Insertion Intermediates Research Articles

Diborane Reductions of CO2 and CS2 Mediated by Dicopper μ-Boryl Complexes of a Robust Bis(phosphino)-1,8-naphthyridine Ligand.

A dinucleating 1,8-naphthyridine ligand featuring fluorene-9,9-diyl-linked phosphino side arms (PNNPFlu) was synthesized and used to obtain the cationic dicopper complexes 2, [(PNNPFlu)Cu2(μ-Ph)][NTf2]; [NTf2] = bis(trifluoromethane)sulfonimide, 6, [(PNNPFlu)Cu2(μ-CCPh)][NTf2], and 3, [(PNNPFlu)Cu2(μ-OtBu)][NTf2]. Complex 3 reacted with diboranes to afford dicopper μ-boryl species (4, with μ-Bcat; cat = catecholate and 5, with μ-Bpin; pin = pinacolate) that are more reactive in C(sp)-H bond activations and toward activations of CO2 and CS2, compared to dicopper μ-boryl complexes supported by a 1,8-naphthyridine-based ligand with di(pyridyl) side arms. The solid-state structures and DFT analysis indicate that the higher reactivities of 4 and 5 relate to changes in the coordination sphere of copper, rather than to perturbations on the Cu-B bonding interactions. Addition of xylyl isocyanide (CNXyl) to 4 gave 7, [(PNNPFlu)Cu2(μ-Bcat)(CNXyl)][NTf2], demonstrating that the lower coordination number at copper is chemically significant. Reactions of 4 and 5 with CO2 yielded the corresponding dicopper borate complexes (8, [(PNNPFlu)Cu2(μ-OBcat)][NTf2]; 9, [(PNNPFlu)Cu2(μ-OBpin)][NTf2]), with 4 demonstrating catalytic reduction in the presence of excess diborane. Related reactions of 4 and 5 with CS2 provided insertion products 10, {[(PNNPFlu)Cu2]2[μ-S2C(Bcat)2]}[NTf2]2, and 11, [(PNNPFlu)Cu2(μ,κ2-S2CBpin)][NTf2], respectively. These products feature Cu-S-C-B linkages analogous to those of proposed CO2 insertion intermediate.

Substrate-driven assembly of a translocon for multipass membrane proteins

Most membrane proteins are synthesized on endoplasmic reticulum (ER)-bound ribosomes docked at the translocon, a heterogeneous ensemble of transmembrane factors operating on the nascent chain1,2. How the translocon coordinates the actions of these factors to accommodate its different substrates is not well understood. Here we define the composition, function and assembly of a translocon specialized for multipass membrane protein biogenesis3. This ‘multipass translocon’ is distinguished by three components that selectively bind the ribosome–Sec61 complex during multipass protein synthesis: the GET- and EMC-like (GEL), protein associated with translocon (PAT) and back of Sec61 (BOS) complexes. Analysis of insertion intermediates reveals how features of the nascent chain trigger multipass translocon assembly. Reconstitution studies demonstrate a role for multipass translocon components in protein topogenesis, and cells lacking these components show reduced multipass protein stability. These results establish the mechanism by which nascent multipass proteins selectively recruit the multipass translocon to facilitate their biogenesis. More broadly, they define the ER translocon as a dynamic assembly whose subunit composition adjusts co-translationally to accommodate the biosynthetic needs of its diverse range of substrates.

Palladium-Catalyzed Insertion of Ethylene and 1,1-Disubstituted Difunctional Olefins: An Experimental and Computational Study.

Insertion or coordination copolymerization of ethylene with di-substituted olefins is challenging and the choice of di-substituted mono-functional olefin versus di-substituted di-functional olefin (DDO) appears to be decisive. Here we show that DDO-inserted species are amenable to ethylene insertion and polymerization. DDOs such as 2-acetamidoacrylic acid (AAA), methyl 2-acetamidoacrylate (MAAA), and ethyl 2-cyanoacrylate (ECA) were treated with palladium complex [{P∧O}PdMe(L)] (P∧O=κ2 -P,O-Ar2 PC6 H4 SO2 O with Ar=2-MeOC6 H4 ; L=C2 H6 OS) and the existence of respective insertion intermediates in moderate yield (up to 37 %) was established. These intermediates were exposed to ethylene and corresponding ethylene-inserted products were isolated and characterized. A careful comparison with three model compounds confirmed ethylene insertion and polymerization. Thus, the combined experimental and computational investigations show that DDO-inserted species can undergo ethylene insertion and polymerization.

Mechanism Studies of Ir-Catalyzed Asymmetric Hydrogenation of Unsaturated Carboxylic Acids.

