Theoretical analysis of the mechanism of palladium(II) acetate-catalyzed oxidative Heck coupling of electron-deficient arenes with alkenes: effects of the pyridine-type ancillary ligand and origins of the meta-regioselectivity

A systematic theoretical study is carried out on the mechanism for Pd(II)-catalyzed oxidative cross-coupling between electron-deficient arenes and alkenes. Two types of reaction pathways involving either a sequence of initial arene C-H activation followed by alkene activation, or the reverse sequence of initial alkene C-H activation followed by arene activation are evaluated. Several types of C-H activation mechanisms are discussed including oxidative addition, σ-bond metathesis, concerted metalation/deprotonation, and Heck-type alkene insertion. It is proposed that the most favored reaction pathway should involve an initial concerted metalation/deprotonation step for arene C-H activation by (L)Pd(OAc)(2) (L denotes pyridine type ancillary ligand) to generate a (L)(HOAc)Pd(II)-aryl intermediate, followed by substitution of the ancillary pyridine ligand by alkene substrate and direct insertion of alkene double bond into Pd(II)-aryl bond. The rate- and regio-determining step of the catalytic cycle is concerted metalation/deprotonation of arene C-H bond featuring a six-membered ring transition state. Other mechanism alternatives possess much higher activation barriers, and thus are kinetically less competitive. Possible competing homocoupling pathways have also been shown to be kinetically unfavorable. On the basis of the proposed reaction pathway, the regioselectivity predicted for a number of monosubstituted benzenes is in excellent agreement with experimental observations, thus, lending further support for our proposed mechanism. Additionally, the origins of the regioselectivity of C-H bond activation is elucidated to be caused by a major steric repulsion effect of the ancillary pyridine type ligand with ligands on palladium center and a minor electronic effect of the preinstalled substituent on the benzene ring on the cleaving C-H bond. This would finally lead to the formation of a mixture of meta and para C-H activation products with meta products dominating while no ortho products were detected. Finally, the multiple roles of the ancillary pyridine type ligand have been discussed. These insights are valuable for our understanding and further development of more efficient and selective transition metal-catalyzed oxidative C-H/C-H coupling reactions.     

Theoretical prediction of a perepoxide intermediate for the reaction of singlet oxygen with trans-cyclooctene contrasts with the two-step no-intermediate ene reaction for acyclic alkenes

B3LYP/6-31G* and CASMP2 calculations have been employed to study the ene reaction of singlet oxygen with trans-cyclooctene. These methods predict that the reaction involves a perepoxide intermediate, whereas alkenes such as tetramethylethylene are predicted by the same methods to occur by a two-step no-intermediate mechanism, with no perepoxide intermediate. The change in mechanism arises because the trans-cyclooctene imposes a substantial strain in the transition state for hydrogen abstraction. The perepoxide is formed through a polarized diradical intermediate that can lead to the observation of alkene isomerization. The polarized diradical also becomes a minimum because of the barrier to abstraction.     

Probing the structural and electronic factors affecting the adsorption and reactivity of alkenes in acidic zeolites using DFT calculations and multivariate statistical methods

Quantum mechanical (QM) cluster calculations have been performed on a model of ZSM-5 at DFT and MP2 levels. We investigated how the adsorption energies and the energetics of alkoxide intermediate formation of six different alkene substrates, ethene, propene, 1-butene, cis/trans butene, and isobutene, vary in this zeolite model. An analysis of the DFT geometric, electronic, and energetic parameters of the zeolite-substrate complexes, transition states, and alkoxide intermediates is performed using principal components analysis (PCA) and partial least squares (PLS). These deliver an insight into the correlated changes that occur between molecular structure and energy along the reaction coordinate between the physisorbed and chemisorbed species within the zeolite. To the best of our knowledge, this is the first occasion multivariate techniques such as PCA or PLS have been employed to profile the changes in electronics, distances, and angles in QM calculations of catalytic systems such as zeolites. We find the calculated adsorption and the alkoxide intermediate energies correlate strongly with the absolute charge on the substrate and the length of the substrate double bond. The transition states' energies are not affected by the zeolite framework as modeled, which explains why they correlate strongly with the gas-phase substrate protonation energy. Our cluster results show that for ethene, propene, 1-butene, and isobutene, the relative energetics associated with the formation of the alkoxide intermediate in ZSM-5 follow the same trends as calculations where the effects of the framework are included.     

