of 1,3-butadiene, leading to doublet C₅ H₇ intermediates with life times longer than the rotation periods. These collision complexes undergo non-statistical unimolecular decomposition through hydrogen atom emission yielding the cyclic cis- and trans-3-vinyl-cyclopropene products with reaction exoergicities of 119±42 kJ mol^-1 . Since this reaction is barrierless, exoergic, and all transition states are located below the energy of the separated reactants, these cyclic C₅ H₆ products are predicted to be accessed even in low-temperature environments, such as in hydrocarbon-rich atmospheres of planets and cold molecular clouds such as TMC-1.

Observation and Kinetic Characterization of Transient Schiff Base Intermediates by CEST NMR Spectroscopy

In aqueous solution, many biochemical reaction pathways involve reaction of an aldehyde with an amine, which progresses through generally unstable, hydrated and dehydrated, Schiff base intermediates that often are unobservable by conventional NMR. There are 4 states in the relevant equilibrium: 1) gem-diol, 2) aldehyde, 3) hemiaminal, and 4) Schiff base. For the reaction between protein amino groups and DOPAL, a highly toxic metabolite of dopamine, the ¹ H resonances of both the hemiaminal and the dehydrated Schiff base can be observed by CEST NMR, even when their populations fall below 0.1 %. CEST NMR reveals the quantitative exchange kinetics between reactants and Schiff base intermediates, explaining why the Schiff base NMR signals are rarely observed. The reactivity of DOPAL with N^α -amino groups is greater than with lysine N^ϵ -amines and, in the presence of O₂ , both types of Schiff base DOPAL-peptide intermediates rapidly react with free DOPAL to irreversibly form dicatechol pyrrole adducts.

Absolute configuration of phomactatriene diterpenoids obtained by Wagner-Meerwein rearrangement of epimeric verticillols

The epimeric diterpenes (+)-(1S,3E,7E,11S,12S)-verticilla-3,7-dien-12-ol (1), isolated from Bursera suntui, and (+)-(1S,3E,7E,11S,12R)-verticilla-3,7-dien-12-ol (2), isolated from Bursera kerberi, gave the same Wagner-Meerwein rearrangement product (-)-(1E,4Z,8Z,11S,12R)-phomacta-1,(15)4,8-triene (3). The Et₂ O:BF₃ -induced transformations evidence that verticillenes and phomactanes, both containing the bicyclo[9.3.1]pentadecane skeleton, are biogenetically related through the verticillen-12-yl cation (A⁺ ), which also is a key intermediate in the biosynthetic pathways to generate antitumor taxanes. Molecular modeling using the Monte Carlo protocol, followed by density functional theory (DFT) geometry optimization employing the hybrid functionals B3LYP and B3PW91, both with the DGDZVP basis set, secured the configuration of 3 as followed from the good agreement between the calculated and experimental vibrational circular dichroism spectra. Similar DFT calculations allowed determining the absolute configuration of (+)-(1R,4R,5R,8S,9S,11S,12R,15R)-1,15:4,5:8,9-triepoxyphomactane (9), which surprisingly derives from epoxidation of the second minimum energy conformer of 3.

Gas Phase Formation of the Interstellar Molecule Methyltriacetylene

Methyltriacetylene - the largest methylated polyacetylene detected in deep space - has been synthesized in the gas phase via the bimolecular reaction of the 1-propynyl radical with diacetylene under single-collision conditions. The barrier-less route to methyltriacetylene represents a prototype of a polyyne chain extension through a radical substitution mechanism and provides a novel low temperature route, in which the propynyl radical piggybacks a methyl group to be incorporated into methylated polyynes. This mechanism overcomes a key obstacle in previously postulated reactions of methyl radicals with unsaturated hydrocarbon, which fail the inclusion of methyl groups into hydrocarbons due to insurmountable entrance barriers thus providing a fundamental understanding on the electronic structure, chemical bonding, and formation of methyl-capped polyacetylenes. These species are key reactive intermediates leading to carbonaceous nanostructures in molecular clouds like TMC-1.

Direct Spectroscopic Detection of Key Intermediates and the Turnover Process in Catalytic H2 Formation by a Biomimetic Diiron Catalyst

[FeFe(Cl₂ -bdt)(CO)₆ ] (1; Cl₂ -bdt=3,6-dichlorobenzene-1,2-dithiolate), inspired by the active site of FeFe-hydrogenase, shows a chemically reversible 2 e^- reduction at -1.20 V versus the ferrocene/ferrocenium couple. The rigid and aromatic bdt bridging ligand lowers the reduction potential and stabilizes the reduced forms, compared with analogous complexes with aliphatic dithiolates; thus allowing details of the catalytic process to be characterized. Herein, time-resolved IR spectroscopy is used to provide kinetic and structural information on key catalytic intermediates. This includes the doubly reduced, protonated complex 1H^- , which has not been previously identified experimentally. In addition, the first direct spectroscopic observation of the turnover process for a molecular H₂ evolving catalyst is reported, allowing for straightforward determination of the turnover frequency.