The Ir-catalyzed asymmetric hydrogenation of olefins is widely used for production of value-added bulk and fine chemicals. The iridium catalysts with chiral spiro phosphine-oxazoline ligands developed in our group show high activity and high enantioselectivity in the hydrogenation of olefins bearing a coordinative carboxyl group, such as α,β-unsaturated carboxylic acids, β,γ-unsaturated carboxylic acids, and γ,δ-unsaturated carboxylic acids. Here we conducted detailed mechanistic studies on these Ir-catalyzed asymmetric hydrogenation reactions by using (E)-2-methyl-3-phenylacrylic acid as a model substrate. We isolated and characterized several key intermediates having Ir-H bonds under the real hydrogenation conditions. Particularly, an Ir(III) migratory insertion intermediate was first isolated in an asymmetric hydrogenation reaction promoted by chiral Ir catalysts. That this intermediate cannot undergo reductive elimination in the absence of hydrogen strongly supports the involvement of an Ir(III)/Ir(V) cycle in the hydrogenation. On the basis of the structure of the Ir(III) intermediate, variable-temperature NMR spectroscopy, and density functional theory calculations, we elucidated the mechanistic details of the Ir-catalyzed hydrogenation of unsaturated carboxylic acids and explained the enantioselectivity of the reactions. These findings experimentally and computationally elucidate the mechanism of Ir-catalyzed asymmetric hydrogenation of olefins with a strong coordinative carboxyl group and will likely inspire further catalyst design.

Invitro reconstitution of co-translational D1 insertion reveals a role of the cpSec-Alb3 translocase and Vipp1in photosystem II biogenesis.

Photosystem II (PS II) is a multi-subunit complex localized in the thylakoid membrane that performs the light-dependent photosynthetic charge separation. The PS II reaction centre comprises, among others, the D1 protein. De novo synthesis and repair of PS II require efficient mechanisms for transport and insertion of plastid encoded D1 into the thylakoid membrane. To elucidate the process of D1 insertion, we used an invitro translation system derived from pea chloroplasts to reconstitute the D1 insertion. Thereby, truncated D1 encoding psbA mRNAs lacking a stop codon were translated in the presence of thylakoid membranes and the translation was stalled by addition of chloramphenicol. The generated ribosome nascent chain complexes (RNCs) were tightly associated with the thylakoids. Subsequently, these D1 insertion intermediates were enriched from solubilized thylakoids by sucrose cushion centrifugation. Immunological analyses demonstrated the presence of the cpSec translocase, Alb3, cpFtsY, cpSRP54 and Vipp1 (vesicle-inducing protein in plastids 1) in the enriched D1 insertion intermediates. A complex formation between cpSecY, Alb3, cpFtsY and Vipp1in thylakoid membranes was shown by gel filtration chromatography, BN (Blue Native)/SDS-PAGE and co-immunoprecipitation experiments. Furthermore, a stimulating effect of recombinant Vipp1 on the formation of a D1 insertion intermediate was observed invitro. These results suggest a co-operative function of these proteins in D1 insertion.

Visualization of a polytopic membrane protein during SecY-mediated membrane insertion.

The biogenesis of polytopic membrane proteins occurs co-translationally on ribosomes that are tightly bound to a membrane-embedded protein-conducting channel: the Sec-complex. The path that is followed by nascent proteins inside the ribosome and the Sec-complex is relatively well established; however, it is not clear what the fate of the N-terminal transmembrane domains (TMDs) of polytopic membrane proteins is when the C-terminal TMDs domains are not yet synthesized. Here, we present the sub-nanometer cryo-electron microscopy structure of an in vivo generated ribosome-SecY complex that carries a membrane insertion intermediate of proteorhodopsin (PR). The structure reveals a pre-opened Sec-complex and the first two TMDs of PR already outside the SecY complex directly in front of its proposed lateral gate. Thus, our structure is in agreement with positioning of N-terminal TMDs at the periphery of SecY, and in addition, it provides clues for the molecular mechanism underlying membrane protein topogenesis.

ChemInform Abstract: Pd(II)‐Catalyzed ortho Trifluoromethylation of Arenes and Insights into the Coordination Mode of Acidic Amide Directing Groups.

A Pd(II)-catalyzed trifluoromethylation of ortho C–H bonds with an array of N-arylbenzamides derived from benzoic acids is reported. N-Methylformamide has been identified as a crucial promoter of C–CF3 bond formation from the Pd center. X-ray characterization of the C–H insertion intermediate has revealed a rare coordination mode of acidic amides as directing groups and the origin of their capacity in directing C–H activation.