Intramolecular hydroboration of unsaturated phosphine boranes

Homoallylic phosphine boranes undergo intramolecular hydroboration upon activation by triflic acid. The reaction occurs via an intermediate B-trifluorosulfonyloxyborane complex such as 15, followed by S(N)1-like or S(N)2-like displacement of the triflate leaving group, apparently leading to the formation of a four-center transition state. In the case of trisubstituted double bonds, as in the substrates 29 and 32, ionic hydrogenation of the alkene competes with internal hydroboration.     

New mechanistic insights into the iridium-phosphanooxazoline-catalyzed hydrogenation of unfunctionalized olefins: a DFT and kinetic study

The reaction mechanism of the iridium-phosphanooxazoline-catalyzed hydrogenation of unfunctionalized olefins has been studied by means of density functional theory calculations (B3LYP) and kinetic experiments. The calculations suggest that the reaction involves an unexpected Ir(III)-Ir(V) catalytic cycle facilitated by coordination of a second equivalent of dihydrogen. Thus, in the rate-determining migratory insertion of the substrate alkene into an iridium-hydride bond, simultaneous oxidative addition of the bound dihydrogen occurs. The kinetic data shows that the reaction is first order with respect to hydrogen pressure. This is interpreted in terms of an endergonic coordination of this second equivalent of dihydrogen, although a rate-determining step, in which coordinated solvent is replaced by dihydrogen, could not be ruled out. Furthermore, the reaction was found to be zeroth order with respect to the alkene concentration. This correlates well with the calculated exothermicity of substrate coordination, and the catalyst is thus believed to coordinate an alkene in the resting state. On the basis of the proposed catalytic cycle, calculations were performed on a full-sized system with 88 atoms to assess the appropriateness of the model calculations. These calculations were also used to explain the enantioselectivity exerted by the catalyst.     

Theoretical study of the gas-phase thermolysis reaction of alkyl (ethyl,isopropyl, and tert-butyl) N,N-dimethylcarbamates and N,N-diethylcarbamates

Theoretical studies on the thermolysis in the gas phase of alkyl N,N-dialkylcarbamates were carried out using ab initio theoretical methods, at the MP2/6-31G(d), MP2/6-31++G(d,p) and MP2/6-311++G(2d,p)//MP2/6-31G(d) levels. The reactions have two steps: the first one corresponds to the formation of an alkene and a neutral dialkylcarbamic acid intermediate via a six-membered cyclic transition state; the second one is the decarboxylation of this intermediate via a four-membered cyclic transition state, leading to carbon dioxide and the corresponding dialkylamine. The progress of the reactions was followed by means of the Wiberg bond indices. The results indicate that the transition states have character intermediate between reactants and products, and the calculated synchronicities show that the reactions are slightly asynchronous. The bond-breaking processes are more advanced than the bond-forming ones, indicating a bond deficiency in the transition states. The rate constants calculated for all the reactions agree very well with the available experimental data.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

Substrate and metal control of barrier heights for oxo transfer to Mo and W bis-dithiolene sites

Reaction coordinates for oxo transfer from the substrates Me(3)NO, Me(2)SO, and Me(3)PO to the biologically relevant Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)(2)](-) where mdt = 1,2-dimethyl-ethene-1,2-dithiolate(2-), and from Me(2)SO to the analogous W(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X-O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction.     

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

The mechanism for the reaction catalyzed by the 4-oxalocrotonate tautomerase (4-OT) enzyme has been studied using a quantum mechanical/molecular mechanical (QM/MM) method developed in our laboratory. Total free energy barriers were obtained for the two steps involved in this reaction. In the first step, Pro-1 acts as a general base to abstract a proton from the third carbon of the substrate, 2-oxo-4-hexenedioate, creating a negative charge on the oxygen at C-2 of this substrate. In the second step, the same hydrogen abstracted by the N-terminal Pro-1 is shuttled back to the fifth carbon of the substrate to form the product, 2-oxo-3-hexenedioate. The calculated total free energy barriers are 14.54 and 16.45 kcal/mol for the first and second steps, respectively. Our calculations clearly show that there is no general acid in the reaction. Arg-39' ', which is hydrogen bonded to the carboxylate group of the substrate, and an ordered water, which moves closer to the site of the charge formed in the transition state and intermediate, play the main role in transition state/intermediate stabilization without acting as general acids in the reaction.     

