H-transfer Step Research Articles

Activity of Different AunSn+1 Staples in the Ligand Exchange of Au23(SR)16- with a Single Foreign Thiolate Ligand.

Ligand exchange has been widely used to synthesize novel thiolated gold nanoclusters and to regulate their specific properties. Herein, density functional theory (DFT) calculations were conducted to investigate the kinetic profiles of the ligand exchange of the [Au23(SCy)16]- nanocluster with an aromatic thiolate (2-napthalenethiol). The three types of staple motifs (i.e., trimetallic Au3S4, monometallic AuS2, and the bridging thiolates) of the Au23 cluster precursor could be categorized into eight groups of S sites with different chemical environments. The ligand exchange of all of them occurs favorably via the SN1-like pathway, with one site starting with the Au-S dissociation and seven other sites starting with the H-transfer steps. By contrast, the SN2-like pathway (i.e., the synergistic SCy-to-SAr exchange prior to the H-transfer step) is unlikely in the target systems. Meanwhile, the Au-S bond on the capping Au atom of the bicapped icosahedral Au15 core is the most active one, while the S sites on Au3S4 (except for the one remote from the metallic core) are all competitive exchanging sites. The ligand exchange activity of the bridging thiolate and the remote S site on Au3S4 is significantly less reactive. The calculation results correlate with the multiple ligand exchange within only a few minutes and the preferential etching of the AuS2 staple with the foreign ligands reported in earlier experiments. The relative activity of different staples might be helpful in elucidating the inherent principles in the ligand exchange-induced size-evolution of metal nanoclusters.

Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu2O2 Active Site of oxy-Tyrosinase.

Tyrosinase is a ubiquitous coupled binuclear copper enzyme that activates O2 toward the regioselective monooxygenation of monophenols to catechols via a mechanism that remains only partially defined. Here, we present new mechanistic insights into the initial steps of this monooxygenation reaction by employing a pre-steady-state, stopped-flow kinetics approach that allows for the direct measurement of the monooxygenation rates for a series of para-substituted monophenols by oxy-tyrosinase. The obtained biphasic Hammett plot and the associated solvent kinetic isotope effect values provide direct evidence for an initial H-transfer from the protonated phenolic substrate to the Cu2O2 core of oxy-tyrosinase. The correlation of these experimental results to quantum mechanics/molecular mechanics calculations provides a detailed mechanistic description of this H-transfer step. These new mechanistic insights revise and expand our fundamental understanding of Cu2O2 active sites in biology.

Chiral Lewis Acid-Catalyzed Norrish Type II Cyclization to Synthesize α-Oxazolidinones via Enantioselective Protonation

Chiral Lewis Acid-Catalyzed Norrish Type II Cyclization to Synthesize α-Oxazolidinones via Enantioselective Protonation

The homogeneous gas-phase formation mechanisms of PCPTs/PCDTs/PCDFs from the radical/radical cross-condensation of 2-CPR and 2-CTPR: a theoretical, mechanistic and kinetics study.

Polychlorinated phenoxathiins (PCPTs) are one group of dioxin-like compounds, which can be considered to be one-oxygen-substituted polychlorinated thianthrene (PCTA) compounds or one-sulfur-substituted polychlorinated dibenzo-p-dioxin (PCDD) compounds. Owing to their high toxicity and wide distribution, clarifying the formation and emission of PCPTs due to combustion and thermal processes can deepen our understanding of the dioxin formation mechanism and allow reduced-emission and dioxin-control strategies to be established. Chlorophenols (CPs) and chlorothiophenols (CTPs) are direct precursors in PCPT formation. In this paper, the homogeneous gas-phase formation mechanisms of PCPTs, as well as polychlorinated dibenzofurans (PCDFs) and polychlorinated dibenzothiophenes (PCDTs), from the cross-condensation of 2-chlorophenoxy radicals (2-CPRs) and 2-chlorothiophenoxy radicals (2-CTPRs) under thermal and combustion conditions were investigated theoretically using a density functional theory (DFT) method. The reaction priorities and effects of water molecules on the formation mechanisms were discussed. The rate constants of crucial elementary steps were calculated from 600–1200 K. The acute and chronic toxicities of the main products were predicted at three trophic levels. This study shows that routes starting with oxygen–carbon condensation are favored over those starting with sulfur–carbon condensation for PCPT formation, and routes ending with Cl loss can occur more easily than those ending with H loss. Water molecules have a negative catalytic effect on CH–S H-transfer steps but a positive catalytic effect on CH–O H-transfer steps.