Vacuum Ultraviolet Photoionization Studies of PtCH2 and H‐Pt‐CH3: A Potential Energy Surface for the Pt+CH4 Reaction

Vacuum Ultraviolet Photoionization Studies of PtCH₂ and H‐Pt‐CH₃: A Potential Energy Surface for the Pt+CH₄ Reaction

Direct Detection of Key Intermediates in Rhodium(I)‐Catalyzed [2+2+2] Cycloadditions of Alkynes by ESI‐MS

The mechanism of the Rh-catalysed [2+2+2] cycloaddition reaction of diynes with monoynes has been examined using ESI-MS and ESI-CID-MS analysis. The catalytic system used consisted of the combination of a cationic rhodium(I) complex with bisphosphine ligands, which generates highly active complexes that can be detected by ESI(+) experiments. ESI-MS on-line monitoring has allowed the detection for the first time of all of the intermediates in the catalytic cycle, supporting the mechanistic proposal based mainly on theoretical calculations. For all ESI-MS experiments, the structural assignments of ions are supported by tandem mass spectrometry analyses. Computer model studies based on density functional theory (DFT) support the structural proposal made for the monoyne insertion intermediate. The collective studies provide new insight into the reactivity of cationic rhodacyclopentadienes, which should facilitate the design of related rhodium-catalysed C-C couplings.

Understanding Reactivity and Stereoselectivity in Palladium-Catalyzed Diastereoselective sp3 C–H Bond Activation: Intermediate Characterization and Computational Studies

The origin of the high levels of reactivity and diastereoselectivity (>99:1 dr) observed in the oxazoline-directed, Pd(II)-catalyzed sp(3) C-H bond iodination and acetoxylation reactions as reported in previous publications has been studied and explained on the basis of experimental and computational investigations. The characterization of a trinuclear chiral C-H insertion intermediate by X-ray paved the way for further investigations into C-H insertion step through the lens of stereochemistry. Computational investigations on reactivities and diastereoselectivities of C-H activation of t-Bu- and i-Pr-substituted oxazolines provided good agreement with the experimental results. Theoretical predictions with DFT calculations revealed that C-H activation occurs at the monomeric Pd center and that the most preferred transition state for C-H activation contains two sterically bulky t-Bu substituents in anti-positions due to steric repulsion and that this transition state leads to the major diastereomer, which is consistent with the structure of the newly characterized C-H insertion intermediate. The structural information about the transition state also suggests that a minimum dihedral angle between C-H bonds and Pd-OAc bonds is crucial for C-H bond cleavage. We have also utilized density functional theory (DFT) to calculate the energies of various potential intermediates and transition states with t-Bu- and i-Pr-substituted oxazolines and suggested a possible explanation for the substantial difference in reactivity between the t-Bu- and i-Pr-substituted oxazolines.

Activation of Propane C-H and C-C Bonds by Gas-Phase Pt Atom: A Theoretical Study

The reaction mechanism of the gas-phase Pt atom with C3H8 has been systematically investigated on the singlet and triplet potential energy surfaces at CCSD(T)//BPW91/6-311++G(d, p), Lanl2dz level. Pt atom prefers the attack of primary over secondary C-H bonds in propane. For the Pt + C3H8 reaction, the major and minor reaction channels lead to PtC3H6 + H2 and PtCH2 + C2H6, respectively, whereas the possibility to form products PtC2H4 + CH4 is so small that it can be neglected. The minimal energy reaction pathway for the formation of PtC3H6 + H2, involving one spin inversion, prefers to start at the triplet state and afterward proceed along the singlet state. The optimal C-C bond cleavages are assigned to C-H bond activation as the first step, followed by cleavage of a C-C bond. The C-H insertion intermediates are kinetically favored over the C-C insertion intermediates. From C-C to C-H oxidative insertion, the lowering of activation barrier is mainly caused by the more stabilizing transition state interaction ΔE≠int, which is the actual interaction energy between the deformed reactants in the transition state.

Pd(II)-Catalyzed Ortho Trifluoromethylation of Arenes and Insights into the Coordination Mode of Acidic Amide Directing Groups

A Pd(II)-catalyzed trifluoromethylation of ortho C-H bonds with an array of N-arylbenzamides derived from benzoic acids is reported. N-Methylformamide has been identified as a crucial promoter of C-CF(3) bond formation from the Pd center. X-ray characterization of the C-H insertion intermediate has revealed a rare coordination mode of acidic amides as directing groups and the origin of their capacity in directing C-H activation.

