Unstable Reaction Intermediates Research Articles

In Situ Polymerization Synthesis of Graphdiyne Nanosheets as Electrode Material and Its Application in NMR Spectroelectrochemistry.

In situ NMR spectroelectrochemistry is extremely powerful in studying redox reactions in real time and identifying unstable reaction intermediates. In this paper, in situ polymerization synthesis of ultrathin graphdiyne (GDY) nanosheets was realized on the surface of copper nanoflower/copper foam (nano-Cu/Cuf)-based electrode with hexakisbenzene monomers and pyridine. Palladium (Pd) nanoparticles were further deposited onto the GDY nanosheets by the constant potential method. By using this GDY composite as electrode material, a new NMR-electrochemical cell was designed for in situ NMR spectroelectrochemistry measurement. The three-electrode electrochemical system consists of a Pd/GDY/nano-Cu/Cuf electrode as the working electrode, a platinum wire as the counter electrode, and a silver/silver chloride (Ag/AgCl) wire as a quasi-reference electrode, which can be dipped into a specially constructed sample tube and adapted for convenient operation in any commercial high-field, variable-temperature FT NMR spectrometer. The application of this NMR-electrochemical cell is illustrated by monitoring the progressive oxidation of hydroquinone to benzoquinone by controlled-potential electrolysis in aqueous solution.

Microfluidics-Assisted Synthesis of Hierarchical Cu2 O Nanocrystal as C2 -Selective CO2 Reduction Electrocatalyst.

Copper-based catalysts have attracted enormous attention due to their high selectivity for C2+ products during the electrochemical reduction of CO2 (CO2 RR). In particular, grain boundaries on the catalysts contribute to the generation of various Cu coordination environments, which have been found essential for C-C coupling. However, smooth-surfaced Cu2 O nanocrystals generally lack the ability for the surface reorganization to form multiple grain boundaries and desired Cu undercoordination sites. Flow chemistry armed with the unparalleled ability to mix reaction mixture can achieve a very high concentration of unstable reaction intermediates, which in turn are used up rapidly to lead to kinetics-driven nanocrystal growth. Herein, the synthesis of a unique hierarchical structure of Cu2 O with numerous steps (h-Cu2 O ONS) via flow chemistry-assisted modulation of nanocrystal growth kinetics is reported. The surface of h-Cu2 O ONS underwent rapid surface reconstruction under CO2 RR conditions to exhibit multiple heterointerfaces between Cu2 O and Cu phases, setting the preferable condition to facilitate C-C bond formation. Notably, the h-Cu2 O ONS obtained the increased C2 H4 Faradaic efficiency from 31.9% to 43.5% during electrocatalysis concurrent with the morphological reorganization, showing the role of the stepped surface. Also, the h-Cu2 O ONS demonstrated a 3.8-fold higher ethylene production rate as compared to the Cu2 O nanocube.

Anhydrous Hydrogen Iodide-Mediated Reductive Indolization of In Situ-Generated Cyclopropyl Hydrazones.

Fischer-type indolization of N-aryl-C-cyclopropyl hydrazones generated in situ followed by chemoselective reduction using tert-butyl iodide as an anhydrous HI generator was developed. This protocol provides indoles bearing carboxylic acid derivative units. A series of control experiments indicated the HI-mediated formation and reduction of spirocyclopropyl indolenines. Anhydrous HI functions as a Brønsted acid as well as a reducing agent, facilitating the successful conversion of unstable reaction intermediates and iodinated mixtures in equilibrium.

Understanding How Coacervates Drive Reversible Small Molecule Reactions to Promote Molecular Complexity

Liquid-liquid phase-separated coacervate droplets give rise to membraneless compartments that play an important role in the spatial organization and reactivity in cells. Due to their molecularly crowded nature and ability to sequester biomolecules, coacervate droplets create distinct environments for enzymatic reaction kinetics and reaction mechanisms that markedly differ from bulk solution. In this work, we use a combination of experiments and quantitative modeling to understand how coacervate droplets promote reversible small molecule reaction chemistry. In particular, we study a model condensation reaction generating an unstable fluorescent imine in polyacrylic acid-polyethylene glycol coacervate droplets over a range of conditions. At equilibrium, the concentration of the imine product in coacervate droplets is approximately 140-fold larger than that in bulk solution, which arises due to preferential partitioning of reactants and products into coacervate droplets and a reaction equilibrium constant that is roughly threefold larger in coacervate droplets than in solution. A reaction-diffusion model is developed to quantitatively describe how competing reaction and partitioning equilibria govern the spatial distribution of the imine product inside coacervate droplets. Overall, our results show that compartmentalization stabilizes kinetically labile reaction products, which enables larger reactant concentrations in coacervate droplets compared to bulk solution. Broadly, these results provide an improved understanding of how biomolecular condensates promote multistep reaction pathways involving unstable reaction intermediates and suggest how coacervates provide a potential abiotic mechanism to promote molecular complexity.