Mechanistic study on the palladium-catalyzed (3 + 2) intramolecular cycloaddition of alk-5-enylidenecyclopropanes

The intramolecular (3 + 2) cycloaddition of alkenylidenecyclopropanes to alkenes under palladium catalysis provides a practical and stereoselective entry into a variety of interesting bicycles. The reaction outcome and stereoselectivity of the process are somewhat dependent on the characteristics of the substrate and of the palladium ligand, which is not easy to justify on the basis of the current mechanistic understanding. We therefore decided to study the different mechanistic alternatives from a theoretical point of view. The energies of the reaction intermediates and transition states for different possible pathways have been explored at DFT level in a model system, and using PH(3) and P(OMe)(3) as ligands. The results obtained suggest that the most favourable reaction pathway involves an initial oxidative addition of Pd(0) at the distal position of the cyclopropane to afford a palladacyclobutane intermediate. The evolution of this intermediate into the final cycloadduct can occur following different paths, the most favorable depending on the configuration and substitution of the alkene cycloaddition partner, and the number of ancillary ligands coordinated to Pd. The computational results are consistent with the experimental observations and provide the basis for proposing which would be the operative mechanistic pathway in different cases. The results also allow us to explain the stereochemical divergences observed in some of the reactions.     

Intramolecularly competitive Ireland-Claisen rearrangements: scope and potential applications to natural product synthesis

A variety of bis-allylic esters were prepared by vinylmetal addition to cycloalkenones followed by esterification either in situ or in a separate operation. For chiral cyclohexenones, the vinyl additions generally occurred with >10:1 diastereoselectivity. Although in some cases the bis-allylic esters proved to be sensitive to silica gel or other adsorbents, all of the esters examined could be isolated in acceptable purity. The Ireland-Claisen rearrangement of the bis-allylic esters occurred with complete regioselectivity via the exocyclic alkene. The alkene stereochemistry and the stereochemistry at C-2 and C-3 of the pentenoic acid products were consistent with a chairlike transition state in the rearrangement. Substituents at the carbons adjacent to the allylic carbinol carbon (i.e., C-2 or C-6 in cyclohexenone-derived substrates) directed the stereochemical course of the rearrangement. The rearrangements generally proceeded so as to place the larger of the C-2 or C-6 substituents in the pseudoequatorial position with respect to the chairlike transition state. For a bis-allylic ester bearing both a C-2-CH(3) and a C-6-OMEM substituent, the rearrangement product resulted from the nominally smaller OMEM substituent occupying a pseudoequatorial position with respect to the chairlike transition state.     

A Short Sequence for the Iterative Synthesis of Fused Polyethers

A simple and efficient four‐step sequence for the synthesis of fused polyether arrays has been developed. Cyclic ethers are installed by sequential alkynyl ether formation, carbocupration, ring‐closing metathesis and hydroboration with acidic workup. Crucially, the alkene required for the subsequent ring formation by ring‐closing metathesis is present in the substrate but is masked in the form of a vinylic silane, which prevents competitive metathesis of the side chain. Generation of the reactive alkene from the unreactive vinylic silane is accomplished by hydroboration and subsequent acid‐mediated Peterson elimination of the intermediate hydroxysilane.     

Combined experimental and theoretical study of the mechanism and enantioselectivity of palladium- catalyzed intermolecular Heck coupling

The asymmetric Heck reaction using P,N-ligands has been studied by a combination of theoretical and experimental methods. The reaction follows Halpern-style selectivity; that is, the major isomer is produced from the least favored form of the pre-insertion intermediate. The initially formed Ph-Pd(P,N) species prefers a geometry with the phenyl trans to N. However, the alternative form, with Ph trans to P, is much less stable but much more reactive. In the preferred transition state, the phenyl moiety is trans to P, but significant electron density has been transferred to the alkene carbon trans to N. The steric interactions in this transition state fully account for the enantioselectivity observed with the ligands studied. The calculations also predict relative reactivity and nonlinear mixing effects for the investigated ligands; these predictions are fully validated by experimental testing. Finally, the low conversion observed with some catalysts was found to be caused by inactivation due to weak binding of the ligand to Pd(0). Adding monodentate PPh3 alleviated the precipitation problem without deteriorating the enantioselectivity and led to one of the most effective catalytic systems to date.     

