Complete Catalytic Cycle Research Articles

Gas‐Phase Catalysis by Atomic and Cluster Metal Ions: The Ultimate Single‐Site Catalysts

Gas-phase experiments with state-of-the-art techniques of mass spectrometry provide detailed insights into numerous elementary processes. The focus of this Review is on elementary reactions of ions that achieve complete catalytic cycles under thermal conditions. The examples chosen cover aspects of catalysis pertinent to areas as diverse as atmospheric chemistry and surface chemistry. We describe how transfer of oxygen atoms, bond activation, and coupling of fragments can be mediated by atomic or cluster metal ions. In some cases truly unexpected analogies of the idealized gas-phase ion catalysis can be drawn with related chemical transformations in solution or the solid state, and so improve our understanding of the intrinsic operation of a practical catalyst at a strictly molecular level.

Catalytic Oxidation of CO with N2O on Gas‐Phase Platinum Clusters

The complete catalytic cycle of CO oxidation with N2O is shown to occur on Ptn+ (see scheme); for Pt7+ it involves six different elementary reactions. Poisoning of the catalyst by sequential addition of CO is observed. The extent of poisoning can be adjusted with the ratio of N2O and CO partial pressures.

NiFe Hydrogenase Active Site Biosynthesis: Identification of Hyp Protein Complexes in Ralstonia eutropha

Biosynthesis of the NiFe hydrogenase active site is a complex process involving the action of the Hyp proteins: HypA-HypF. Here we investigate the mechanism of NiFe site biosynthesis in Ralstonia eutropha by examining the interactions between HypC, HypD, HypE, and HypF1. Using an affinity purification procedure based on the Strep-tag II, we purified HypC and HypE from different genetic backgrounds as complexes with other hydrogenase-related proteins and characterized them using immunological analysis. Copurification of HypC and HoxH, the active site-containing subunit of the soluble hydrogenase in R. eutropha, from several different genetic backgrounds suggests that this complex forms early in the maturation process. With respect to the Hyp proteins, it is shown that HypE and HypF1 formed a stable complex both in vivo and in vitro. Furthermore, HypC and HypD functioned as a unit. Together, they were able to interact with HypE to form a range of complexes probably varying in stoichiometry. The HypC/HypD/HypE complexes did not involve HypF1 but appeared to be more stable when HypF1 was also present in the cells. We hypothesize that HypF1 is able to modify some component of the HypC/HypD/HypE complex. Since we have also seen that HypF1 and HypE form a complex, it is likely that HypF1 modifies HypE. On the basis of these results, we propose a complete catalytic cycle for HypE. First, it is modified by HypF1, and then it can form a complex with HypC/HypD. This activated HypE/HypC/HypD complex could then decompose by donating active site components to the immature hydrogenase and regenerate unmodified HypE.

Why Are Olefins Oxidized by RuO4under Cleavage of the Carbon−Carbon Bond whereas Oxidation by OsO4Yieldscis-Diols?

Quantum chemical calculations using gradient-corrected (B3LYP) density functional theory have been carried out to investigate the mechanism of the oxidative cleavage of alkenes by ruthenium tetraoxide. The initial reaction of the tetraoxide with the olefin occurs via a [3+2] cycloaddition as in the case of osmium tetraoxide. The results clearly show that the bond cleavage does not take place at the primary adduct, but much later in the reaction path. After the formation of the ruthenium(VI)dioxo-2,5-dioxolane, the reaction proceeds with the addition of a second olefin to yield ruthenium(IV)-bis(2,5-dioxolane), which in turn becomes oxidized first to rutheniumoxo(VI)-bis(2,5-dioxolane) 6(Ru) and then to ruthenium(VIII)-dioxo-bis(2,5-dioxolane) 7(Ru). Only in complexes containing the metal center in the formal oxidation state +VIII are low activation barriers for C-C bond cleavage and exothermic formation of carbonyl compounds as products calculated. The lowest activation barrier, DeltaH(++) = 2.5 kcal/mol, is calculated for the C-C bond breaking reaction of 7(Ru) which is predicted as the pivotal intermediate of the oxidation reaction. The calculations of the oxidation reaction with OsO(4) show that those reactions where the oxidation state of the metal increases have larger activation barriers for M = Ru than for M = Os, while reactions which reduce the oxidation state have a lower activation barrier for ruthenium compounds. Also, reactions which increase the oxidation state of the metal are in the case of M = Os more exothermic than for M = Ru. In this work, all important points of the potential energy surface (PES) are reported, and the complete catalytic cycle for the oxidative cleavage of olefins by ruthenium tetraoxide is presented.