Formation and Stabilization Mechanisms of Enols on Pt through Multiple Hydrogen Bonding

Lateral interactions between coadsorbed molecules on surfaces might trigger specific reaction pathways and stabilize otherwise energetically unstable reaction intermediates. These phenomena can crucially affect the overall activity and selectivity of catalytic processes and can be employed for purposeful functionalization of surfaces to improve their catalytic efficiency. In this report, we present a study on the atomistic-level details of intermolecular interactions between acetophenone adsorbates on Pt. We show that these interactions trigger an important reaction of keto–enol tautomerization producing an enol reaction intermediate, which is envisaged to enable low-barrier hydrogenation of simple carbonyl compounds. By combining scanning tunneling microscopy and infrared reflection–absorption spectroscopy, we found that several types of hydrogen-bonded oligomer species can be formed, including ketone–enol dimers and ketone–enol–enol trimers. Their evolution exhibits a strong temperature dependence, sugg...

In situ ultrafast 2D NMR spectroelectrochemistry for real-time monitoring of redox reactions.

The in situ implementation of an electrochemical cell (EC) inside a nuclear magnetic resonance (NMR) spectrometer is extremely powerful to study redox reactions in real time and identify unstable reaction intermediates. Unfortunately, the implementation of an electrochemical device near the sensitive volume of an NMR probe significantly affects the quality of the NMR signal, inducing significant line broadening resulting in peak overlap and partial loss of the multiplet structures. Two-dimensional (2D) NMR spectroscopy allows one to bypass signal overlapping by spreading the peaks along two orthogonal dimensions, while providing precious information in terms of structural elucidation. Nevertheless, the acquisition of 2D NMR data suffers from long acquisition durations which are incompatible with fast redox processes taking place in solution. Here, we present a new approach to deal with this issue, consisting of coupling EC-NMR with ultrafast 2D spectroscopy, capable of recording 2D spectra much faster than conventional 2D NMR. This approach is applied to the real-time monitoring of a model reaction. Fast correlation spectroscopy (COSY) spectra are recorded every 3 min in the course of the 80 min reaction, leading to the unambiguous identification of one reaction intermediate and two reaction products. The evolution of 2D NMR peak volumes in the course of time provides further insight into the mechanism of this reaction involving an unstable intermediate. This study demonstrates the feasibility and the relevance of coupling in situ spectroelectrochemistry with ultrafast 2D spectroscopy to monitor real-time electrochemical reactions in the NMR tube.

A chirped-pulse Fourier-transform microwave/pulsed uniform flow spectrometer. I. The low-temperature flow system.

We report the development of a new instrument that combines chirped-pulse microwave spectroscopy with a pulsed uniform supersonic flow. This combination promises a nearly universal detection method that can deliver isomer and conformer specific, quantitative detection and spectroscopic characterization of unstable reaction products and intermediates, product vibrational distributions, and molecular excited states. This first paper in a series of two presents a new pulsed-flow design, at the heart of which is a fast, high-throughput pulsed valve driven by a piezoelectric stack actuator. Uniform flows at temperatures as low as 20 K were readily achieved with only modest pumping requirements, as demonstrated by impact pressure measurements and pure rotational spectroscopy. The proposed technique will be suitable for application in diverse fields including fundamental studies in spectroscopy, kinetics, and reaction dynamics.

