Structures Of Reaction Intermediates Research Articles

Cerium Photocatalyst in Action: Structural Dynamics in the Presence of Substrate Visualized via Time-Resolved X-ray Liquidography.

[Ce(III)Cl6]3-, with its earth-abundant metal element, is a promising photocatalyst facilitating carbon-halogen bond activation. Still, the structure of the reaction intermediate has yet to be explored. Here, we applied time-resolved X-ray liquidography (TRXL), which allows for direct observation of the structural details of reaction intermediates, to investigate the photocatalytic reaction of [Ce(III)Cl6]3-. Structural analysis of the TRXL data revealed that the excited state of [Ce(III)Cl6]3- has Ce-Cl bonds that are shorter than those of the ground state and that the Ce-Cl bond further contracts upon oxidation. In addition, this study represents the first application of TRXL to both photocatalyst-only and photocatalyst-and-substrate samples, providing insights into the substrate's influence on the photocatalyst's reaction dynamics. This study demonstrates the capability of TRXL in elucidating the reaction dynamics of photocatalysts under various conditions and highlights the importance of experimental determination of the structures of reaction intermediates to advance our understanding of photocatalytic mechanisms.

Scanning tunneling microscopy under chemical reaction at solid–liquid and solid–gas interfaces

The task of bridging the pressure gap between ideal ultrahigh vacuum conditions and more realistic reaction conditions involving gas and liquid phases is crucial in surface and interfacial chemistry. Scanning tunneling microscopy (STM) has played a key role in addressing this challenge by enabling atomic-scale probing of the interface. STM enabled us to study surface structure, electronic structure, atomic manipulation, dynamics of molecules and atoms, and chemical properties of the surface at the atomic scale. Over the past four decades, the field of STM has undergone explosive growth. This review article focuses on recent advances in operando STM, specifically in the study of solid–liquid and solid–gas interfaces. It highlights the latest works in ambient-pressure STM, which has enabled the observation of atomic features under various gas and reaction conditions. This information sheds light on the surface mobility of adsorbates and atomic structures of reaction intermediates. The review also addresses research on electrochemical STM, which investigates the evolution of surface morphology under electrochemical processes and provides insights into atomic-scale reaction mechanisms. Finally, the article outlines future challenges and perspectives for operando STM techniques.

Modelling complex molecular interactions in catalytic materials for energy storage and conversion in nuclear magnetic resonance

Nuclear magnetic resonance (NMR) is a non-destructive and atom-specific specific tool that has become a burgeoning analytic method for understanding the detailed molecular interactions in catalysis and energy storage materials. However, the observation of diverse chemical shifts arising from complex molecular interactions makes the interpretation of NMR spectroscopy increasingly challenging, in particular for a novel system without standards for comparison. Density functional theory-NMR (DFT-NMR) is an indispensable tool to mitigate these challenges and provide detailed 3D molecular structures that relate materials and reaction intermediate structures, and information about chemical interactions, dynamics, and reaction mechanisms. This review provides a fundamental background in DFT-NMR relating to theory development, critical parameters for calculating NMR properties, computational accuracy, and the current capabilities. A variety of practical examples from the fields of catalysis and energy storage, including CO2 capture, are summarized to illustrate the capabilities of DFT-NMR application to date. Last but not least, cautionary notes on the application of these strategies are presented for researchers modeling their own systems.

Chemical kinetics modeling for combustion of Al in CO2

A detailed reaction mechanism for the oxidation of aluminum with CO2 in the gas phase has been investigated. Quantum chemical calculations were performed to obtain molecular structures of reaction intermediates and transition states on the reaction pathways. A highly accurate method was applied to calculate potential energies and thermodynamic properties for the molecular structures. The rate coefficients of each reaction path were also obtained from calculations on the chemical reaction theory. A detailed chemical kinetic model was constructed from obtained rate coefficients and thermodynamic properties of molecules. Chemical kinetic analysis showed the Al + CO2 ⇔ AlO + CO reaction and Al2 + CO2 ⇔ Al2O + CO reaction were predominant in that reaction system.