Pivotal Electron Delivery Effect of the Cobalt Catalyst in Photocarboxylation of Alkynes: A DFT Calculation

Photocarboxylation of alkyne with carbon dioxide represents a highly attractive strategy to prepare functionalized alkenes with high efficiency and atomic economy. However, the reaction mechanism, especially the sequence of elementary steps (leading to different reaction pathways), reaction modes of the H-transfer step and carboxylation step, spin and charge states of the cobalt catalyst, etc., is still an open question. Herein, density functional theory calculations are carried out to probe the mechanism of the Ir/Co-catalyzed photocarboxylation of alkynes. The overall catalytic cycle mainly consists of four steps: reductive-quenching of the Ir catalyst, hydrogen transfer (rate-determining step), outer sphere carboxylation, and the final catalyst regeneration step. Importantly, the cobalt catalyst can facilitate the H-transfer by an uncommon hydride coupled electron transfer (HCET) process. The pivotal electron delivery effect of the Co center enables a facile H-transfer to the α-C(alkyne) of the aryl group, resulting in the high regioselectivity for β-carboxylation.

Visible-Light-Mediated [2+2+1] Carbocyclization Reactions of 1,7-Enynes with Bromofluoroacetate to Form Fused Monofluorinated Cyclopenta[c]quinolin-4-ones.

Herein, we describe a new protocol for photoinduced radical [2+2+1] carbocyclization reactions of 1,7-enynes with bromofluoroacetate. These reactions, which proceed via a cascade involving fluoroalkylation, 6-exo-dig and 5-endo-trig cyclizations, H-transfer step, and oxidative dehydrogenation, provide an efficient and general route to a variety of fused monofluorinated cyclopenta[c]quinolin-4-one derivatives.

A guinea pig for conformer selectivity and mechanistic insights into dissociative ionization by photoelectron photoion coincidence: fluorocyclohexane.

We studied fluorocyclohexane (C6H11F, FC6) by double imaging photoelectron photoion coincidence spectroscopy in the 9.90-13.90 eV photon energy range. The photoelectron spectrum can identify species isomer and, in this case, even conformer selectively. Ab initio results indicated that the axial conformer has two, close-lying cation electronic states. With the help of Franck-Condon simulations of the vibrational fine structure, we determined the origin of three transitions, (i) axial FC6 → axial FC6+ of C1 symmetry (X[combining tilde]+, A'' in CS), (ii) equatorial FC6 → equatorial FC6+ of C1 symmetry (X[combining tilde]+, A'' in CS), and (iii) axial FC6 → A' axial FC6+ of CS symmetry (Ã+) as 10.12 ± 0.01, 10.15 ± 0.01 and 10.15 ± 0.02 eV, respectively. At slightly higher energies, the FC6 cation starts fragmenting by HF loss (E0 = 10.60 eV), followed by sequential CH3 (E0 = 10.71 eV) or C2H4 (E0 = 11.06 eV) loss. Surprisingly, the methyl-loss step has an effective barrier of only 0.11 eV, and yet it is a slow process at threshold. Based on the statistical model, this is explained by isomerization and stabilization of the C6H10+ intermediate. The highest energy channel observed, vinyl fluoride (C2H3F) loss yielding C4H8+ appears in the breakdown diagram at 12 eV, which agrees with the computed threshold to cyclobutane cation formation. However, the model predicted a ca. 1 eV competitive shift for this parallel channel, i.e., an E0 = 11.23 eV. This led us to explore the potential energy surface to find a lower-lying fragmentation channel including H-transfer steps. Rate constant measurements and statistical modeling thus yield fundamental insights into the reaction mechanism beyond what is immediately seen in the mass spectra.

Cooperative Catalysis of Chiral Guanidine and Rh2(OAc)4 in Asymmetric O-H Insertion of Carboxylic Acid: A Theoretical Investigation.

We reported a mechanistic study on asymmetric O-H insertion reaction of α-diazoester with carboxylic acid using Rh2(OAc)4/chiral guanidine-amide as the cocatalyst by density functional theory [B3LYP-D3(BJ)/def2-TZVP//B3LYP-D3(BJ)/[6-31G**, SDD] (SMD, Et2O)]. The catalytic reaction included two stages: (i) formation of Rh-carbene species, subsequently by the construction of C-O bond forming enol and (ii) chiral guanidinium salt-assisted H-transfer to the enol. In cooperative catalysis, Rh2(OAc)4 helped to form an enol intermediate via high-reactivity Rh-carbene species, while the in situ-formed guanidium carboxylate acted as a chiral proton shuttle to construct a hydrogen bonding net for the stereo-determinant protonation. The repulsions between the phenyl group of the enol intermediate and the cyclohexyl as well as the ortho-substituted isopropyl group of chiral guanidine played important roles in controlling stereoselectivity. A disadvantageous steric arrangement in si-face attack weakened the stabilizing electrostatic and orbital interaction of reacting species in the H-transfer step, enhancing the pathway to form a predominant product with R-configuration in the two competing pathways. A model was proposed to explain the asymmetric induction of chiral guanidine-amide in protonation.

Computational Insight into the Mechanism of Ruthenium(II)-Catalyzed α-Alkylation of Arylmethyl Nitriles Using Alcohols.

The ruthenium(II)-catalyzed α-alkylation reaction of arylmethyl nitriles (phenylacetonitrile) using alcohols (ethanol) in toluene has been extensively investigated by means of SMD-M06-2X/6-311G(d,p)-LANL2dz (LAnL2dz for Ru, 6-311G(d,p) for other atoms) calculations. Detailed mechanistic schemes have been proposed and discussed. The catalytically active Ru(II) complex was generated by the base-induced KCl elimination from the catalyst precursor [(PNPPh)RuHCl(CO)]. The overall Ru(II) catalytic cycle consists of three basic processes: (1) ethanol-to-aldehyde transformation catalyzed by the 16-electron unsaturated ruthenium pincer catalyst; (2) a 16-electron unsaturated ruthenium pincer catalyst catalyzed condensation reaction of arylmethyl nitrile with aldehyde, which leads to PhC(CN)=CHCH3; (3) hydrogenation of PhC(CN)=CHCH3, which leads to the formation of the α-alkylated arylmethyl nitrile product (PhCH(CH2CH3)CN). The DFT results revealed that the rate-determining barrier of the overall reaction was 23.9 kcal/mol of the H-transfer step in the third process. The reaction of PhC(CN)=CHCH3 with the dihydride Ru complex, which is generated in the ethanol-to-aldehyde transformation process, is the more preferable hydrogenation mechanism than hydrogenation of vinyl nitrile-Ru complex by H2. Using alcohol as the reactant not only fulfills the requirement of the borrowing-H strategy but also lowers the barriers of the H-migration steps.

Reactivity and selectivity descriptors of dioxygen activation routes on metal oxides

The activation of dioxygen at typically isolated two-electron reduced centers can lead to the formation of electrophilic superoxo or peroxo species, providing an essential route to form reactive O2-derived species in biological, organometallic, and heterogeneous catalysts. Alternatively, O2 activation can proceed via outer sphere routes, circumventing the formation of bound peroxo (OO*) species during oxidation catalysis by forming H2O2(g), which can react with another reduced center to form H2O. The electronic and binding properties of metal oxides that determine the relative rates of these activation routes are assessed here by systematic theoretical treatments using density functional theory (DFT). These methods are combined with conceptual frameworks based on thermochemical cycles and crossing potential models to assess the most appropriate descriptors for the activation barriers for each route using Keggin polyoxometalates as illustrative examples. In doing so, we show that inner sphere routes, which form OO* species via O2 activation on the O-vacancies (*) formed in the reduction part of redox cycles, are mediated by early transition states that only weakly sense the oxide binding properties. Outer sphere routes form H2O2(g) via O2 activation on OH pairs (H/OH*) formed by dissociation of H2O on O-vacancies; their rates and activation barriers reflect the rates of the first H-atom transfer from H/OH* to O2. The activation barriers for this H-transfer step depend on the binding energy of more weakly-bound H-atom in H/OH* pairs (HAE2) and on the OOH-surface interaction energy at its product state (Eint0). The Eint0 values are similar among oxides unless a large charge-balancing cation is present and interacts with OOH; consequently, HAE2 acts as an appropriate descriptor of the outer sphere dynamics. HAE2 also determines the thermodynamics of H2O dissociation on O-vacancies, which influence the inner and outer sphere rates by setting the relative coverage of * and H/OH*. These results, in turn, show that HAE2 is a complete descriptor of the reactivity and selectivity of oxides for O2 activation; the O-atoms in more reducible oxides (more negative HAE2) exhibit a greater preference for the inner sphere routes and for the formation of electrophilic OO* intermediates that mediate epoxidation and O-insertion reactions during catalytic redox cycles. Large charge-balancing cations locally modify Eint0 values that determine the outer sphere rates and thus can be used to alter the preference of O-atoms to either inner or outer sphere routes.

Catalytic Hydrogenation of p-Chloronitrobenzene to p-Chloroaniline Mediated by γ-Mo2N.

Promoting the production of industrially important aromatic chloroamines over transition-metal nitrides catalysts has emerged as a prominent theme in catalysis. This contribution provides an insight into the reduction mechanism of p-chloronitrobenzene (p-CNB) to p-chloroaniline (p-CAN) over the γ-Mo2N(111) surface by means of density functional theory calculations. The adsorption energies of various molecularly adsorbed modes of p-CNB were computed. Our findings display that, p-CNB prefers to be adsorbed over two distinct adsorption sites, namely, Mo-hollow face-centered cubic (fcc) and N-hollow hexagonal close-packed (hcp) sites with adsorption energies of −32.1 and −38.5 kcal/mol, respectively. We establish that the activation of nitro group proceeds through direct pathway along with formation of several reaction intermediates. Most of these intermediaries reside in a significant well-depth in reference to the entrance channel. Central to the constructed mechanism is H-transfer steps from fcc and hcp hollow sites to the NO/–NH groups through modest reaction barriers. Our computed rate constant for the conversion of p-CNB correlates very well with the experimental finding (0.018 versus 0.033 s–1 at ∼500 K). Plotted species profiles via a simplified kinetics model confirms the experimentally reported high selectivity toward the formation of p-CAN at relatively low temperatures. It is hoped that thermokinetics parameters and mechanistic pathways provided herein will afford a molecular level understanding for γ-Mo2N-mediated conversion of halogenated nitrobenzenes into their corresponding nitroanilines; a process that entails significant industrial applications.

Theoretical Investigation on Direct Vinylogous Aldol Reaction of Isatin Catalyzed by Chiral-N, N'-dioxide Sc(III) Complex

