Copper-cascade catalysis: synthesis of 3-functionalized indoles

A three-component reaction of indoles, sulfonyl azides and terminal alkynes afforded 3-functionalized indoles in a single step via copper-cascade catalysis.     

Efficient synthesis of 3-substituted indoles through a domino gold(I) chloride catalyzed cycloisomerization/C3-functionalization of 2-(alkynyl)anilines

An efficient synthesis of 3-substituted indoles by a sequential approach involving gold(I) chloride catalyzed cycloisomerization/bis-addition and conjugate addition of 2-(alkynyl)anilines has been accomplished. A variety of 2-(alkynyl)anilines, aldehydes, isatins and nitroolefins undergo this overall process in good to excellent yields. This methodology represents an effective alternative to the classical C3-functionalization of indoles.     

Mechanism of the aminolysis of methyl benzoate: a computational study

Density functional and ab initio methods were applied in examining the possible mechanistic pathways for the reaction of methyl benzoate with ammonia. Transition state structures and energies were determined for concerted and neutral stepwise mechanisms. The theoretical results show that the two possible pathways have similar activation energies. The general base catalysis of the process was also examined. The predictions reveal that the catalytic process results in considerable energy savings and the most favorable pathway of the reaction is through a general-base-catalyzed neutral stepwise mechanism. The structure and transition vectors of the transition states indicate that the catalytic role of ammonia is realized by facilitating the proton-transfer processes. Comparison of the energetics of the aminolysis for methyl benzoate and methyl formate shows the more favorable process to be that for the aliphatic ester. The differing reactivity of the two esters is explained in terms of the electrostatic potential values at the atoms of the ester functionality.     

Revisiting the reduction of indoles by hydroboranes: A combined experimental and computational study

A combined experimental and density functional computational study was used to probe the mechanism for the reduction of indoles using simple borane BH₃·DMS (DMS?=?dimethyl sulfide). Experimental and computational studies all steer to the formation of the reduced species 1-BH₂-indolines as the resting state for this reaction, as opposed to the historically presumed formation of the unreduced 1-BH₂-indoles, before the addition of a proton source to form the final product indolines. Furthermore, it was observed that molecular H₂ was generated and consumed in the reaction. Computations put forward hydroboration followed by protodeborylation as the very reasonable mechanistic route for the formation of experimentally observed major intermediate 1-BH₂ indolines. For the H₂ consumption in the reaction, computations suggest the frustrated Lewis pair-type heterolytic splitting of H₂ by a bis(3-indolinyl)borane intermediate.     

Gold catalysis on immobilized substrates: a heteroannulation approach to the solid-supported synthesis of indoles

A gold-catalyzed cyclization of immobilized 2-alkynylanilines was developed as the key step in the synthetic sequence for the preparation of 2-substituted indoles. These results demonstrate the potential of the unexplored combination of gold catalysis and solid-phase organic synthesis.     

Mechanism of the palladium-catalyzed addition of arylboronic acids to enones: a computational study

The palladium(II)-catalyzed addition of arylboronic acids to β,β-disubstituted enones has been investigated with the BP86 density functional. The results show that the mechanism requires three steps: transmetalation, alkene insertion, and protonation. The alkene insertion is the rate-determining step. For unactivated alkenes, the Heck-type β-hydride elimination is more favored than protonation.     

InBr3-catalyzed sulfonation of indoles: a facile synthesis of 3-sulfonyl indoles

Indoles react smoothly with sulfonyl chlorides in the presence of a catalytic amount of indium tribromide at ambient temperature to afford the corresponding 3-arylsulfonyl indole derivatives in high yields with high regioselectivity.     

Mechanism of the Morita-Baylis-Hillman reaction: a computational investigation

Accurate calculations are presented on the mechanism of the MBH reaction, focusing on the reaction between methyl acrylate and benzaldehyde, catalyzed by a tertiary amine. We address the mechanism under protic solvent-free conditions, but also consider how the mechanism and rate-limiting step change in the presence of alcohols. We have carefully calibrated the DFT method used in the calculations by carrying out high-level G3MP2 calculations on a model system. All of our calculations also treat the effect of solvent, described as a dielectric continuum. In the absence of protic solvent, we predict that deprotonation of the alpha-position is the rate-determining step and occurs through a cyclic transition state, with proton transfer to a hemiacetal alkoxide formed by addition of a second equivalent of aldehyde to the intermediate alkoxide. As first suggested by McQuade, this mechanism explains the observed second-order kinetics with respect to aldehyde concentration in the absence of protic solvent. In contrast, in the presence of methanol, we find a slightly lower energy pathway, in which the alcohol serves as a shuttle to transfer the proton from carbon to oxygen. Overall, the barrier to reaction for the latter mechanism is of 24.6 kcal/mol with respect to reactants at the B3LYP level of theory. The relative energy for the addition transition state of the amine-acrylate betaine adduct to the aldehyde is much lower, at 16.0 kcal/mol relative to reactants, so C-C bond formation should not be rate-limiting, except perhaps for some aliphatic aldehydes or imines. We discuss the implications of this mechanism for the design of asymmetric versions of the MBH reaction, given the overwhelming importance of the proton-transfer step.     