Peroxovanadate imidazole complexes as catalysts for olefin epoxidation: density functional study of dynamics, 51V NMR chemical shifts, and mechanism.

A density functional study of [VO(O(2))(2)(Im)](-) (1, Im = imidazole) is presented, calling special attention to effects of dynamics and solvation on the (51)V chemical shift. According to Car-Parrinello molecular dynamics simulations, rotation of the Im ligand can be fast in the gas phase, but is more hindered in aqueous solution. In the latter, bonding between Im and V is reinforced, and dynamic averaging of GIAO-B3LYP magnetic shieldings affords a gas-to-liquid shift of ca. -100 ppm for delta((51)V). A complete catalytic cycle has been characterized for olefin epoxidation mediated by 1, using H(2)O(2) as oxidant. The rate-determining step is indicated to be initial oxygen atom transfer from 1 to the substrate via a spiro-like transition state. Substituent effects on this barrier are examined, and a significant decrease (by 2-6 kcal/mol) is revealed upon removal of the Im proton or upon complexation with a H-bond acceptor. Implications for the mechanism of the oxidative chemistry of vanadium-dependent haloperoxidases and requirements for prospective biomimetic analogues are discussed.

Sketching a path through the hydrocarbon oxidation maze

The selective oxidation of hydrocarbons such as methane, propane, and propene remains one of the grand challenges of catalytic chemistry. It is our thesis that the structures and energetics of stationary points along probable kinetic pathways can provide important conceptual data for catalyst development. Further, we suggest that a wide range of theoretical methodologies are required to tackle this important problem. To support these hypotheses the results of a range of modern electronic structure methods including complete active space-perturbation theory to second order (CASPT2), a range of density functionals (DFT), and a new approach, the approximate pair theory (APT) are described. Studies on ethylene oxidation by CrCl2O2, isobutane oxidation by CrCl2O2, and propene oxidation by bismuth molybdate are used to illustrate one path for obtaining theoretical insights consistent with experimental observation and of predictive value. Specific findings include a novel saddle point for ethylene epoxidation with implications for selective methane oxidation, direct support for this novel alkane oxidation mode, and the energetics for the complete catalytic cycle of the bismuth molybdate propene oxidation.

Mechanism of the ruthenium-catalyzed formation of pyrane-2-one and their sulfur and selen analogs from acetylene and CX2(X = O, S, Se): a theoretical study

Complete catalytic cycles for the (actual or potential) cycloaddition of acetylene with CX2 (X = O, S, Se), mediated by CpRu(COD)Cl as the precatalyst, are proposed on the basis of DFT/B3LYP calculations. The common initial step is the replacement of labile COD by two molecules of acetylene to afford a bisacetylene complex. Oxidative coupling of the acetylene ligands results in the formation a coordinatively saturated metallacyclopentatriene complex. This metallacycle adds the CX bond of CX2 directly to the RuC bond in a concerted fashion, forming an unusual bicyclic carbene intermediate. The activation energies for this addition are 14.2, 15.3 and 30.0 kcal mol−1 for X = O, S and Se, respectively, thus rendering the CSe2 addition the most difficult. In a subsequent reductive elimination a coordinatively unsaturated metallaheteronorbornene intermediate is formed, which eventually rearranges into RuCpCl complexes bearing pyrane-2-one, thiopyrane-2-thione and selenopyrane-2-selenone ligands coordinated in an η4 fashion. The energy barrier for the reductive elimination step decreases in the order O > S > Se, being 28.1, 17.7 and 14.6 kcal mol−1, respectively. Overall, the reaction with CS2 is thus the most favorable. Completion of the cycles is achieved by an exothermic displacement of the respective heterocyclic product by two acetylene molecules, regenerating the bisacetylene complex.

