An aggregation inhibitor specific to oligomeric intermediates of Aß42 derived from phage display libraries of stable, small proteins.

The self-assembly of amyloid ß peptide (Aß) to fibrillar and oligomeric aggregates is linked to Alzheimer's disease. Aß binders may serve as inhibitors of aggregation to prevent the generation of neurotoxic species and for the detection of Aß species. A particular challenge involves finding binders to on-pathway oligomers given their transient nature. Here we construct two phage­display 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 Aß40 and Aß42 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 loop­insertion YLTIRLM as an inhibitor of the secondary nucleation of Aß42 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 Aß40 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.

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

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 (Br2DNiR) 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.

Catalytic wet peroxide oxidation of phenol through mesoporous silica-pillared clays supported iron and/or titanium incorporated catalysts.

Catalytic performances of Silica Pillared Clay (SPC) supports synthesized in different silica amounts both from standard SWy-2 clay mineral and Hançili region bentonite rock (HWB), and iron (Fe) and/or titanium (Ti) incorporated SPCs in different combinations were evaluated in various advanced Catalytic Wet Peroxide Oxidation (CWPO) of phenol. Host clay mineral type led to different oxidation performances and metal loading created significant increases in the catalytic performance. CWPO performance of Fe-loaded SPCs was better than Ti-loaded ones, so oxidation parameters for Fe-SPCs were studied in detail. Catalyst amount and rise in temperature increased phenol conversion values significantly, and catalysts were more effective in lower pH reaction medium. Aromatic intermediates such as catechol, hydroquinone and benzoquinone formed at the beginning of oxidation were oxidized to carboxylic acids with an advancing oxidation time. The presence of carboxylic acids such as oxalic and formic acid resulted in relatively low total organic carbon (TOC) conversion values. The highest catalytic activity was obtained with high silica content Fe-SPCs synthesized with both host clays. Complete conversion was nearly achieved within 60 min with an experimental condition of T = 30 °C, pH = 3.7 and catalyst/solution ratio = 2 g/L for SWy-2 based catalyst by applying either CWPO or PCWPO (Photo Catalytic Wet Peroxide Oxidation) techniques. SCWPO (Sono Catalytic Wet Peroxide Oxidation) technique also yielded this value at the same oxidation conditions for HWB based catalyst. TOC conversion values at 240 min oxidation time were determined as 33% and 48% for SWy-2 based catalyst with CWPO and PCWPO techniques, respectively, and 37% for HWB based catalyst with SCWPO technique. SWy-2 based catalyst still retained its performance after 3 cycles.

Gold N-Heterocyclic Carbene Catalysts for the Hydrofluorination of Alkynes Using Hydrofluoric Acid: Reaction Scope, Mechanistic Studies and the Tracking of Elusive Intermediates.

An efficient and chemoselective methodology deploying gold-N-heterocyclic carbene (NHC) complexes as catalysts in the hydrofluorination of terminal alkynes using aqueous HF has been developed. Mechanistic studies shed light on an in situ generated catalyst, formed by the reaction of Brønsted basic gold pre-catalysts with HF in water, which exhibits the highest reactivity and chemoselectivity. The catalytic system has a wide alkyl substituted-substrate scope, and stoichiometric as well as catalytic reactions with tailor-designed gold pre-catalysts enable the identification of various gold species involved along the catalytic cycle. Computational studies aid in understanding the chemoselectivity observed through examination of key mechanistic steps for phosphine- and NHC-coordinated gold species bearing the triflate counterion and the elusive key complex bearing a bifluoride counterion.

Low-Coordination Single Au Atoms on Ultrathin ZnIn2 S4 Nanosheets for Selective Photocatalytic CO2 Reduction towards CH4.

Selective CO2 photoreduction to hydrocarbon fuels such as CH4 is promising and sustainable for carbon-neutral future. However, lack of proper binding strengths with reaction intermediates makes it still a challenge for photocatalytic CO2 methanation with both high activity and selectivity. Here, low-coordination single Au atoms (Au1 -S2 ) on ultrathin ZnIn2 S4 nanosheets was synthesized by a complex-exchange route, enabling exceptional photocatalytic CO2 reduction performance. Under visible light irradiation, Au1 /ZnIn2 S4 catalyst exhibits a CH4 yield of 275 µmol g-1 h-1 with a selectivity as high as 77 %. As revealed by detailed characterizations and density functional theory calculations, Au1 /ZnIn2 S4 with Au1 -S2 structure not only display fast carrier transfer to underpin its superior activity, but also greatly reduce the energy barrier for protonation of *CO and stabilize the *CH3 intermediate, thereby leading to the selective CH4 generation from CO2 photoreduction.

Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands.

Recently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N2-derived ligands at three sites in the catalytic FeMo cluster, replacing the three [Formula: see text] bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381-1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain directions than others. This, together with the questionable use of anisotropic B factors, give atoms an elongated shape, which may look like diatomic atoms. In terms of standard electron-density maps and real-space Z scores, a resting-state structure with no dissociated sulfide ligands fits the raw data better than the interpretation suggested by the crystallographers. The anomalous electron density at 7100 eV is weaker for the putative N2 ligands, but not lower than for several of the [Formula: see text] bridging sulfide ions and not lower than what can be expected from a statistical analysis of the densities. Therefore, we find no convincing evidence for any N2 binding to the FeMo cluster. Instead, a standard resting state without any dissociated ligands seems to be the most likely interpretation of the structure. Likewise, we find no support that the homocitrate ligand should show monodentate binding.

Nonstatistical Reaction Dynamics.

Nonstatistical dynamics is important for many chemical reactions. The Rice-Ramsperger-Kassel-Marcus (RRKM) theory of unimolecular kinetics assumes a reactant molecule maintains a statistical microcanonical ensemble of vibrational states during its dissociation so that its unimolecular dynamics are time independent. Such dynamics results when the reactant's atomic motion is chaotic or irregular. Intrinsic non-RRKM dynamics occurs when part of the reactant's phase space consists of quasiperiodic/regular motion and a bottleneck exists, so that the unimolecular rate constant is time dependent. Nonrandom excitation of a molecule may result in short-time apparent non-RRKM dynamics. For rotational activation, the 2J + 1 K levels for a particular J may be highly mixed, making K an active degree of freedom, or K may be a good quantum number and an adiabatic degree of freedom. Nonstatistical dynamics is often important for bimolecular reactions and their intermediates and for product-energy partitioning of bimolecular and unimolecular reactions. Post-transition state dynamics is often highly complex and nonstatistical.

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.

Electrocatalytic Refinery for Sustainable Production of Fuels and Chemicals.

Compared to modern fossil-fuel-based refineries, the emerging electrocatalytic refinery (e-refinery) is a more sustainable and environmentally benign strategy to convert renewable feedstocks and energy sources into transportable fuels and value-added chemicals. A crucial step in conducting e-refinery processes is the development of appropriate reactions and optimal electrocatalysts for efficient cleavage and formation of chemical bonds. However, compared to well-studied primary reactions (e.g., O2 reduction, water splitting), the mechanistic aspects and materials design for emerging complex reactions are yet to be settled. To address this challenge, herein, we first present fundamentals of heterogeneous electrocatalysis and some primary reactions, and then implement these to establish the framework of e-refinery by coupling in situ generated intermediates (integrated reactions) or products (tandem reactions). We also present a set of materials design principles and strategies to efficiently manipulate the reaction intermediates and pathways.

Observation of the Reaction Intermediates of Methanol Dehydrogenation by Cationic Vanadium Clusters.

A mass spectrometric study of the reactions of vanadium cationic clusters with methanol in a low-pressure collision cell is reported. For comparison, the reaction of methanol with cobalt cationic clusters was studied. For vanadium, the main reaction products are fully dehydrogenated species, and partial dehydrogenation and non-dehydrogenation species are observed as minors, for which the relative intensities increase with cluster size and also at low cluster source temperature cooled by liquid nitrogen; no dehydrogenation products were observed for cobalt clusters. Quantum chemical calculations explored the reaction pathways and revealed that the fully dehydrogenation products of the reaction between Vn + and methanol are Vn (C)(O)+ , in which C and O are separated owing to the high oxophilicity of vanadium. The partial dehydrogenation and non-dehydrogenation species were verified to be reaction intermediates along the reaction pathway, and their most probable structures were proposed.

Temperature-Dependent CO2 Electroreduction over Fe-N-C and Ni-N-C Single-Atom Catalysts.