Nano structures of group 13-15 mixed heptamer clusters: a computational study

The structural and thermodynamic characteristics of lowest-energy structures of group 13-15 mixed heptamers in two distinct series [(HM)(k)(HM')(l)(NH)(7)] (M, M' = B, Al, Ga and k + l = 7) and [(HGa)(7)(YH)(m)(Y'H)(n)] (Y,Y' = N, P, As and m + n = 7) have been systematically investigated using the density functional approach. Our main goal is to get knowledge of the preferential bonding patterns of the first three rows of group 13-15 elements for the construction of mixed heptameric clusters. Structural parameters, thermodynamic properties of oligomerization reaction, band gaps, and dipole moments of the 18 lowest-energy structures of the studied heptamers in each series are compared to their corresponding binary parents, that is, [(HM)(7)(NH)(7)] and [(HGa)(7)(YH)(7)]. The stability of different isomer structures is discussed to reveal the competitiveness of group 13 and 15 bonding. Mixed heptamers are predicted to be thermodynamically more stable compared to a mixture of monomers. However, the favorability for the generation of mixed heptamers strongly depends on the nature of inserted metal and nonmetal pairs of group 13-15. Moreover, it is found that among all studied heptamers the smaller band gaps correspond to arsenic containing species which are close to the semiconducting regime, around 4.62-4.98 eV.     

Platinum-catalysed bisindolylation of allenes: a complementary alternative to gold catalysis

Pt versus Au: Platinum-catalysed addition of nucleophiles to allenes follows a distinctly different pathway to the process catalysed by gold(I) complexes; the platinum catalyst leads to different products with indoles involving a bisindolylation reaction, whereas gold(I) gives allyl indoles from a single addition (see scheme).     

The mechanism of water oxidation catalysis promoted by [tpyRu(IV)=O]2L3+: a computational study

The resting state of the recently reported water oxidation catalyst [tpyRu(II)-OH(2)](2)L(3+) (tpy = terpyridine; L = bipyridylpyrazolylic anion) ([2,2](3+)) must be activated by a series of proton-coupled oxidations in which four protons and four electrons are removed overall to afford the catalytically competent species [tpyRu(IV)O](2)L(3+) ([4,4](3+)). We have examined all of the plausible redox intermediates utilizing density functional theory coupled to a continuum solvation model. Our calculations reproduce well the first three redox potentials under pH = 1 conditions, and a reasonable correlation between theory and experiment is found for the fourth irreversible redox process that accompanies O(2) generation. The computed oxidation potentials to access [5,4](4+) and [5,5](5+), 1.875 and 2.032 V vs NHE, respectively, exclude the otherwise plausible possibilities of the catalytically active species having a higher oxidation state. [4,4](3+) has an antiferromagnetically coupled ground state in which one ruthenium has two unpaired electrons antiparallel to those of the other ruthenium. As we found in our previous work, two radicaloid terminal oxygen moieties with different spin orientations that are induced by spin polarization from the electron-deficient Ru(IV) centers are found. Two mechanistic scenarios are relevant and interesting for the key O-O bond formation event: intramolecular oxo-oxo coupling and coupling between one terminal oxo and the oxygen atom of the incoming water substrate. The intramolecular oxo-oxo coupling is facile, with a low barrier of 13.9 kcal mol(-1), yielding a peroxo intermediate. The necessary subsequent addition of water in an associative substitution mechanism to cleave one of the Ru-peroxo bonds, however, is found to be impractical at room temperature, with a barrier of DeltaG(double dagger) = 30.9 kcal mol(-1). Thus, while plausible, the intramolecular oxo-oxo coupling is unproductive for generating molecular dioxygen. The intermolecular O-O coupling is associated with a high barrier (DeltaG(double dagger) = 40.2 kcal mol(-1)) and requires the assistance of an additional proton, which lowers the barrier dramatically to 24.5 kcal mol(-1).     

Aerobic oxygenation of phenylboronic acid promoted by thiol derivatives under gold-free conditions: a warning against gold nanoparticle catalysis

Oxygenation of phenylboronic acid to phenol is promoted by thiol derivatives such as 2-aminothiophenol under aerobic conditions in water without metal catalyst. A plausible mechanism involves autoxidation of thiol to generate hydrogen peroxide in situ, which converts phenylboronic acid into phenol under basic conditions. Since thiols are often utilized as protective ligands for gold nanoparticles (AuNPs), this result is a warning that excess thiols and free thiols liberated from the Au surface could participate in aerobic oxidations catalyzed by thiol-protected AuNPs.     

Mechanism of OH radical hydration: a comparative computational study of liquid and supercritical solvent

Flexible models of the radical and water molecules including short-range interaction of hydrogen atoms have been employed in molecular dynamic simulation to understand mechanism of (●)OH hydration in aqueous systems of technological importance. A key role of H-bond connectivity patterns of water molecules has been identified. The behavior of (●)OH(aq) strongly depends on water density and correlates with topological changes in the hydrogen-bonded structure of water driven by thermodynamic conditions. Liquid and supercritical water above the critical density exhibit the radical localization in cavities existing in the solvent structure. A change of mechanism has been found at supercritical conditions below the critical density. Instead of cavity localization, we have identified accumulation of water molecules around (●)OH associated with the formation of a strong H-donor bond and diminution of non-homogeneity in the solvent structure. For all the systems investigated, the computed hydration number and the internal energy of hydration Δ(h)U showed approximately linear decrease with decreasing density of the solvent but a degree of radical-water hydrogen bonding exhibited non-monotonic dependence on density. The increase in the number of radical-water H-acceptor bonds is associated with diminution of extended nets of four-bonded water molecules in compressed solution at ~473 K. Up to 473 K, the isobaric heat of hydration in compressed liquid water remains constant and equal to -40 ± 1 kJ mol(-1).     

First principles computational study for understanding the interactions between ssdna and gold nanoparticles: adsorption of methylamine on gold nanoparticulate surfaces

We conducted a computational adsorption study of methylamine on various surface models of a gold nanoparticle which is facetted by multiple [111] and [100] planes. In addition to these flat surfaces, our models include the stepped surfaces (ridges) formed along the intersections of these planes. Binding on the flat surfaces was fairly weak, but substantially stronger on the ridges by an average of 4.4 kcal/mol. This finding supports the idea that ssDNA's interaction with gold nanoparticles occurs through the amines on the purine/pyrimidine rings. Also, this typically undesirable interaction between DNA and gold nanoparticles is expected to increase as the particle size decreases. Our analysis suggests that particle size is an important controlling parameter to reduce this interaction.     

Mechanism and diastereoselectivity of aziridine formation from sulfur ylides and imines: a computational study

A computational investigation of the title reaction involving semistabilized (R = Ph) and stabilized (R = CO2Me) sulfur ylides has been performed using DFT methods including a continuum model of solvent. Our results provide support for the generally accepted mechanism and are in very good agreement with observed cis/trans selectivities. This study shows that betaine formation is nonreversible, and that selectivity is thereby determined at the initial addition step, in the case of semistabilized ylides. Our analysis indicates moreover that addition TS structures are governed by the steric strain induced by the N-sulfonyl group, which favors the transoid approach in the case of syn betaine formation and the cisoid mode of addition in anti TSs. The observed low trans selectivity is accounted for by the favorable Coulombic interactions and stabilization by C-H...O hydrogen bonding allowed in the cisoid anti addition TS. In the case of stabilized ylides, the endothermicity of betaine formation combined with the high barrier to ring closure render the elimination step rate- and selectivity-determining. Accordingly, the low cis selectivity observed in stabilized ylide reactions is explained by the lower steric strain in the elimination step generated by the formation of the cis aziridine (as compared to the trans case).     

A simple,direct synthesis of 3-vinylindoles from the carbocation-catalysed dehydrative cross-coupling of ketones and indoles. A combined experimental and computational study

A straightforward synthesis of a library of largely new 3-vinylindoles via a clean dehydrative coupling reaction between ketones and indoles has been developed. Highly stable, non-nucleophilic aryl(2-methylindol-3-yl)methylium salts have been used as efficient Lewis acid catalysts. The advantages of the reaction are the use of equimolar amounts of inexpensive and easily available reagents, the low catalyst amount, high atom efficiency, the production of only one molecule of water as a by-product and the mild reaction conditions. Computational studies of two specific reaction mechanism instances show that both steric and electronic effects heavily influence the nature of the final products, whether a methyl group in position 2 of the indole is present or absent.     

Sequential coupling/desilylation-coupling/cyclization in a single pot under Pd/C-Cu catalysis: synthesis of 2-(hetero)aryl indoles

A new one-pot synthesis of 2-(hetero)aryl indoles via sequential C-C coupling followed by C-Si bond cleavage and a subsequent tandem C-C/C-N bond forming reaction is described. A variety of functionalized indole derivatives were prepared by conducting this four step reaction under Pd/C-Cu catalysis. The methodology involved coupling of (trimethylsilyl)acetylene with iodoarenes in the presence of 10% Pd/C-CuI-PPh(3) and triethylamine in MeOH, followed by treating the reaction mixture with K(2)CO(3) in aqueous MeOH, and finally coupling with o-iodoanilides. The single crystal X-ray data of a synthesized indole derivative is presented. Application of the methodology, in vitro pharmacological properties of the synthesized compound, along with a docking study is described.     

Isolation of a cyclopropane-containing product from the rearrangement of a 3-aza-3-ene-1,5-diyne under acid catalysis

A 3-aza-enediyne that undergoes rapid aza-Bergman rearrangement was treated with trifluoromethanesulfonic acid in the presence of 1,4-cyclohexadiene in an attempt to trap the putative 2,5-didehydropyridinium aza-Bergman intermediate. No pyridine products were detected; rather, a cyclopropane derivative of 1,4-cyclohexadiene derived from a 5-oxazolylcarbene was isolated.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.