Key Mechanistic Features of Enantioselective C–H Bond Activation Reactions Catalyzed by [(Chiral Mono-N-Protected Amino Acid)–Pd(II)] Complexes

Monoprotected chiral amino acids have recently been established as a class of ligand scaffolds for effecting Pd-catalyzed enantioselective C-H bond activation reactions. However, to elucidate the mechanistic details and controlling factors of these reactions, more comprehensive studies are needed. In this work we report computational investigations into the key mechanistic features of enantioselective C-H bond activation reactions catalyzed by a [chiral (mono-N-protected amino acid)-Pd(II)] complex. Structural analysis points to a C-H insertion intermediate in which the nitrogen atom of the ligand is bound as a neutral σ-donor. The formation of this C-H insertion intermediate could, in principle, proceed via a "direct C-H cleavage" or via "initial N-H bond cleavage followed by C-H cleavage". The computational studies presented herein show that the pathway initiated by N-H bond cleavage is more kinetically favorable. It is shown that the first step of the reaction is the N-H bond cleavage by the coordinated acetate group (OAc). In the next stage, the weakly coordinated OAc(-) (the second acetate group) activates the ortho-C-H bond of the substrate and transfers the H-atom from the C-atom to the bound N-atom of the ligand. As a result, a new Pd-C bond is formed and the carbamate is converted from X-type to L-type ligand. The absolute configuration of the products that are predicted on the basis of the calculated energies of the transition states matches the experimental data. The calculated enantioselectivity is also comparable with the experimental result. On the basis of these data, the origin of the enantioselectivity can be largely attributed to steric repulsions in the transition states.

ChemInform Abstract: Photochemically Promoted Transition Metal‐Free Cross‐Coupling of Acylsilanes with Organoboronic Esters.

Intermolecular carbon−carbon bond formation between acylsilanes and organoboronic esters was achieved by photoirradiation under almost neutral, transition metal-free conditions. In this reaction, siloxycarbenes generated by photoisomerization of acylsilanes reacted with boronic esters to give the formal B−C bond insertion intermediates, which underwent unique rearrangement to afford the cyclic α-alkoxyboronic esters. Acidic treatment of the resulting crude products under air furnished the cross-coupled ketones in good yields.

Photochemically Promoted Transition Metal-Free Cross-Coupling of Acylsilanes with Organoboronic Esters

Intermolecular carbon-carbon bond formation between acylsilanes and organoboronic esters was achieved by photoirradiation under almost neutral, transition metal-free conditions. In this reaction, siloxycarbenes generated by photoisomerization of acylsilanes reacted with boronic esters to give the formal B-C bond insertion intermediates, which underwent unique rearrangement to afford the cyclic α-alkoxyboronic esters. Acidic treatment of the resulting crude products under air furnished the cross-coupled ketones in good yields.

Why is Pt4+ the Least Efficient Cationic Cluster in Activating the C−H Bond in Methane? Two-State Reaction Computational Investigation

The two-state reaction mechanism of Pt4+ with CH4 on the quartet and doublet potential energy surfaces has been investigated at the B3LYP level. Crossing points between the potential energy surfaces are located using different methods, and possible spin inversion processes are discussed by means of spin−orbit coupling (SOC) calculations. As a result, after the C−H insertion intermediates, two distinct H2 elimination reaction paths have been found, and the second C−H bond broken is regarded as the rate-determining step for two reaction paths. For the first pathway, there is a minimal energy crossing point (MECP) between the two surfaces, where the reacting system will change its spin multiplicities from the quartet state to the doublet state near this crossing region because the magnitude of the spin multiplicity mixing increases in a small energy gap between high- and low-spin states and will greatly enhance the probability of the intersystem crossing. The single P1ISC and double P2ISC passes estimated at MECP (SOC = 201.25 cm−1) are approximately 0.51 and 0.76, respectively. Not only will the reaction overcome a spin-change-induced barrier (ca. 6 kcal/mol) but it also will overcome an adiabatic barrier (ca. 24.7−20.8 kcal/mol), which will greatly reduced the efficiency of the reaction system. As for the second reaction path, similarly, there is a crossing seam between CP-2 and CP-3, the spin-change-induced barrier is very high, about 15.86−18.86 kcal/mol, which also indicates a less favorable process kinetically. Therefore, the lack of a thermodynamic driving force is an important factor contributing to the low efficiency of the reaction system. These conclusions are consistent with the experimental observations.