Genomic mapping of DNA-repair reaction intermediates in living cells with engineered DNA structure-trap proteins.

Diverse DNA structures occur as reaction intermediates in various DNA-damage and -repair mechanisms, most of which results from replication stress. We harness the power of proteins evolutionarily optimized to bind and "trap" specific DNA reaction-intermediate structures, to quantify the structures, and discern the mechanisms of their occurrence in cells. The engineered proteins also allow genomic mapping of sites at which specific DNA structures occur preferentially, using a structure-trapping protein and ChIP-seq- or Cut-and-Tag-like methods. Genome-wide identification of sites with recurrent DNA-damage intermediates has illuminated mechanisms implicated in genome instability, replication stress, and chromosome fragility. Here, we describe X-seq, for identifying sites of recurrent four-way DNA junctions or Holliday-junctions (HJs). X-seq uses an engineered, catalysis-defective mutant of Escherichia coli RuvC HJ-specific endonuclease, RuvCDefGFP. X-seq signal indicates sites of recombinational DNA repair or replication-fork stalling and reversal. We also describe methods for genomic mapping of 3'-single-stranded DNA ends with SsEND-seq, in E. coli. Both methods allow genomic profiling of DNA-damage and -repair intermediates, which can precede genome instability, and are expected to have many additional applications including in other cells and organisms.

Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules.

Several important Gram-negative bacterial pathogens possess surface capsular layers composed of hypervariable long-chain polysaccharides linked via a conserved 3-deoxy-β-D-manno-oct-2-ulosonic acid (β-Kdo) oligosaccharide to a phosphatidylglycerol residue. The pathway for synthesis of the terminal glycolipid was elucidated by determining the structures of reaction intermediates. In Escherichia coli, KpsS transfers a single Kdo residue to phosphatidylglycerol; this primer is extended using a single enzyme (KpsC), possessing two cytidine 5'-monophosphate (CMP)-Kdo-dependent glycosyltransferase catalytic centers with different linkage specificities. The structure of the N-terminal β-(2→4) Kdo transferase from KpsC reveals two α/β domains, supplemented by several helices. The N-terminal Rossmann-like domain, typically responsible for acceptor binding, is severely reduced in size compared with canonical GT-B folds in glycosyltransferases. The similar structure of the C-terminal β-(2→7) Kdo transferase indicates a past gene duplication event. Both Kdo transferases have a narrow active site tunnel, lined with key residues shared with GT99 β-Kdo transferases. This enzyme provides the prototype for the GT107 family.

Benzo-Fused Periacenes or Double Helicenes? Different Cyclodehydrogenation Pathways on Surface and in Solution.

Controlling the regioselectivity of C–H activation in unimolecular reactions is of great significance for the rational synthesis of functional graphene nanostructures, which are called nanographenes. Here, we demonstrate that the adsorption of tetranaphthyl-p-terphenyl precursors on metal surfaces can completely change the cyclodehydrogenation route and lead to obtaining planar benzo-fused perihexacenes rather than double [7]helicenes during solution synthesis. The course of the on-surface planarization reactions is monitored using scanning probe microscopy, which unambiguously reveals the formation of dibenzoperihexacenes and the structures of reaction intermediates. The regioselective planarization can be attributed to the flattened adsorption geometries and the reduced flexibility of the precursors on the surfaces, in addition to the different mechanism of the on-surface cyclodehydrogenation from that of the solution counterpart. We have further achieved the on-surface synthesis of dibenzoperioctacene by employing a tetra-anthryl-p-terphenyl precursor. The energy gaps of the new nanographenes are measured to be approximately 2.1 eV (dibenzoperihexacene) and 1.3 eV (dibenzoperioctacene) on a Au(111) surface. Our findings shed new light on the regioselectivity in cyclodehydrogenation reactions, which will be important for exploring the synthesis of unprecedented nanographenes.