Unstable Reaction Intermediates and Hysteresis during the Catalytic Cycle of 5-Aminolevulinate Synthase: Implications from Using Pseudo and Alternate Substrates and a Promiscuous Enzyme Variant

5-Aminolevulinate (ALA), an essential metabolite in all heme-synthesizing organisms, results from the pyridoxal 5'-phosphate (PLP)-dependent enzymatic condensation of glycine with succinyl-CoA in non-plant eukaryotes and α-proteobacteria. The predicted chemical mechanism of this ALA synthase (ALAS)-catalyzed reaction includes a short-lived glycine quinonoid intermediate and an unstable 2-amino-3-ketoadipate intermediate. Using liquid chromatography coupled with tandem mass spectrometry to analyze the products from the reaction of murine erythroid ALAS (mALAS2) with O-methylglycine and succinyl-CoA, we directly identified the chemical nature of the inherently unstable 2-amino-3-ketoadipate intermediate, which predicates the glycine quinonoid species as its precursor. With stopped-flow absorption spectroscopy, we detected and confirmed the formation of the quinonoid intermediate upon reacting glycine with ALAS. Significantly, in the absence of the succinyl-CoA substrate, the external aldimine predominates over the glycine quinonoid intermediate. When instead of glycine, L-serine was reacted with ALAS, a lag phase was observed in the progress curve for the L-serine external aldimine formation, indicating a hysteretic behavior in ALAS. Hysteresis was not detected in the T148A-catalyzed L-serine external aldimine formation. These results with T148A, a mALAS2 variant, which, in contrast to wild-type mALAS2, is active with L-serine, suggest that active site Thr-148 modulates ALAS strict amino acid substrate specificity. The rate of ALA release is also controlled by a hysteretic kinetic mechanism (observed as a lag in the ALA external aldimine formation progress curve), consistent with conformational changes governing the dissociation of ALA from ALAS.

Isoclast Active Manufacture: In Situ Spectroscopic Investigation of the Unstable Products of Cyanamide and Sodium Hypochlorite Reactions

Isoclast Active is a new insecticide manufactured by Dow AgroSciences LLC. In an effort to lower the cost of manufacture of Isoclast Active, we have studied the reaction which produces N-cyano sulfilimine, which is the precursor to Isoclast Active. The reaction involves the oxidative coupling of cyanamide with the sulfide intermediate using sodium hypochlorite. In this study, we demonstrated that a transient intermediate species is produced by the reaction between bleach and cyanamide. On the basis of in situ Raman, IR, and NMR spectroscopic evidence we propose that the intermediate is the anionic form of N-chlorocyanamide: ClN––C≡N. The degradation of this intermediate species was found to be highly sensitive to its environment and leads to a complicated mixture of products. This work also demonstrates that in situ Raman and IR spectroscopy are powerful and invaluable tools for monitoring reactions/processes involving unstable reaction intermediates for kinetic modeling and process R&D.

Real Time Determination of the Electronic Structure of Unstable Reaction Intermediates during Au2O3 Reduction.

Chemical reactions are always associated with electronic structure changes of the involved chemical species. Determining the electronic configuration of an atom allows probing its chemical state and gives understanding of the reaction pathways. However, often the reactions are too complex and too fast to be measured at in situ conditions due to slow and/or insensitive experimental techniques. A short-lived Au2O compound has been detected for the first time under in situ conditions during the temperature-programmed reduction of Au2O3. A time-resolved resonant inelastic X-ray scattering experiment (RIXS) allowed the determination of changes in the Au electronic structure, enabling a better understanding of the reaction mechanism of Au(III) reduction. On the basis of time-resolved RIXS data analysis combined with genetic algorithm methodology, we determined the electronic structure of the metastable Au2O intermediate species. The data analysis showed a notably larger value for the lattice constant of the intermediate Au as compared to the theoretical predictions. With support of DFT calculations, we found that such a structure may indeed be formed and that the expanded lattice constant is due to the termination of Au2O on the Au2O3 structure.

Direct Observation of Unstable Reaction Intermediates by Acid‐Base Complex Formation

The structures of several unstable or metastable reaction intermediates that were photoproduced in crystals were analyzed by using X-ray techniques. The presence of enough void space around the reactive group(s) is an essential factor for the reaction to occur with retention of the single-crystal form. To expand the void space, an acid group (COOH) was substituted onto the reactant molecule and acid-base complex crystals were prepared with several amines, such as dibenzylamine and dicyclohexylamine. Following the formation of such acid-base complexes in crystals, the metastable structures of nitrenes and red species of photochromic salicylideneanilines have been successfully analyzed by using X-ray techniques. Moreover, the structure of a Pt complex anion in the excited state has been analyzed, which formed acid-base complex crystals with various alkylammonium cations. The formation of acid-base complexes will be a powerful tool for directly observing the structure of unstable or metastable reaction intermediates by using X-ray techniques.