Reaction temperature is an important parameter to tune the selectivity and activity of electrochemical CO2 reduction reaction (CO2 RR) due to different thermodynamics of CO2 RR and competitive hydrogen evolution reaction (HER). In this work, temperature-dependent CO2 RR over Fe-N-C and Ni-N-C single-atom catalysts are investigated from 303 to 343 K. Increasing the reaction temperature improves and decreases CO Faradaic efficiency over Fe-N-C and Ni-N-C catalysts at high overpotentials, respectively. CO current density over Fe-N-C catalyst increases with temperature, then gets into a plateau at 323 K, finally reaches the maximum value of 185.8 mA cm-2 at 343 K. While CO current density over Ni-N-C catalyst achieves the maximum value of 252.5 mA cm-2 at 323 K, and then drops significantly to 202.9 mA cm-2 at 343 K. Temperature programmed desorption results and density functional theory calculations reveal that the difference of temperature-dependent variation on CO Faradaic efficiency and current density between Fe-N-C and Ni-N-C catalysts results from the varied adsorption strength of key reaction intermediates during CO2 RR.

Mechanistic Investigation of Photochemical Reactions by Mass Spectrometry.

This Minireview highlights the application of electrospray ionization mass spectrometry (ESI-MS) to investigating photochemical reactions. We show possible approaches to on-line ESI-MS monitoring of photocatalytic reactions and give examples of the characterization of short-lived photochemical intermediates by ion spectroscopy. The minireview also exemplifies in-depth mass spectrometric studies of photoisomerization reactions and photofragmentation reactions. Apart from mechanistic studies, the coupling of photochemistry and mass spectrometry is a powerful approach to studying structure and properties of biomolecules. We show several examples focused on investigation of intrinsic properties of model biomolecules.

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.

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.

Self-Immolation of a Bacterial Dehydratase Enzyme by its Epoxide Product.

Disabling the bacterial capacity to cause infection is an innovative approach that has attracted significant attention to fight against superbugs. A relevant target for anti-virulence drug discovery is the type I dehydroquinase (DHQ1) enzyme. It was shown that the 2-hydroxyethylammonium derivative 3 has in vitro activity since it causes the covalent modification of the catalytic lysine residue of DHQ1. As this compound does not bear reactive electrophilic centers, how the chemical modification occurs is intriguing. We report here an integrated approach, which involves biochemical studies, X-ray crystallography and computational studies on the reaction path using combined quantum mechanics/molecular mechanics Umbrella Sampling Molecular Dynamics, that evidences that DHQ1 catalyzes its self-immolation by transforming the unreactive 2-hydroxyethylammonium group in 3 into an epoxide that triggers the lysine covalent modification. This finding might open opportunities for the design of lysine-targeted irreversible inhibitors bearing a 2-hydroxyethylammonium moiety as an epoxide proform, which to our knowledge has not been reported previously.

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 Ag ) 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.

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.

Computer Modeling of N-Acetylglutamate Synthase: From Primary Structure to Elemental Stages of Catalysis.

Three-dimensional full-atom model of the enzyme complex with acetyl-CoA and substrate was constructed on the basis of the primary sequence of amino acid residues of N-acetyl glutamate synthase. Bioinformatics approaches of computer modeling were applied, including multiple sequence alignment, prediction of co-evolutionary contacts, and ab initio folding. On the basis of the results of calculations by classical molecular dynamics and combined quantum and molecular mechanics (QM/MM) methods, the structure of the active site and the reaction mechanism of N-acetylglutamate formation are described. Agreement of the structures of the enzyme-product complexes obtained in computer modeling and in the X-ray studies validates the reliability of modeling predictions.

Remote Participation during Glycosylation Reactions of Galactose Building Blocks: Direct Evidence from Cryogenic Vibrational Spectroscopy.

The stereoselective formation of 1,2-cis-glycosidic bonds is challenging. However, 1,2-cis-selectivity can be induced by remote participation of C4 or C6 ester groups. Reactions involving remote participation are believed to proceed via a key ionic intermediate, the glycosyl cation. Although mechanistic pathways were postulated many years ago, the structure of the reaction intermediates remained elusive owing to their short-lived nature. Herein, we unravel the structure of glycosyl cations involved in remote participation reactions via cryogenic vibrational spectroscopy and first principles theory. Acetyl groups at C4 ensure α-selective galactosylations by forming a covalent bond to the anomeric carbon in dioxolenium-type ions. Unexpectedly, also benzyl ether protecting groups can engage in remote participation and promote the stereoselective formation of 1,2-cis-glycosidic bonds.