First-Principles Study of Oxygen Reduction Reaction at Defective TiO2 Surfaces

As future alternatives to Pt-based materials, group-IV oxides have been proposed for electrocatalysts against the oxygen reduction reaction (ORR) in acid solution [1]. Those oxides are abundant and electrochemically stable while Pt is scarce and soluble in acid solution. Although pristine oxides are nonreactive, they can be made reactive by introducing defects. For example, in the case of TiO2, doping Nb atoms and introducing oxygen vacancies (VOs) makes the oxide reactive [2]. However, the microscopic mechanisms of the reaction at defective oxide surfaces are still not well understood. In order to improve our understandings on the ORR at defective oxides, we have performed density functional theory simulations. We have studied defective TiO2 as an example of defective oxides. A challenge in theoretical study of the reaction on defective oxides is high complexities of the surfaces. At defective oxide surfaces, there are many possible active sites, defect configurations and adsorbed structures of reaction intermediates. In order to elucidate the reaction on the surface, extensive investigations are mandatory. For an extensive investigation, we have studied two major polymorphs of TiO2 (rutile and anatase), several defect configurations, several surface orientations and many adsorbed structures of intermediates. As for surface orientations, we have studied the rutile (110) surface, the anatase (101), (100), (001) and (001)-(1x4) reconstructed surfaces. In total, we investigated the total energies of about 500 configurations. By calculating the free energies of reaction intermediates using PBE+U functional with computational hydrogen electrode model, we found the followings. (1) At Nb-doped TiO2 surfaces, calculated free energy of OH* intermediate is very low. This indicates that this surface is poisoned by OH* intermediate and nonreactive against ORR. The strong adsorption is because the adsorbed OH captures an electron from Ti3+ generated by a NbTi defect and thus produced OH- is very stable. (2) At oxygen-deficient surfaces (VO surfaces), the calculated free energy of O* intermediate at VO site is very low, so the VO surface seems to be nonreactive and poisoned by O* intermediate. This is because the O* intermediate can capture two electrons from two Ti3+, which arise by making VO on the surface, and the resulting surface are very stable because they are pristine surfaces. Our calculations indicate that both the Nb-doped surface and Vo surface are likely to be nonreactive. (3) If we take the OH poison of Ti3+ existing surface into consideration, it is natural that there exists the OH poisoned VO surface (VO+2OH* surface), where the Vo site is unoccupied and the two surface Ti sites are adsorbed by OH* intermediates. On this surface, there are no Ti3+ because OH* intermediates capture electrons from Ti3+s, and so the VO site may be reactive. Indeed, at the VO+2OH* surface, the calculated adsorption strength of O* intermediate is moderate, this means the surface is likely to be reactive. The calculated free energies of the entire reaction intermediates suggest that the anatase (001) surface has much higher reactivity than other surfaces. These results indicate that the VO site without Ti3+ is the most likely reactive site of the ORR on defective TiO2 surfaces. K. Ota, Y. Ohgi, K. Matsuzawa, S. Mitsushima and A. Ishihara, ECS Transaction 45(2), 27 (2012).A. Ishihara, M. Hamazaki, M. Arao, M. Matsumoto, H. Imai, Y. Kohno, K. Matsuzawa, S. Mitsushima and K. Ota, J. Electrochem. Soc. 163, F603 (2016).