Accumulation of tetrahedral intermediates in cholinesterase catalysis: a secondary isotope effect study

In a previous communication, kinetic β-deuterium secondary isotope effects were reported that support a mechanism for substrate-activated turnover of acetylthiocholine by human butyrylcholinesterase (BuChE) wherein the accumulating reactant state is a tetrahedral intermediate ( Tormos , J. R. ; et al. J. Am. Chem. Soc. 2005 , 127 , 14538 - 14539 ). In this contribution additional isotope effect experiments are described with acetyl-labeled acetylthiocholines (CL(3)COSCH(2)CH(2)N(+)Me(3); L = H or D) that also support accumulation of the tetrahedral intermediate in Drosophila melanogaster acetylcholinesterase (DmAChE) catalysis. In contrast to the aforementioned BuChE-catalyzed reaction, for this reaction the dependence of initial rates on substrate concentration is marked by pronounced substrate inhibition at high substrate concentrations. Moreover, kinetic β-deuterium secondary isotope effects for turnover of acetylthiocholine depended on substrate concentration, and gave the following: (D3)k(cat)/K(m) = 0.95 ± 0.03, (D3)k(cat) = 1.12 ± 0.02 and (D3)βk(cat) = 0.97 ± 0.04. The inverse isotope effect on k(cat)/K(m) is consistent with conversion of the sp(2)-hybridized substrate carbonyl in the E + A reactant state into a quasi-tetrahedral transition state in the acylation stage of catalysis, whereas the markedly normal isotope effect on k(cat) is consistent with hybridization change from sp(3) toward sp(2) as the reactant state for deacylation is converted into the subsequent transition state. Transition states for Drosophila melanogaster AChE-catalyzed hydrolysis of acetylthiocholine were further characterized by measuring solvent isotope effects and determining proton inventories. These experiments indicated that the transition state for rate-determining decomposition of the tetrahedral intermediate is stabilized by multiple protonic interactions. Finally, a simple model is proposed for the contribution that tetrahedral intermediate stabilization provides to the catalytic power of acetylcholinesterase.     

Linear and branched phospha[n]triangulanes

Novel, highly stable, linear and branched mono- and diphospha[n]triangulanes were synthesized in high yields by the CuCl-catalyzed phosphinidene addition to spirocyclopropanated methylenecyclopropanes and bicyclopropylidenes. The effect of spirofusion on the electronic properties of these esthetically attractive phosphacycles is apparent from X-ray single crystal structure analyses, which reveals a tightening of the phosphirane ring on additional spirocyclopropanation, and from the NMR features that show deshielded chemical shifts for the ring-phosphorus and -carbon atoms. Steric factors play a role in the addition reaction when the substrate alkene carries a second sphere of spirocyclopropane rings and causes the formation of 2-phosphabicyclo[3.2.0]heptenes in small amounts. These by-products most probably result from addition of the [PhP(Cl)W(CO)(5)]-Cu-L (L=alkene or solvent) reagent to the spirocyclopropanated bicyclopropylidene to give an intermediate sigma-complex, which subsequently, facilitated by steric factors, undergoes a cyclopropylcarbinyl to cyclobutyl ring expansion followed by a [1,3]-sigmatropic shift.     

Rhodium phosphine-π-arene intermediates in the hydroamination of alkenes

A detailed mechanistic study of the intramolecular hydroamination of alkenes with amines catalyzed by rhodium complexes of a biaryldialkylphosphine is reported. The active catalyst is shown to contain the phosphine ligand bound in a κ(1), η(6) form in which the arene is π-bound to rhodium. Addition of deuterated amine to an internal olefin showed that the reaction occurs by trans addition of the N-H bond across the C═C bond, and this stereochemistry implies that the reaction occurs by nucleophilic attack of the amine on a coordinated alkene. Indeed, the cationic rhodium fragment binds the alkene over the secondary amine, and the olefin complex was shown to be the catalyst resting state. The reaction was zero-order in substrate, when the concentration of olefin was high, and a primary isotope effect was observed. The primary isotope effect, in combination with the observation of the alkene complex as the resting state, implies that nucleophilic attack of the amine on the alkene is reversible and is followed by turnover-limiting protonation. This mechanism constitutes an unusual pathway for rhodium-catalyzed additions to alkenes and is more closely related to the mechanism for palladium-catalyzed addition of amide N-H bonds to alkenes.     

Transition‐State Stabilization by a Secondary Substrate–Ligand Interaction: A New Design Principle for Highly Efficient Transition‐Metal Catalysis

A library of monodentate phosphane ligands, each bearing a guanidine receptor unit for carboxylates, was designed. Screening of the library gave some excellent catalysts for regioselective hydroformylation of β,γ‐unsaturated carboxylic acids. A terminal alkene, but‐3‐enoic acid, was hydroformylated with a linear/branched (l/b) regioselectivity up to 41. An internal alkene, pent‐3‐enoic acid was hydroformylated with regioselectivity up to 18:1. Further substrate selectivity (e.g., acid vs. methyl ester) and reaction site selectivity (monofunctionalization of 2‐vinylhept‐2‐enoic acid) were also achieved. Exploration of the structure–activity relationship and a practical and theoretical mechanistic study gave us an insight into the nature of the supramolecular guanidinium–carboxylate interaction within the catalytic system. This allowed us to identify a selective transition‐state stabilization by a secondary substrate–ligand interaction as the basis for catalyst activity and selectivity.     

The stereochemistry of 1,3-dipolar cycloaddition of internally H-bonded chiral methylenenitrones

A study of diastereoselectivity in the cycloaddition reactions of a series of mono- and disubstituted alkenes with two chiral, internally H-bonded methylenenitrones has been carried out. The high degree of stereochemical control in the presence of anhydrous magnesium bromide has been explained in terms of a metal chelated transition state. Intramolecular cycloaddition involving a methylenenitrone containing an alkene moiety linked to a nitrogen gave a stereoselective addition product.     

Stereochemical memory effects in alkene radical cation/anion contact ion pairs: effect of substituents, and models for diastereoselectivity

A series of 12 stereochemically defined 2,m-dimethyl- and 2,m,n-trimethyl-6-benzylamino-2-nitro-3-(diphenylphosphatoxy)hexanes have been synthesized and their cyclization reactions leading to di- and trisubstituted N-benzyl pyrrolidines examined in the presence of tributyltin hydride and azoisobutyronitrile in benzene at reflux. The cyclizations are interpreted in terms of generation of an alkyl radical by abstraction of the nitro group with a stannyl radical. The phosphate leaving group is then expelled in a heterolytic cleavage to give a contact alkene radical cation/phosphate anion pair. For the majority of the examples studied, the cyclizations are best understood in terms of nucleophilic attack by the amine on the opposite face of the alkene radical cation to the one shielded by the leaving group, within the confines of the initial contact ion pair, resulting in overall cyclization with inversion of configuration. Dependent on the relative stereochemistry of the substituents, the cyclization is envisaged as taking place through either chair-like or twist-boat-like transition states with the maximum number of substituents pseudo-equatorial. The model breaks down when cyclization on the initial contact ion pair would engender significant destabilizing steric interactions, especially (1,3)A strain in the alkene radical cation. In these cases a fully equilibrated Beckwith-Houk-type transition state provides a satisfactory model. Interesting examples of matching and mismatching in the Corey-type oxazaborolidine-mediated reduction of alkyl (methyl-1-nitroethyl) ketones by a beta-methyl group in the alkyl chain are reported, and the mismatching is attributed to a developing syn-pentane interaction in the transition state.     

Acid-mediated aryl migration reaction of C-3 aryl substituted pyrrolidinoindolines

Aryl migration reactions of C-3 aryl substituted pyrrolidinoindoline compounds to provide highly conjugated C-2 aryl indole compounds have been discovered. The developed reactions have a wide substrate scope and proceed in high yield under simple acidic conditions. A unique cationic cyclopropane intermediate as the transition state is proposed.     

Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.

BACKGROUND: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates. RESULTS: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 A and 2.0 A resolution, respectively. The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual 2,5B conformation. CONCLUSIONS: The 2,5B conformation found for the alpha-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the 4C1 chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this clan of glycoside hydrolases.