結晶相反応の動的構造解析と化学反応性の解明

It was found that a chiral alkyl group bonded to the cobalt atom in a cobalt complex crystal was racemized with retention of the single crystal form on exposure to visible light. Such reactions, which are called crystalline-state reactions, have been found in a variety of cobalt complex crystals. The concept of reaction cavity was introduced to explain the reaction rate quantitatively and the chirality of the photo-product. The new diffractometers and detectors were made for rapid data collection. The reaction mechanism was also elucidated using neutron diffraction analysis. The unstable reaction intermediates were analyzed using cryo-trapping method. The excited-state structures were obtained at the equilibrium state between ground and excited states.

Ligand migration through the internal hydrophobic cavities in human neuroglobin

Neuroglobin (Ngb), a member of the globin superfamily, was found in the brain of vertebrates and is suggested to play a neuroprotective function under hypoxic conditions by scavenging nitrogen monoxide (NO) through a dioxygenase activity. In order for such a reaction to efficiently take place and to minimize the release of reactive intermediates in the cytosol, the cosubstrates O(2) and NO and other unstable reaction intermediates should bind sequentially to docking sites in the protein matrix. We have characterized the accessibility of these sites by analyzing the geminate CO rebinding kinetics to the heme moiety observed upon nanosecond flash photolysis of the Ngb-CO complex encapsulated in silica gels. The geminate rebinding phase showed a remarkable complexity, revealing the presence of a system of secondary docking sites where ligands are stored for hundreds of microseconds. Most kinetics steps display little temperature dependence, demonstrating that ligands can easily migrate through the cavities, except for the slowest reaction intermediate, possibly reflecting a structural conformational change reshaping the system of cavities. This conformational change is unrelated with distal His E7 binding to the heme, as it persists for the HE7L mutant. Overall, data are consistent with the presence of a discrete system of docking sites, possibly acting as reservoirs for the putative cosubstrates and for other reactive species involved in the physiologically relevant reaction.

X-ray observation of a transient hemiaminal trapped in a porous network

X-ray crystallography is the method of choice for the direct structural analysis of crystalline compounds. Extending its use to the in situ mapping of chemical transformations could provide valuable insights, as illustrated by time-resolved X-ray crystallography studies; however, the transient nature of unstable reaction intermediates often poses a significant challenge. It has recently been demonstrated that standard chemical reactions can occur within the pores of porous coordination networks and that the robust crystallinity of these networks facilitates in situ X-ray analysis of the adducts and products. Here we show that such systems even enable X-ray observations of reaction intermediates that are usually transient and non-isolable. Our proof-of-concept demonstration examines the simple and ubiquitous reaction between an amine and an aldehyde, which normally form a very short-lived hemiaminal that then yields the Schiff-base product. The mechanism of this reaction has been exhaustively examined, but the hemiaminal intermediate has only rarely been observed. We first determine the structure of a porous network with an aromatic amine embedded in it, then diffuse an aldehyde substrate into the material to transform the amine into a hemiaminal intermediate that is kinetically trapped and thus amenable to X-ray analysis, and finally raise the temperature of the system to obtain the imine product and determine its structure. These results establish that porous network materials provide a means of obtaining sequential X-ray-based snapshots of the structural transformations that occur during chemical reactions.

Molecular crystal balls

Sorcerers have long gazed into crystal balls to conjure up information. Chemists are also getting in on the act, using porous crystals to trap unstable reaction intermediates and to reveal their structures.

Actin disassembly by cofilin, coronin, and Aip1 occurs in bursts and is inhibited by barbed-end cappers

Turnover of actin filaments in cells requires rapid actin disassembly in a cytoplasmic environment that thermodynamically favors assembly because of high concentrations of polymerizable monomers. We here image the disassembly of single actin filaments by cofilin, coronin, and actin-interacting protein 1, a purified protein system that reconstitutes rapid, monomer-insensitive disassembly (Brieher, W.M., H.Y. Kueh, B.A. Ballif, and T.J. Mitchison. 2006. J. Cell Biol. 175:315–324). In this three-component system, filaments disassemble in abrupt bursts that initiate preferentially, but not exclusively, from both filament ends. Bursting disassembly generates unstable reaction intermediates with lowered affinity for CapZ at barbed ends. CapZ and cytochalasin D (CytoD), a barbed-end capping drug, strongly inhibit bursting disassembly. CytoD also inhibits actin disassembly in mammalian cells, whereas latrunculin B, a monomer sequestering drug, does not. We propose that bursts of disassembly arise from cooperative separation of the two filament strands near an end. The differential effects of drugs in cells argue for physiological relevance of this new disassembly pathway and potentially explain discordant results previously found with these drugs.

Structure and Reactivity of a Thermostable Prokaryotic Nitric-oxide Synthase That Forms a Long-lived Oxy-Heme Complex

In an effort to generate more stable reaction intermediates involved in substrate oxidation by nitric-oxide synthases (NOSs), we have cloned, expressed, and characterized a thermostable NOS homolog from the thermophilic bacterium Geobacillus stearothermophilus (gsNOS). As expected, gsNOS forms nitric oxide (NO) from l-arginine via the stable intermediate N-hydroxy l-arginine (NOHA). The addition of oxygen to ferrous gsNOS results in long-lived heme-oxy complexes in the presence (Soret peak 427 nm) and absence (Soret peak 413 nm) of substrates l-arginine and NOHA. The substrate-induced red shift correlates with hydrogen bonding between substrate and heme-bound oxygen resulting in conversion to a ferric heme-superoxy species. In single turnover experiments with NOHA, NO forms only in the presence of H(4)B. The crystal structure of gsNOS at 3.2 AA of resolution reveals great similarity to other known bacterial NOS structures, with the exception of differences in the distal heme pocket, close to the oxygen binding site. In particular, a Lys-356 (Bacillus subtilis NOS) to Arg-365 (gsNOS) substitution alters the conformation of a conserved Asp carboxylate, resulting in movement of an Ile residue toward the heme. Thus, a more constrained heme pocket may slow ligand dissociation and increase the lifetime of heme-bound oxygen to seconds at 4 degrees C. Similarly, the ferric-heme NO complex is also stabilized in gsNOS. The slow kinetics of gsNOS offer promise for studying downstream intermediates involved in substrate oxidation.

Structural Motifs and Reactivity of Small Molecules Containing Subvalent Group 13 Elements: Matrix Isolation and Quantum Chemical Studies

AbstractFor Abstract see ChemInform Abstract in Full Text.

Cold-spray ionization mass spectrometry: principle and applications.

A direct solution analysis method, cold-spray ionization (CSI) mass spectrometry (MS), a variant of electrospray (ESI) MS operating at low temperature (ca -80 to 10 degrees C), allows the facile and precise characterization of labile organic species, especially those in which non-covalent bonding interactions are prominent. We applied this method to investigations of the solution structures of many labile organic species, including unstable reagents and reaction intermediates, asymmetric catalysts, supramolecules and even primary biomolecules. Remarkable analytical results were obtained for highly ordered supramolecules using the CSI method. Whereas conventional ESI is not applicable to these compounds because of their instability to heat and/or air, CSI affords multiply charged molecular ions with many solvent molecules attached. Investigation of the constitution of Grignard reagents in solution is extremely challenging, but CSI-MS allowed us to identify one of the key structures in THF solution. Recently, this method was adopted for investigations of the solution structures of primary biomolecules such as nucleosides, amino acids, sugars and lipids, revealing singly charged Na(+) adducts of large clusters (chain structures), presumably linked by non-covalent interactions, including hydrogen bonding and/or hydrophobic interactions. The principle of the CSI method and applications of the method to a wide variety of labile organic species and primary biomolecules in solution are described.

Structural motifs and reactivity of small molecules containing subvalent Group 13 elements: matrix isolation and quantum chemical studies

This review analyses some aspects of the variety of different structures small molecular compounds of the subvalent Group 13 elements can adopt. The discussion of experimental work restricts itself to matrix isolation studies. The experimental results are compared with those obtained for related (more stable) molecules using experimental methods other than matrix isolation and with the results of quantum chemical studies. Special consideration is given to the structural changes between homologues. All the molecules dealt with represent highly unstable species or reaction intermediates which can nevertheless be retained and characterized at leisure with the aid of the matrix-isolation technique. The combination of experimental spectroscopic information and detailed quantum chemical calculations can be used as a framework to analyse in detail the molecular and electronic structures of these species, most of which were sighted only very recently in experiments. Trends and differences in reactivity will also be considered, where information (experimental or theoretical) is available.