Structure—Reactivity Relationships in the Cyclo‐Oligomerization of 1,3‐Butadiene Catalyzed by Zerovalent Nickel Complexes

AbstractFor Abstract see ChemInform Abstract in Full Text.

Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.

The complete catalytic cycle of EcoRV endonuclease has been observed by combining fluorescence anisotropy with fluorescence resonance energy transfer (FRET) measurements. Binding, bending, and cleavage of substrate oligonucleotides were monitored in real time by rhodamine-x anisotropy and by FRET between rhodamine and fluorescein dyes attached to opposite ends of a 14-mer DNA duplex. For the cognate GATATC site binding and bending are found to be nearly simultaneous, with association and bending rate constants of (1.45-1.6) x 10(8) M(-1) s(-1). On the basis of the measurement of k(off) by a substrate-trapping approach, the equilibrium dissociation constant of the enzyme-DNA complex in the presence of inhibitory calcium ions was calculated as 3.7 x 10(-12) M from the kinetic constants. Further, the entire DNA cleavage reaction can be observed in the presence of catalytic Mg(2+) ions. These measurements reveal that the binding and bending steps occur at equivalent rates in the presence of either Mg(2+) or Ca(2+), while a slow decrease in fluorescence intensity following bending corresponds to k(cat), which is limited by the cleavage and product dissociation steps. Measurement of k(on) and k(off) in the absence of divalent metals shows that the DNA binding affinity is decreased by 5000-fold to 1.4 x 10(-8) M, and no bending could be detected in this case. Together with crystallographic studies, these data suggest a model for the induced-fit conformational change in which the role of divalent metal ions is to stabilize the sharply bent DNA in an orientation suitable for accessing the catalytic transition state.

Density functional theory study of the ethylene epoxidation over Ti-substituted silicalite (TS-1)

The mechanism of ethylene epoxidation with hydrogen peroxide over Ti-substituted silicalite (TS-1) catalyst was investigated by using both the cluster and embedded cluster approaches at the B3LYP/6-31G(d) level of theory. The complete catalytic cycle was determined. The epoxidation of ethylene consists of three steps. First, the chemisorption of H2O2 at the Ti active site forms the oxygen donating TiOOH species and then the transfer of an oxygen atom from the TiOOH species to the adsorbed ethylene. The final step is the dehydration of the TiOH species to regenerate to active center. The oxygen atom transfer step was found to be the rate-limiting step with the zero-point energy corrected barrier of 17.0 kcal/mol using the embedded cluster model at B3LYP/6-31G(d) level of theory, which is in agreement with the experimental estimate of about 16.7 kcal/mol. Regeneration of the active center by dehydration of the TiOOH species was found to have a rather small barrier and the overall process is exothermic. Our results also show that inclusion of the effects of the zeolite crystal framework is crucial for obtaining quantitative energetic information. For instance, the Madelung potential increases the barrier of the oxygen atom transfer step by 5.0 kcal/mol.

Mechanism for the cyclotrimerization of alkynes and related reactions catalyzed by CpRuCl.

A complete catalytic cycle for the cyclotrimerization of acetylene with the CpRuCl fragment has been proposed and discussed based on DFT/B3LYP calculations, which revealed a couple of uncommon intermediates. The first is a metallacyclopentatriene complex RuCp(Cl)(C(4)H(4)) (B), generated through oxidative coupling of two alkyne ligands. It adds another alkyne in eta(2) fashion to give an alkyne complex (C). No less than three successive intermediates could be located for the subsequent arene formation. The first, an unusual five- and four-membered bicyclic ring system (D), rearranges to a very unsymmetrical metallaheptatetraene complex (E), which in turn provides CpRuCl(eta(2)-C(6)H(6)) (F) via a reductive elimination step. The asymmetry of E, including Cp ring slippage, removes the symmetry-forbidden character from this final step. Completion of the cycle is achieved by an exothermic displacement (21.4 kcal mol(-)(1)) of the arene by two acetylene molecules regenerating A. In addition to acetylene, the reaction of B with ethylene and carbon disulfide, the latter taken as a model for a molecule lacking hydrogen atoms, has also been investigated, and several parallels noted. In the case of the coordinated alkene, facile C-C coupling to the alpha carbon of the metallacycle is feasible due to an agostic assistance, which tends to counterbalance the reduced degree of unsaturation. Carbon disulfide, on the other hand, does not coordinate to ruthenium, but a C=S bond adds instead directly to the Ru=C bond. The final products of the reactions of B with acetylene, ethylene, and carbon disulfide are, respectively, benzene, cyclohexadiene, and thiopyrane-2-thione, the activation energies being lower for acetylene.

Mechanism of copper(I)-catalyzed cyclopropanation: a DFT study calibrated with copper(I) alkene complexes

The complete catalytic cycle of copper-catalyzed cyclopropanation is investigated by density functional model calculations. The study focuses on obtaining accurate relative stabilities of the ligand–metal cores of all catalytic intermediates and transition states. The copper iminophosphanamide [H 2P(NH 2) 2κ 2 N]Cu serves as model fragment, since three copper catalyst key intermediates with an iminophosphanamide ligand have been isolated or detected. The electronic structure of the active intermediates, copper(I) carbenes of the d 10-ML 3 type, and their reactivity towards ethene and vinyl alcohol is investigated. The reliability of the computed data is confirmed by their comparison with experimental data of [ t-Bu 2P(NSiMe 3) 2κ 2 N]Cu alkene and alkyne complexes, using relative ligand binding strengths and alkene ligand rotation barriers. The uncharged nature of the model complexes minimizes solvation artifacts and thus renders the evaluation of associative and dissociative ligand exchange pathways possible. The associative alkene ligand exchange with diazoalkane to a κ N,κ O-diazoalkane complex, subsequent intramolecular rearrangement to a κ C-complex and N 2 extrusion are identified on the most probable pathway to the electrophilic copper(I) carbene complexes of the Fischer type. They are predicted to react with alkenes to labile cupracyclobutanes with a planar N 2Cu IIIC 2 core, which undergo facile reductive elimination of a cyclopropane derivative.

Theoretical study on the mechanism of iron carbonyls mediated isomerization of allylic alcohols to saturated carbonyls.

The conversion of allylic alcohols to enols mediated by Fe(CO)(3) has been studied through density functional theoretical calculations. From the results obtained a complete catalytic cycle has been proposed in which the first intermediate is the [(allyl alcohol)Fe(CO)(3)] complex. This intermediate evolves to the [(enol)Fe(CO)(3)] complex through two consecutive 1,3-hydrogen shifts involving a pi-allyl hydride intermediate. The highest Gibbs energy transition state corresponds to the partial decoordination ot the enol ligand prior to the coordination of a new allyl alcohol molecule that regenerates the first intermediate. Alternative processes for the [(enol)Fe(CO)(3)] complex such as [Fe(CO)(3)]-mediated enol-aldehyde transformation and enol isomerization have also been considered. The results obtained show that the former process is unfavourable, whereas the enol isomerization may compete with the enol decoordination step of the catalytic cycle.

A theoretical study on the complete catalytic cycle of the hetero-Pauson-Khand-type [2+2+1] cycloaddition reaction of ketimines, carbon monoxide and ethylene catalyzed by iron carbonyl complexes.

The [2+2+1] cycloaddition reaction of 1,4-diazabutadienes, carbon monoxide and ethylene catalyzed by iron carbonyl complexes produces pyrrolidin-2-one derivatives. Only one of the two imine moieties is activated during the catalysis. The mechanism of this cycloaddition reaction is studied by density functional theory at the B3LYP/6-311++G(d,p) level of theory. In accordance with experimental results, a [(diazabutadiene)Fe(CO)(3)] complex of square-pyramidal geometry is used as the starting compound S of the catalytic cycle. Based on experimental experience, the reaction with ethylene is considered to take place before any interaction with carbon monoxide. According to the computational results, the reaction does not proceed by ligand dissociation followed by addition of ethylene and subsequent intramolecular activation steps but by the approach of an ethylene molecule from the base of the square-pyramidal complex. This reaction yields an intermediate I(4) in which ethylene is coordinated to the iron centre and a new C-C bond between ethylene and one of the imine groups is formed. The insertion of a terminal carbon monoxide ligand into the metal-carbon bond between ethylene and iron produces the key intermediate I(7). The reaction proceeds by metal-assisted formation of a lactam P. The catalytic cycle is closed by a ligand-exchange reaction in which the diazabutadiene ligand substitutes P with reformation of S. This reaction pathway is found to be energetically favored over a reductive elimination. It leads to the experimentally observed heterocyclic product P and a reactive [Fe(CO)(3)] fragment.

Propylene polymerization with a bisiminepyridine iron complex: activation with Ph 3C [B(C 6F 5) 4] and AlR 3; iron hydride species in the catalytic cycle

In this work, the complex 2,6-bis [1-(2-isopropyl-6-methylphenylimino)ethyl]-pyridineiron(II)dichloride was used for propylene polymerization. Activation with Ph 3C [B(C 6F 5) 4] and subsequent treatment with triisobutylaluminium or triethylaluminium generated a very active polymerization catalyst for propylene. The kinetics of this polymerization reaction were investigated with mass-flowmeters. Further we show propagation-time-profiles of this reaction. Depending on the nature of the aluminiumalkyl we are able to determine different aliphatic endgroups in the polymer using 13 C NMR spectroscopy. Addition of hydrogen to the polymerization leads to higher activities and allows us to formulate a complete catalytic reaction cycle containing an iron hydride species. This cycle comprises one starting cycle and two propagation cycles which can be controlled with the aluminiumtrialkyl-propylene ratio.

Proton and electron pathways in the bacterial nitric oxide reductase.

Electron- and proton-transfer reactions in bacterial nitric oxide reductase (NOR) have been investigated by optical spectroscopy and electrometry. In liposomes, NOR does not show any generation of an electric potential during steady-state turnover. This electroneutrality implies that protons are taken up from the same side of the membrane as electrons during catalysis. Intramolecular electron redistribution after photolysis of the partially reduced CO-bound enzyme shows that the electron transfer in NOR has the same pathway as in the heme-copper oxidases. The electron is transferred from the acceptor site, heme c, via a low-spin heme b to the binuclear active site (heme b3/FeB). The electron-transfer rate between hemes c and b is (3 +/- 2) x 10(4) s(-1). The rate of electron transfer between hemes b and b3 is too fast to be resolved (>10(6) s(-1)). Only electron transfer between heme c and heme b is coupled to the generation of an electric potential. This implies that the topology of redox centers in NOR is comparable to that in the heme-copper cytochrome oxidases. The optical and electrometric measurements allow identification of the intermediate states formed during turnover of the fully reduced enzyme, as well as the associated proton and electron movement linked to the NO reduction. The first phase (k = 5 x 10(5) s(-1)) is electrically silent, and characterized by the disappearance of absorbance at 433 nm and the appearance of a broad peak at 410 nm. We assign this phase to the formation of a ferrous NO adduct of heme b3. NO binding is followed by a charge separation phase (k = 2.2 x 10(5) s(-1)). We suggest that the formation of this intermediate that is not linked to significant optical changes involves movement of charged side chains near the active site. The next step creates a negative potential with a rate constant of approximately 3 x 10(4) s(-1) and a weak optical signature. This is followed by an electrically silent phase with a rate constant of 5 x 10(3) s(-1) leading to the last intermediate of the first turnover (a rate constant of approximately 10(3) s(-1)). The fully reduced enzyme has four electrons, enough for two complete catalytic cycles. However, the protons for the second turnover must be taken from the bulk, resulting in the generation of a positive potential in two steps. The optical measurements also verify two phases in the oxidation of low-spin hemes. Based on these results, we present mechanistic models of NO reduction by NOR. The results can be explained with a trans mechanism rather than a cis model involving FeB. Additionally, the data open up the possibility that NOR employs a P450-type mechanism in which only heme b3 functions as the NO binding site during turnover.

Alumina-Supported Copper Chloride: 4. Effect of Exposure to O2 and HCl

A complete catalytic cycle was performed on CuCl2/Al2O3 catalyst for ethylene oxychlorination at 500 K. X-ray absorption near-edge spectroscopy, extended X-ray absorption fine structure, electron paramagnetic resonance, and IR of adsorbed CO were used to demonstrate that the ethylene oxychlorination reaction, C2H4+2HCl+1/2 O2→C2H4Cl2+H2O, follows a three-step mechanism: (i) reduction of CuCl2 to CuCl (2CuCl2+C2H4→C2H4Cl2+2CuCl), (ii) oxidation of CuCl to give an oxychloride (2CuCl+1/2 O2→Cu2OCl2), and (iii) closure of the catalytic circle by rechlorination with HCl, restoring the original CuCl2 (Cu2OCl2+2HCl→2CuCl2+H2O). The dispersing/sintering effect of the different reagents on the active phase has been also investigated.

The CuCl2/Al2O3 Catalyst Investigated in Interaction with Reagents

Alumina supported CuCl2, the basic catalyst for ethylene oxychlorination, has been investigated by UV-Vis spectroscopy, EPR, EXAFS and XANES in a wide range (0.25-9.0 wt%) of Cu concentration. We have evidenced that, at low Cu content, the formation of a surface aluminate species takes place. The formation of this surface copper aluminate stops at 0.95 wt% Cu / 100 m2; at higher Cu concentrations excess copper chloride precipitates directly from solution during the drying step forming an highly dispersed CuCl2.H2O, phase, overlapping progressively the surface aluminate. Depletion tests and IR spectroscopy of adsorbed NO have demonstrated that the latter is the only active phase. A complete catalytic cycle has then been performed on CuCl2/Al2O3 catalyst. EPR, XANES and EXAFS, have been used to demonstrate that the ethylene oxychlorination reaction: C2H4 + 2HCl + ½ O2 --> C2H4Cl2 + H2O follows a three steps mechanism: (i) reduction of CuCl2 to CuCl (2CuCl2 + C2H4 --> C2H4Cl2 + 2CuCl), (ii) oxidation of CuCl to give an oxychloride (2CuCl + ½ O2 --> Cu2OCl2) and (iii) closure of the catalytic circle by rechlorination with HCl, restoring the original CuCl2 (Cu2OCl2 + 2HCl --> 2CuCl2 + H2O). Finally, we have shown that time resolved, in situ, spectroscopy is a very promising technique to investigate the interplay between catalyst activity and oxidation state of copper.

Time course of reactions controlled and gated by intramolecular dynamics of proteins: predictions of the model of random walk on fractal lattices.

Computer simulations of random walk on the Sierpinski gasket and percolation clusters demonstrate that the short, initial condition-dependent stage of protein involving reactions can dominate the progress of the reaction over the main stage described by the standard kinetics. This phenomenon takes place if the intramolecular conformational transition dynamics modeled by the stochastic process is slow enough and the initial conformational substate of the protein already belongs to the transition state of the reaction. Both conditions are realized in two kinds of experiments: small ligand rebinding to protein after laser flash photolysis and direct recording of single protein channel activity. The model considered suggests simple analytical formulae that can explain the time behavior of the processes observed and its variation with temperature. The initial condition-dependent stage, and not the stage described by the standard kinetics, is expected as responsible for the coupling of component reactions in the complete catalytic cycles and more complex processes of biological free energy transduction.

The catalytic cycle of the escherichia coli SecA ATPase comprises two distinct preprotein translocation events.

SecA is the ATP-dependent force generator in the Escherichia coli precursor protein translocation cascade, and is bound at the membrane surface to the integral membrane domain of the preprotein translocase. Preproteins are thought to be translocated in a stepwise manner by nucleotide-dependent cycles of SecA membrane insertion and de-insertion, or as large polypeptide segments by the protonmotive force (Deltap) in the absence of SecA. To determine the step size of a complete ATP- and SecA-dependent catalytic cycle, translocation intermediates of the preprotein proOmpA were generated at limiting SecA translocation ATPase activity. Distinct intermediates were formed, spaced by intervals of approximately 5 kDa. Inhibition of the SecA ATPase by azide trapped SecA in a membrane-inserted state and shifted the step size to 2-2.5 kDa. The latter corresponds to the translocation elicited by binding of non-hydrolysable ATP analogues to SecA, or by the re-binding of partially translocated polypeptide chains by SecA. Therefore, a complete catalytic cycle of the preprotein translocase permits the stepwise translocation of 5 kDa polypeptide segments by two consecutive events, i.e. approximately 2.5 kDa upon binding of the polypeptide by SecA, and another 2.5 kDa upon binding of ATP to SecA.