Theoretical study for the reaction of CH3CN with O(P3)

The low-lying triplet and singlet potential energy surfaces of the O((3)P)+CH(3)CN reaction have been studied at the G3(MP2)//B3LYP/6-311+G(d,p) level. On the triplet surface, six kinds of pathways are revealed, namely, direct hydrogen abstraction, C-addition/elimination, N-addition/elimination, substitution, insertion, and H-migration. Multichannel Rice-Ramsperger-Kassel-Marcus theory and transition-state theory are employed to calculate the overall and individual rate constants over a wide range of temperatures and pressures. It is predicted that the direct hydrogen abstraction and C-addition/elimination on triplet potential energy surface are dominant pathways. Major predicted end products include CH(3)+NCO and CH(2)CN+OH. At atmospheric pressure with Ar and N(2) as bath gases, CH(3)C(O)N (IM1) formed by collisional stabilization is dominated at T<700 K, whereas CH(3) and NCO produced by C-addition/elimination pathway are the major products at the temperatures between 800 and 1500 K; the direct hydrogen abstraction leading to CH(2)CN+OH plays an important role at higher temperatures in hydrocarbon combustion chemistry and flames, with estimated contribution of 64% at 2000 K. Furthermore, the calculated rate constants are in good agreement with available experimental data over the temperature range 300-600 K. The kinetic isotope effect has also been calculated for the triplet O((3)P)+CH(3)CN reaction. On the singlet surface, the atomic oxygen can easily insert into C-H or C-C bonds of CH(3)CN, forming the insertion intermediates s-IM8(HOCH(2)CN) and s-IM5(CH(3)OCN) or add to the carbon atom of CN group in CH(3)CN, forming the addition intermediate s-IM1(CH(3)C(O)N); both approaches were found to be barrierless. It is indicated that the singlet reaction exhibits a marked difference from the triplet reaction. This calculation is useful to simulate experimental investigations of the O((3)P)+CH(3)CN reaction in the singlet state surface.

Computational study of oxygen atom (3P and 1D) reactions with CF3CN

Singlet and triplet potential energy surfaces for the reactions of oxygen atoms ((3)P and (1)D) with CF(3)CN have been studied computationally to evaluate the reaction mechanisms, possible products, and rate constants. On the triplet surface, six kinds of pathway are revealed, namely: direct fluorine abstraction, C-addition/elimination, N-addition/elimination, substitution, insertion and F-migration. The results show that the reaction should occur mainly through the C-addition/elimination mechanism involving the chemically activated CF(3)C(O)N* intermediate, and the major products are CF(3) and NCO. The rate constants for C-addition/elimination channel of the reaction of O((3)P) with CF(3)CN have been determined by using RRKM statistical rate theory and compared with the experimental data. On the singlet surface, the atomic oxygen can easily insert into the C-F or C-C bond of CF(3)CN, forming the insertion intermediates FOCF(2)CN and CF(3)OCN, and O((1)D) can add to the carbon or nitrogen atom of the CN group in CF(3)CN, forming the addition intermediates CF(3)C(O)N and CF(3)CNO; both approaches are found to be barrierless. The decomposition and isomerization of some intermediates were also modeled at the QCISD(T)/6-311+G(2df)//B3LYP/6-311+G(d) level for the better understanding of the O((1)D) with CF(3)CN chemistry. The decomposition products CF(3) and NCO arising from CF(3)OCN and CF(3)NCO are the dominant species. Further comparison with similar reactions is also summarized.

Pd(II)-catalyzed enantioselective C-H olefination of diphenylacetic acids.

Pd(II)-catalyzed enantioselective C-H olefination of diphenylacetic acid substrates has been achieved through the use of monoprotected chiral amino acid ligands. The absolute configuration of the resulting olefinated products is consistent with that of a proposed C-H insertion intermediate.

Methane C−H Bond Activation by Gas-Phase Th+and U+: Reaction Mechanisms and Bonding Analysis

Th+ is the only actinide ion that activates exothermically the strong C−H bonds of methane in the gas phase. In contrast, U+, as well as all of the rest of the experimentally studied An+ cations, is inert in the reaction with CH4. In this work, the activation of methane by thorium and uranium monocations was investigated using two different density functional theory approaches. The reaction mechanisms and the corresponding potential energy profiles were analyzed in detail. From the formation of the initial ion−molecule adduct, the Th++CH4 reaction pathway evolves completely along the doublet spin surface, whereas that of U++CH4 involves solely the quartet bare cation ground spin state. The bonding properties of all of the species involved in the reaction pathways were investigated in terms of diverse analyses including natural bond orbital, atoms in molecules, and electron localization function. The dehydrogenation products (Th+═CH2 and U+═CH2) as well as the last insertion intermediates are characterized by the presence of α-agostic geometries.