Highly Efficient Supramolecular Catalysis by Endowing the Reaction Intermediate with Adaptive Reactivity

A new strategy of highly efficient supramolecular catalysis is developed by endowing the reaction intermediate with adaptive reactivity. The supramolecular catalyst, prepared by host-guest complexation between 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) and cucurbit[7]uril (CB[7]), was used for biphasic oxidation of alcohols. Cationic TEMPO⁺ , the key intermediate, was stabilized by the electrostatic effect of CB[7] in aqueous phase, thus promoting the formation of TEMPO⁺ and inhibiting side reactions. Moreover, through the migration into the organic phase, TEMPO⁺ was separated from CB[7] and recovered the high reactivity to drive a fast oxidation of substrates. The adaptive reactivity of TEMPO⁺ induced an integral optimization of the catalytic cycle and greatly improved the conversion of the reaction. This work highlights the unique advantages of dynamic noncovalent interactions on modulating the activity of reaction intermediates, which may open new horizons for supramolecular catalysis.

Gas-Phase Synthesis of the Elusive Cyclooctatetraenyl Radical (C8 H7 ) via Triplet Aromatic Cyclooctatetraene (C8 H8 ) and Non-Aromatic Cyclooctatriene (C8 H8 ) Intermediates

The 1,2,4,7-cyclooctatetraenyl radical (C₈ H₇ ) has been synthesized for the very first time via the bimolecular gas-phase reaction of ground-state carbon atoms with 1,3,5-cycloheptatriene (C₇ H₈ ) on the triplet surface under single-collision conditions. The barrier-less route to the cyclic 1,2,4,7-cyclooctatetraenyl radical accesses exotic reaction intermediates on the triplet surface, which cannot be synthesized via classical organic chemistry methods: the triplet non-aromatic 2,4,6-cyclooctatriene (C₈ H₈ ) and the triplet aromatic 1,3,5,7-cyclooctatetraene (C₈ H₈ ). Our approach provides a clean gas-phase synthesis of this hitherto elusive cyclic radical species 1,2,4,7-cyclooctatetraenyl via a single-collision event and opens up a versatile, unconventional path to access this previously largely obscure class of cyclooctatetraenyl radicals, which have been impossible to access through classical synthetic methods.

Enzyme Activation with a Synthetic Catalytic Co-enzyme Intermediate: Nucleotide Methylation by Flavoenzymes

To facilitate production of functional enzymes and to study their mechanisms, especially in the complex cases of coenzyme-dependent systems, activation of an inactive apoenzyme preparation with a catalytically competent coenzyme intermediate is an attractive strategy. This is illustrated with the simple chemical synthesis of a flavin-methylene iminium compound previously proposed as a key intermediate in the catalytic cycle of several important flavoenzymes involved in nucleic acid metabolism. Reconstitution of both flavin-dependent RNA methyltransferase and thymidylate synthase apoproteins with this synthetic compound led to active enzymes for the C5-uracil methylation within their respective transfer RNA and dUMP substrate. This strategy is expected to be of general application in enzymology.

Transient Clustering of Reaction Intermediates during Wet Etching of Silicon Nanostructures

Wet chemical etching is a key process in fabricating silicon (Si) nanostructures. Currently, wet etching of Si is proposed to occur through the reaction of surface Si atoms with etchant molecules, forming etch intermediates that dissolve directly into the bulk etchant solution. Here, using in situ transmission electron microscopy (TEM), we follow the nanoscale wet etch dynamics of amorphous Si (a-Si) nanopillars in real-time and show that intermediates generated during alkaline wet etching first aggregate as nanoclusters on the Si surface and then detach from the surface before dissolving in the etchant solution. Molecular dynamics simulations reveal that the molecules of etch intermediates remain weakly bound to the hydroxylated Si surface during the etching and aggregate into nanoclusters via surface diffusion instead of directly diffusing into the etchant solution. We confirmed this model experimentally by suppressing the formation of nanoclusters of etch intermediates on the Si surfaces by shielding the hydroxylated Si sites with large ions. These results suggest that the interaction of etch intermediates with etching surfaces controls the solubility of reaction intermediates and is an important parameter in fabricating densely packed clean 3D nanostructures for future generation microelectronics.

Mass Spectrometric and Vibrational Characterization of Reaction Intermediates in [Ru(bpy)(tpy)(H2 O)]2+ Catalyzed Water Oxidation

Mass spectrometry coupled with an in-line electrochemical electrospray ionization source is used to capture some of the reaction intermediates formed in the [Ru(bpy)(tpy)(H₂ O)]²⁺ (bpy=2,2'-bipyridine, tpy=2,2':6',2"-terpyridine) catalyzed water oxidation reaction. By controlling the applied electrochemical potential, we identified the parent complex, as well as the first two oxidation complexes, identified as [Ru(bpy)(tpy)(OH)]²⁺ and [Ru(bpy)(tpy)(O)]²⁺ . The structures of the parent and first oxidation complexes are probed directly in the mass spectrometer by using infrared predissociation spectroscopy of D₂ -tagged ions. Comparisons between experimental vibrational spectra and density functional theory calculations confirmed the identity and structure of these two complexes. Moreover, the frequency of the O-H stretching mode in [Ru(bpy)(tpy)(OH)]²⁺ shows that this complex features a Ru-OH interaction that is more covalent than ionic.

Selective Hydrogenation of Acrolein Over Pd Model Catalysts: Temperature and Particle-Size Effects

The selectivity in the hydrogenation of acrolein over Fe₃ O₄ -supported Pd nanoparticles has been investigated as a function of nanoparticle size in the 220-270 K temperature range. While Pd(111) shows nearly 100 % selectivity towards the desired hydrogenation of the C=O bond to produce propenol, Pd nanoparticles were found to be much less selective towards this product. In situ detection of surface species by using IR-reflection absorption spectroscopy shows that the selectivity towards propenol critically depends on the formation of an oxopropyl spectator species. While an overlayer of oxopropyl species is effectively formed on Pd(111) turning the surface highly selective for propenol formation, this process is strongly hindered on Pd nanoparticles by acrolein decomposition resulting in CO formation. We show that the extent of acrolein decomposition can be tuned by varying the particle size and the reaction temperature. As a result, significant production of propenol is observed over 12 nm Pd nanoparticles at 250 K, while smaller (4 and 7 nm) nanoparticles did not produce propenol at any of the temperatures investigated. The possible origin of particle-size dependence of propenol formation is discussed. This work demonstrates that the selectivity in the hydrogenation of acrolein is controlled by the relative rates of acrolein partial hydrogenation to oxopropyl surface species and of acrolein decomposition, which has significant implications for rational catalyst design.

Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms

Menaquinone (MQ) is an essential component of the respiratory chains of many pathogenic organisms, including Mycobacterium tuberculosis (Mtb). The first committed step in MQ biosynthesis is catalyzed by 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD), a thiamin diphosphate (ThDP)-dependent enzyme. Catalysis proceeds through two covalent intermediates as the substrates 2-oxoglutarate and isochorismate are successively added to the cofactor before final cleavage of the product. We have determined a series of crystal structures of Mtb-MenD that map the binding of both substrates, visualizing each step in the MenD catalytic cycle, including both intermediates. ThDP binding induces a marked asymmetry between the coupled active sites of each dimer, and possible mechanisms of communication can be identified. The crystal structures also reveal conformational features of the two intermediates that facilitate reaction but prevent premature product release. These data fully map chemical space to inform early-stage drug discovery targeting MenD.

Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase

Cofactor-free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near-atomic resolution crystallography supported by in crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor-free uricase catalyzes uric acid degradation via a C5(S)-(hydro)peroxide intermediate. Low X-ray doses break specifically the intermediate C5-OO(H) bond at 100 K, thus releasing O2 in situ, which is trapped above the substrate radical. The dose-dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick-starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.

Role of active-site residues Tyr55 and Tyr114 in catalysis and substrate specificity of Corynebacterium diphtheriae C-S lyase

In recent years, there has been increased interest in bacterial methionine biosynthesis enzymes as antimicrobial targets because of their pivotal role in cell metabolism. C-S lyase from Corynebacterium diphtheriae is a pyridoxal 5'-phosphate-dependent enzyme in the transsulfuration pathway that catalyzes the α,β-elimination of sulfur-containing amino acids, such as L-cystathionine, to generate ammonia, pyruvate, and homocysteine, the immediate precursor of L-methionine. In order to gain deeper insight into the functional and dynamic properties of the enzyme, mutants of two highly conserved active-site residues, Y55F and Y114F, were characterized by UV-visible absorbance, fluorescence, and CD spectroscopy in the absence and presence of substrates and substrate analogs, as well as by steady-state kinetic studies. Substitution of Tyr55 with Phe apparently causes a 130-fold decrease in K(d)(PLP) at pH 8.5 providing evidence that Tyr55 plays a role in cofactor binding. Moreover, spectral data show that the mutant accumulates the external aldimine intermediate suggesting that the absence of interaction between the hydroxyl moiety and PLP-binding residue Lys222 causes a decrease in the rate of substrate deprotonation. Mutation of Tyr114 with Phe slightly influences hydrolysis of L-cystathionine, and causes a change in substrate specificity towards L-serine and O-acetyl-L-serine compared to the wild type enzyme. These findings, together with computational data, provide useful insights in the substrate specificity of C-S lyase, which seems to be regulated by active-site architecture and by the specific conformation in which substrates are bound, and will aid in development of inhibitors.

On the mechanism of bifunctional squaramide-catalyzed organocatalytic Michael addition: a protonated catalyst as an oxyanion hole

A joint experimental-theoretical study of a bifunctional squaramide-amine-catalyzed Michael addition reaction between 1,3-dioxo nucleophiles and nitrostyrene has been undertaken to gain insight into the nature of bifunctional organocatalytic activation. For this highly stereoselective reaction, three previously proposed mechanistic scenarios for the critical CC bond-formation step were examined. Accordingly, the formation of the major stereoisomeric products is most plausible by one of the bifunctional pathways that involve electrophile activation by the protonated amine group of the catalyst. However, some of the minor product isomers are also accessible through alternative reaction routes. Structural analysis of transition states points to the structural invariance of certain fragments of the transition state, such as the protonated catalyst and the anionic fragment of approaching reactants. Our topological analysis provides deeper insight and a more general understanding of bifunctional noncovalent organocatalysis.

A linker strategy for trans-FRET assay to determine activation intermediate of NEDDylation cascade

Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research and is a valuable tool for elucidating molecular interactions in vitro and in vivo. Quantitative FRET analysis is a powerful method for determining biochemical parameters and molecular distances at nanometer levels. Recently, we reported theoretical developments and experimental procedures for determining the dissociation constant, Kd and enzymatic kinetics parameters, Kcat and KM, of protein interactions with the engineered FRET pair, CyPet and YPet. The strong FRET signal from this pair made these developments possible. However, the direct link of fluorescent proteins with proteins of interests may interfere with the folding of some fusion proteins. Here, we report a new protein engineering strategy for improving FRET signals by adding a linker between the fluorescent protein and the targeted protein. This improvement allowed us to follow the covalent conjugation of NEDD8 to its E2 ligase in the presence of E1 and ATP, which was difficult to determine without linker. Three linkers, LAEAAAKEAA, TSGSPGLQEFGT, and LAAALAAA, which are alpha helix or random coil, all significantly improved the FRET signals. Our results show a general methodology for improving trans-FRET signals to effectively determine biochemical reaction intermediates.

Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium

X-ray crystallography reveals chitinase from the psychrophilic bacterium Moritella marina to be an elongated molecule which in addition to the catalytic β/α-barrel domain contains two Ig-like domains and a chitin-binding domain, all linked in a chain. A ligand-binding study using NAG oligomers showed the enzyme to be active in the crystal lattice and resulted in complexes of the protein with oxazolinium ion (the reaction intermediate) and with NAG2, a reaction product. The characteristic motif DXDXE, containing three acidic amino-acid residues, which is a signature of type 18 chitinases, is conserved in the enzyme. Further analysis of the unliganded enzyme with the two protein-ligand complexes and a comparison with other known chitinases elucidated the roles of other conserved residues near the active site. Several features have been identified that are probably important for the reaction mechanism, substrate binding and the efficiency of the enzyme at low temperatures. The chitin-binding domain and the tryptophan patch on the catalytic domain provide general affinity for chitin, in addition to the affinity of the binding site; the two Ig-like domains give the protein a long reach over the chitin surface, and the flexible region between the chitin-binding domain and the adjacent Ig-like domain suggests an ability of the enzyme to probe the surface of the substrate, while the open shallow substrate-binding groove allows easy access to the active site.

Synthesis and Spectroscopic Characterization of Diphenylargentate, [(C6H5)2Ag](.)

We present the structural and optical properties of the isolated diphenylargentate anion, which has been synthesized by multistage mass spectrometry in a quadrupole ion trap. The experimental photodetachment spectrum has been obtained by action spectroscopy. Comparison with quantum chemical calculations of the electronic absorption spectrum allows for a precise characterization of the spectroscopic features, showing that in the low-energy regime, the optical properties of diphenylargentate bear a significant resemblance to those of atomic silver.

Structural basis for the catalytic mechanism of human phosphodiesterase 9

The phosphodiesterases (PDEs) are metal ion-dependent enzymes that regulate cellular signaling by metabolic inactivation of the ubiquitous second messengers cAMP and cGMP. In this role, the PDEs are involved in many biological and metabolic processes and are proven targets of successful drugs for the treatments of a wide range of diseases. However, because of the rapidity of the hydrolysis reaction, an experimental knowledge of the enzymatic mechanisms of the PDEs at the atomic level is still lacking. Here, we report the structures of reaction intermediates accumulated at the reaction steady state in PDE9/crystal and preserved by freeze-trapping. These structures reveal the catalytic process of a PDE and explain the substrate specificity of PDE9 in an actual reaction and the cation requirements of PDEs in general.