The mechanism and enantio- as well as diastereo-selectivity of asymmetric direct aldol reaction of isatin with α-angelica lactone catalyzed by chiral N, N'-dioxide-Sc(OTf)3 were studied at the B3LYP(SMD, THF)/6-31G(d,p) level. The calculations indicated that the reaction occurred along stepwise mechanism, that is, CC bond formation followed by H-transfer from α-angelica lactone to carbonyl group of isatin. The H-transfer step was predicted to be the rate-determining step(RDS), with the energy barrier of 23.3 ∼ 26.2 kcal mol−1 for four stereoisomeric products. The ortho-isopropyl groups of amide in ligand blocked the reacting site from re-face of isatin and induced the re-face of α-angelica lactone to approach to the si-face of isatin, leading to the predominant product with 3S, 2′S-configuration. In this asymmetric catalysis, the interaction energy term (ΔEint), especially stabilizing orbital energy (ΔEoi) and electrostatic energy (ΔVelstat), were the main contributors to the enantioselectivity of the reaction, while the activation strain energy (ΔEstrain) of α-angelica substrate enhanced the diastereodifferentiation of the two competing pathways, contributing to high diastereomeric ratio (d.r.). The turnover frequency (TOF) along the favorable si-face pathway was predicted to be 2.76 × 10−21 s−1, with the rate constant of k(T) = 7.5 × 10−2 exp(-108390/RT) dm3 mol−1 s−1 over 258.15 K ∼ 358.15 K temperature range. These results provided explanation for the good reactivity as well as excellent asymmetric induction of chiral N, N'-dioxide-Sc(OTf)3 in direct aldol reaction of isatin.

Revised Theoretical Model on Enantiocontrol in Phosphoric Acid Catalyzed H-Transfer Hydrogenation of Quinoline

The enantioselective H-transfer hydrogenation of quinoline by Hantzsch ester is a relevant example of Brønsted acid catalyzed cascade reactions, with phosphoric acid being a privileged catalyst. The generally accepted mechanism points out the hydride transfer step as the rate- and stereodetermining step, however computations based on these models do not totally fit with experimental observations. We hereby present a computational study that enlightens the stereochemical outcome and quantitatively reproduces the experimental enantiomeric excesses in a series of H-transfer hydrogenations. Our calculations suggest that the high stereocontrol usually attained with BINOL-derived phosphoric acids results mostly from the steric constraints generated by an aryl substituent of the catalyst, which hinders the access of the Hantzsch ester to the catalytic site and enforces approach through a specific way. It relies on a new model involving the preferential assembly of one of the stereomeric complexes formed by the chiral phosphoric acid and the two reaction partners. The stereodetermining step thus occurs prior to the H-transfer step.

The Distant Double Bond Determines the Fate of the Carboxylic Group in the Dissociative Photoionization of Oleic Acid.

The valence threshold photoionization of oleic acid has been studied using synchrotron VUV radiation and imaging photoelectron photoion coincidence (iPEPICO) spectroscopy. An oleic acid aerosol beam was impacted on a copper thermodesorber, heated to 130 °C, to evaporate the particles quantitatively. Upon threshold photoionization, oleic acid produces the intact parent ion first, followed by dehydration at higher energies. Starting at ca. 10 eV, a large number of fragment ions slowly rise suggesting several fragmentation coordinates with quasi-degenerate activation energies. However, water loss is the dominant low-energy dissociation channel, and it is shown to be closely related to the unsaturated carbon chain. In the lowest-barrier process, one of the four allylic hydrogen atoms is transferred to the carboxyl group to form the leaving water molecule and a cyclic ketone fragment ion. A statistical model to analyze the breakdown diagram and measured rate constants yields a 0 K appearance energy of 9.77 eV, which can be compared with the density functional theory result of 9.19 eV. Alternative H-transfer steps yielding a terminal C=O group are ruled out based on energetics and kinetics arguments. Some of the previous photoionization mass spectrometric studies also reported 2 amu and 26 amu loss fragment ions, corresponding to hydrogen and acetylene loss. We could not identify such peaks in the mass spectrum of oleic acid.

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase

Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assistedsynthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction.KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.

Active sites and mechanisms for H2O2 decomposition over Pd catalysts

A combination of periodic, self-consistent density functional theory (DFT-GGA-PW91) calculations, reaction kinetics experiments on a SiO2-supported Pd catalyst, and mean-field microkinetic modeling are used to probe key aspects of H2O2 decomposition on Pd in the absence of cofeeding H2 We conclude that both Pd(111) and OH-partially covered Pd(100) surfaces represent the nature of the active site for H2O2 decomposition on the supported Pd catalyst reasonably well. Furthermore, all reaction flux in the closed catalytic cycle is predicted to flow through an O-O bond scission step in either H2O2 or OOH, followed by rapid H-transfer steps to produce the H2O and O2 products. The barrier for O-O bond scission is sensitive to Pd surface structure and is concluded to be the central parameter governing H2O2 decomposition activity.

Theoretical study on the reaction mechanism of cyclopropenylidene with cyclic CnH2nO (n = 2, 3) compounds: Ring expansion process

The ring expansion reaction mechanisms between cyclopropenylidene and cyclic CnH2nO (n=2, 3) compounds have been systematically investigated employing the second-order Møller-Plesset perturbation theory (MP2) method in order to better understand the reactivity of cyclopropenylidene with epoxy compounds (oxirane and epoxypropane). Geometry optimizations and vibration analyses have been performed for the stationary points on the potential energy surfaces of the system. The calculated results show that cyclopropenylidene can insert into oxirane at its CO bond and into epoxypropane at its CO or CC bond. From the kinetic viewpoint, it is easier for cyclopropenylidene to insert into the CO bond of oxirane than that of the CO bond of epoxypropane. For insertion into epoxypropane, it is easier for cyclopropenylidene to insert into its CO bond than CC bond. Through the first insertion step and the second ring-opened step, spiro and carbene intermediates can been formed between cyclopropenylidene and epoxy compounds, respectively. Through the following two H-transfer steps, carbene intermediate forms the products of allenes and alkynes, respectively. From the thermodynamics viewpoint, the allenes are the dominant product for the title reaction.

Theoretical study on the reaction mechanism of cyclopropenylidene with azacyclopropane: ring expansion process

The reaction mechanism between cyclopropenylidene and azacyclopropane has been systematically investigated by employing the second-order Moller–Plesset perturbation theory (MP2) method to better understand the reactivity of cyclopropenylidene with the three-membered ring compound azacyclopropane. Geometry optimization and vibrational analysis have been performed for the stationary points on the potential energy surfaces of the system. It was found that, in the first step of this reaction, cyclopropenylidene can insert into azacyclopropane at its C–N bond to form a spiro intermediate. In the second, ring-opening step, a carbene intermediate is formed. Through the following two H-transfer steps, the carbene intermediate forms an allene [pathway (1)] or alkyne [pathway (2)] product. From the kinetic viewpoint, the pathway with alkyne formation is easier than that with allene formation. From the thermodynamic viewpoint, the allene is the dominant product because the reaction is exothermic (287.8 kJ mol−1). .

Theoretical study of the ring expansion reaction mechanism of cyclopropenylidene with azetidine

The mechanism for the ring expansion reaction between cyclopropenylidene and azetidine was systematically investigated employing second-order Møller-Plesset perturbation theory (MP2) in order to better understand the reactivity of cyclopropenylidene with the four-membered ring compound azetidine. Geometry optimizations and vibrational analyses were performed for the stationary points on the potential energy surfaces of the system. The results of our calculations show that cyclopropenylidene can insert into azetidine at its C-N or C-C bond. From a kinetic viewpoint, it is easier for cyclopropenylidene to insert into the C-N bond of azetidine than into the C-C bond. During the first insertion step and the second ring-opening step, it forms spiro and carbene intermediates, respectively. In the following two H-transfer steps, the carbene intermediate forms allenes and alkynes, respectively, as products. From a thermodynamic perspective, allenes are the dominant product because the reaction is exothermic by 373.4 kJ/mol⁻¹.

Mechanistic Role of Water on the Rate and Selectivity of Fischer–Tropsch Synthesis on Ruthenium Catalysts

Water increases Fischer-Tropsch synthesis (FTS) rates on Ru through H-shuttling processes. Chemisorbed hydrogen (H*) transfers its electron to the metal and protonates the O-atom of CO* to form COH*, which subsequently hydrogenates to *HCOH* in the kinetically relevant step. H2 O also increases the chain length of FTS products by mediating the H-transfer steps during reactions of alkyl groups with CO* to form longer-chain alkylidynes and OH*.