A sapphire single-crystal cell for in situ neutron powder diffraction of solid-gas reactions

Solid-gas reactions play an important role in many technologically important processes from ore smelting to hydrogen storage and the synthesis of functional materials. In situ investigations are very useful for unraveling basic steps of such reactions, rationalizing them and gaining control. For investigating time-resolved solid-gas reactions, we have constructed a gas pressure cell for elastic neutron diffraction. By proper orientation of a single-crystal sapphire tube as sample holder, Bragg peaks from the container material can be completely avoided, thus yielding high-quality powder diffraction data with very clean diffraction background. This enables the extraction of high precision crystal structure data as a function of gas pressure and temperature (laser heating) in time-resolved studies. The potential of the gas pressure cell is demonstrated by in situ studies of the reaction of solids with hydrogen, which yielded detailed models of the reaction pathways including high quality crystal structures of reaction intermediates and products. These were used to predict successfully the existence of further metal hydrides, to explain unusual bonding properties, and to optimize the synthesis of metastable compounds.

Impact of zeolite-Y framework on the geometry and reactivity of Ru (III) benzimidazole complexes – A DFT study

A detailed comparative Density Functional Theory (DFT) study is made to understand the structural changes of the guest complex due to steric and electronic interactions with the host framework. In this study, Ru(III) benzimidazole and 2- ethyl Ru(III) benzimidazole complexes encapsulated in a supercage of zeolite Y. The zeolitic framework integrity is not disturbed by the intrusion of the large guest complex. A blue shift in the d–d transition observed in the UV-Visible spectroscopic studies of the zeolite encapsulated complexes and they shows a higher catalytic efficiency. Encapsulation of zeolite matrix makes the metal center more viable to nucleophilic attack and favors the phenol oxidation reaction. Based on the theoretical calculations, transition states and structures of reaction intermediates involved in the catalytic cycles are derived.

Bond Order Conservation Strategies in Catalysis Applied to the NH3 Decomposition Reaction

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. We have applied this approach together with linear scaling of adsorption energies to obtain the energetics of the NH3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. This information is used to establish a microkinetic model for the formation of N2 and H2, thus providing insight into the components of the reaction that determines the activity.

Collisions of FeO+ with H2 and He in a Cryogenic Ion Trap

The nominal temperature range of cryogenic radio-frequency ion traps has recently been extended down to T=2.3 K. Whereas in situ He tagging of mass-selected ions embedded in dense helium buffer gas is becoming common for recording IR spectra through photofragmentation of small and large ions, much less activity is devoted to the field of cold chemistry, which in this contribution means the two orders of magnitude extending from 300 to below 3 K. The importance of this temperature range for understanding the dynamics of bi- and termolecular reactions is illustrated with new results for the time-honored reaction of FeO+ with H2 obtained with the cryogenic ion trap ISORI in Prague. The rate coefficient for forming Fe+ +H2 O increases steeply with decreasing temperature. In addition more product channels open up, such as the stabilized reaction-intermediate complexes H2 FeO+ and Hen -FeO+ formed by ternary association with He. For the FeOH+ +H channel only a minor signal is observed. The rate coefficients provide deep insight into lifetimes, bottlenecks, and barriers impeding almost completely the exothermic, but spin-forbidden, reaction at room temperature. For some of the He-tagged ions, IR predissociation spectra are recorded. A breakthrough is obtaining the first spectrum of [(H2 )FeO]+ , synthesized and tagged in situ with He. These results pave the way to study the structures of reaction intermediates stabilized in the gas phase by means of collisions with helium.

Theoretical study on gas decomposition mechanism of SF6 by quantum chemical calculation

Sulfur hexafluoride has excellent insulating and arc-suppression properties, and is widely used in gas-insulated switchgear. Under high voltage discharge condition, SF6 decomposes into various by-products according to discharge scenarios. The formation mechanism of decomposition products is so far not clear. For most of the studies, experimental measurements are used to speculate the reaction mechanism, and those research is postulated with great arbitrariness. Quantum chemical calculation by using high precision simulation theory is a very effective method to reveal the microcosmic mechanism of complex chemical reaction. Therefore, in this paper, we used high level quantum chemical method (B3P86/6-31G∗∗) to study the mechanism of decomposition reaction and products, in presence of trace air or H2O. The decomposition products include SO2, H2S, and HF. For each reaction product, we provide a detailed generation pathway, including the data and energy structure of reaction intermediates and transition states. The simulation results can explain the experimental results accurately, and provide new understanding and support for the judgment of the discharge reaction state and subsequent electrical aging. These results are very helpful to build SF6/H2O/O2 reaction model, and indicate the electrical aging process from microcosmic angle.

Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering.

Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.

Direct observation of bond formation in solution with femtosecond X-ray scattering.

The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ∼500femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein.

Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.

X-ray absorption spectroscopy with time-tagged photon counting: application to study the structure of a Co(i) intermediate of H2 evolving photo-catalyst.

In order to probe the structure of reaction intermediates of photochemical reactions a new setup for laser-initiated time-resolved X-ray absorption (XAS) measurements has been developed. With this approach the arrival time of each photon in respect to the laser pulse is measured and therefore full kinetic information is obtained. All X-rays that reach the detector are used to measure this kinetic information and therefore the detection efficiency of this method is high. The newly developed setup is optimized for time-resolved experiments in the microsecond range for samples with relatively low metal concentration (∼1mM). This setup has been applied to study a multicomponent photocatalytic system with a Co(dmgBF(2))(2) catalyst (dmg(2-) = dimethylglyoximato dianion), [Ru(bpy)(3)](2+) chromophore (bpy = 2,2'-bipyridine) and methyl viologen as the electron relay. On the basis of the analysis of hundreds of Co K-edge XAS spectra corresponding to different delay times after the laser excitation of the chromophore, the presence of a Co(i) intermediate is confirmed. The calculated X-ray transient signal for a model of Co(i) state with a 0.14 Å displacement of Co out of the dmg ligand plane and with the closest solvent molecule at a distance of 2.06 Å gives reasonable agreement with the experimental data.

Enantioselective Henry Reaction Catalyzed by “Ship in a Bottle” Complexes

Two chiral Schiff-base complexes of copper(II) have been successfully encapsulated inside the cavity of zeolite-NaY via a "ship in a bottle" synthesis method. The presence of the two complexes inside the cages of zeolite-Y has been confirmed based on various spectrochemical and physicochemical techniques, viz. FTIR, UV-vis/DRS, ESR, XPS, CV, EDX, SEM, and TGA. Zeolite-encapsulated chiral copper(II) Schiff-base complexes are found to give a high-enantioselective (84% ee, R conformation) nitro-aldol product at -20 °C. The encapsulated copper complexes are found to show higher catalytic efficiency than their homogeneous counterparts under identical conditions. Density functional theory (DFT) calculation has been implemented to understand the effect of the zeolite matrix on structural, electronic, and reactivity properties of the synthesized complexes. Theoretical calculation predicts that upon encapsulation into the zeolite matrix the Cu center becomes more susceptible to nucleophilic attack, favoring a nitro-aldol reaction. A plausible mechanism is suggested based on the experimental and theoretical results. The structures of reaction intermediates and transition state(s) involved in the catalytic cycle are derived using DFT.

Development of 4-aminoquinoline-1,3,5-triazine conjugates as potent antibacterial agent through facile synthetic route

A series of novel hybrid 4-aminoquinoline-1,3,5-triazine derivatives were developed and subsequently tested against representative Gram-positive and Gram-negative microorganisms for determination of their antibacterial activity. Screening results indicate that, title molecule exhibit moderate to potent activity in comparison to standard. These hybrid derivatives were synthesized through a facile synthetic routes and structure of reaction intermediates as well as target molecules were recognised with the aid of various spectroscopic techniques viz., FTIR, NMR, mass and elemental analysis.

Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: SUBSTRATE CLEAVAGE, ENOLATE STABILIZATION, AND SUBSTRATE SPECIFICITY

Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8-2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3-C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg(70) assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg(70) stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate.