New coordination compounds of palladium(II) with iminodiacetic acid

Summary Iminodiacetic acid (IDA) forms 1:1 or 1:2 complexes with Pdll at room temperature and pH 6.0. The solid compounds have been characterized by elemental analysis, titrimetry, magnetic measurements, i.r. spectroscopy and thermal studies. The far i.r. spectra show peaks that can be assigned to Pd-Cl, Pd-N and Pd-O vibrations. On the basis of these studies tentative structures for the isolated substances are proposed.     

Crystal structure of diammine(malonato)palladium(II)

Diammine(malonato)palladium(II) is synthesized by the reaction of [Pd(NH₃)₄](NO₃)₂ with malonic acid, and its crystal structure is determined by single crystal X-ray diffraction. Distorted coordination square of the Pd(II) atom is formed by two N atoms of two ammonia molecules and two O atoms of bidentate malonate ligand. The average Pd-N and Pd-O distances are 2.018(7) ? and 2.014(2) ?, respectively. The molecules are stacked in such a way that the planes of coordination squares are parallel with the Pd...Pd distances between the nearest neighbors in a stack of 4.039 ?.     

Kinetic and computational analysis of the palladium(II)-catalyzed asymmetric allylic trichloroacetimidate rearrangement: development of a model for enantioselectivity

The asymmetric rearrangement of allylic trichloroacetimidates catalyzed by palladium(II) complexes of the COP family is a powerful method for the preparation of enantioenriched chiral allylic amines from prochiral allylic alcohols. A detailed kinetic analysis of this reaction was performed to elucidate the rate- and enantiodetermining step of this important reaction. The results of these studies support a cyclization-induced rearrangement mechanism and prompted DFT studies (B3LYP/LACVP**+) of C-N bond formation, believed to be the enantiodetermining step of this catalytic cycle. On the basis of these calculations, a model for enantioinduction was developed, in which the planar chirality of the catalyst controls the enantioselectivity. These studies should allow the rational design of more enantioselective catalysts.     

Organocatalytic claisen rearrangement: theory and experiment

A combined computational and experimental study on the Claisen rearrangement of a 2-alkoxycarbonyl-substituted allyl vinyl ether in the presence of thioureas as potential noncovalent organocatalysts has been performed. DFT calculations employing different basis sets were utilized to predict a catalytic cycle for the thiourea-catalyzed Claisen rearrangement. The nature of the transition state in the presence and absence of thioureas was studied in detail. Critical geometrical data of the transition state that are indicators for the relative barrier height of the Claisen rearrangement are discussed. Although we did observe a significant transition state stabilization, due to endergonic conformational changes and endergonic complexation the overall effect on the barrier is small, in accordance with experimental results.     

Ligand-Controlled Regiodivergence in Nickel-Catalyzed Vinylcyclopropane Rearrangement

A ligand-controlled regiodivergence in Ni-catalyzed rearrangement of vinylcyclopropanes to 1,4- or 1,5-disubstituted cyclopentenes is reported. The 1,4- or 1,5-disubstituted cyclopentene is selectively obtained depending on the choice of ligands. Detailed kinetic studies and density functional theory calculations on the catalytic cycle revealed that the product selectivity is determined at the reductive elimination step from the six-membered η₁-allyl intermediate.     

Probing O-dealkylation and deamination aging processes in tabun-conjugated AChE: a computational study

The mechanisms of the aging process of tabun-conjugated acetylcholinesterase were explored using density functional theory calculations. The free energy surfaces were calculated for O-dealkylation (C–O bond breaking) and deamination (P–N bond breaking) pathways for the aging process of tabun-conjugated acetylcholinesterase as suggested by mass and crystallographic studies. Initially, the calculations were performed using tabun-conjugated serine (SUN) molecule. O-dealkylation mechanism proceeds via one-step S_N2 type process, whereas the deamination process proceeds via two steps addition–elimination reaction at the phosphorus center of SUN molecule. The recent proposal of another deamination mechanism using human butyrylcholinesterase (hBChE) conjugated with N-mono methyl analogue of tabun (TA4) has also been explored (Nachon et al. in Chem Biol Interact 187:44–48, 2010). The rate-determining activation barrier calculated for this deamination mechanism (26.3 kcal/mol) was comparable with O-dealkylation process (26.9 kcal/mol) with B3LYP/6-31+G* level of theory. To examine the influence of catalytic residue His447, additional calculations were performed with imidazole group of His447 residue. The incorporation of imidazole group of catalytic residue His447 showed marked decrease in the free energies of activation for all the studied aging processes of tabun-inhibited serine. The aging mechanisms have been explored with TA4-inhibited serine, and calculated results showed that the deamination with the rearrangement process is markedly preferred in this case, which supports the Nachon et al. proposal based on the crystallographic studies.     

Oxide surface-promoted Pd-complex catalysis for intramolecular O-activated alkene hydroamination: catalyst preparation, characterization, and performance

Supported Pd-P and Pd-N complexes prepared by a selective reaction of Pd-monomer precursors with SiO2, Al2O3 and TiO2 surfaces and characterized by EXAFS, XPS, XRF and gas analysis exhibited oxide surface-promoted catalysis for the catalytic intrahydroamination of 3-amino propanol vinyl ether to produce a cyclic amine.     

Oxidative carbonylation of phenol with a Pd-O/CeO2-nanotube catalyst

CeO2 nanotubes (CeO2-NT) were synthesized using carbon nanotubes as template by a liquid phase deposition and hydrothermal method. X-ray diffraction, transmission electron microscopy, and N2 adsorption-desorption were used to characterize the CeO2-NT. The wall of CeO2-NT was composed of small interconnected nanocrystallites ranging from 4 to 9 nm in size. The specific surface area of CeO2-NT was 108.8 m2/g with an outer diameter of 25 nm and length > 300 nm. Supported Pd cata-lyst, Pd-O/CeO2-NT, was prepared using CeO2-NT as the support. Temperature-programmed reduc-tion analysis showed that the surface oxygen on Pd-O/CeO2-NT could be reduced at low tempera-ture, therefore it showed high activity in the reaction. Pd-O/CeO2-NT was used as the catalyst for the oxidative carbonylation of phenol. It has better activity and DPC selectivity than Pd-O/CeO2-P, which was prepared by supporting Pd on zero dimensional CeO2particles. Under the optimized conditions, phenol conversion was 67.7% with 93.3% DPC selectivity with Pd-O/CeO2-NT. However, its catalyt-ic activity decreased when the catalyst was used for the second time. This was attributed to the destruction of the tubular structure of Pd-O/CeO2-NT and Pd leaching during the reaction.     

Kinetics and mechanism of the reactions of Pd(II) complexes with azoles and diazines. Crystal structure of [Pd(bpma)(H2O)](ClO4)2.2H2O

Substitution reactions of the complexes [Pd(bpma)(H2O)]2+, [Pd(bpma)Cl]+, [Pd(dien)(H2O)]2+ and [Pd(dien)Cl]+, where bpma = bis(2-pyridylmethyl)amine and dien = diethylentriamine or 1,5-diamino-3-azapentane, with some nitrogen-donor ligands such as triazole, pyrazole, pyrimidine, pyrazine and pyridazine, were studied in an aqueous 0.10 M NaClO4 at pH 2.8 using variable-temperature and -pressure stopped-flow spectrophotometry. The second-order rate constants indicate that the Pd(II) complexes of bpma, viz. [Pd(bpma)(H2O)]2+ and [Pd(bpma)Cl]+, are more reactive than the complexes of dien, viz. [Pd(dien)(H2O)]2+ and [Pd(dien)Cl]+. Also, the aqua complexes, [Pd(bpma)(H2O)]2+ and [Pd(dien)(H2O)]2+, are much more reactive than the corresponding chloro complexes. The most reactive nucleophile of the five-membered rings is triazole and for the six-membered rings the most reactive one is pyridazine. Activation parameters were determined for all reactions and the negative entropies and volumes of activation (Delta S++, Delta V++) support an associative ligand substitution mechanism. The crystal structure of [Pd(bpma)(H2O)](ClO4)2.2H2O was determined by X-ray diffraction. Crystals are monoclinic with the space group P2(1)/c. The coordination geometry of [Pd(bpma)(H2O)]2+ is distorted square-planar. The Pd-N (central) bond distance, 1.958(5) A, is shorter than the other two Pd-N distances, 2.007(5) and 2.009(5) A. The Pd-O distance is 2.043(5) A.     

All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction

To elucidate the catalytic power of enzymes, we analyzed the reaction profile of Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM) by all electron quantum chemical calculations using the fragment molecular orbital (FMO) method. To the best of our knowledge, this is the first report of ab initio-based quantum chemical calculations of the entire enzyme system, where we provide a detailed analysis of the catalytic factors that accomplish transition-state stabilization (TSS). FMO calculations deliver an ab initio-level estimate of the intermolecular interaction between the substrate and the amino acid residues of the enzyme. To clarify the catalytic role of Arg90, we calculated the reaction profile of the wild-type BsCM as well as Lys90 and Cit90 mutant BsCMs. Structural refinement and the reaction path determination were performed at the ab initio QM/MM level, and FMO calculations were applied to the QM/MM refined structures. Comparison between three types of reactions established two collective catalytic factors in the BsCM reaction: (1) the hydrogen bonds connecting the Glu78-Arg90-substrate cooperatively control the stability of TS relative to the ES complex and (2) the positive charge on Arg90 polarizes the substrate in the TS region to gain more electrostatic stabilization.     

Toward a catalytic cycle for the Mn-salen mediated alkene epoxidation: a computational approach

BP86 density functional calculations for the title reaction are presented, where a model catalyst with hypochlorite as oxygen-containing counter ligand, (ClO)(O)Mn(acacen') (acacen' = -O(CH)3N-C2H4-N(CH)3O-), is employed. The epoxidation reaction on potential energy surfaces corresponding to an overall spin-density of two and four unpaired electrons is investigated. The presence of the hypochlorite ligand is found to cause the reaction to proceed under conservation of spin. Further, the oxygen-containing counter ligand causes reoxidation of the Mn-center, thus closing the catalytic cycle. A catalytic scheme is therefore proposed, which includes a step of regeneration of the catalytically active species. Energetic estimates including corrections for solvent effects are presented for the relevant steps constituting the proposed catalytic scheme.     

Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement

The oxy-Cope rearrangement reaction in the antibody AZ28 is investigated using ab initio molecular orbital calculations and molecular mechanical molecular dynamics simulations. This antibody, AZ28, is known as one of the few systems where the mature catalytic antibody shows a negative correlation between the transition state analogue (TSA) binding affinity and the catalytic rate of the oxy-Cope rearrangement compared to the germ line catalytic antibody. The ab initio optimized structure shows that the transition state structure has a more planar configuration than the TSA. The favorable electrostatic interactions between AZ28 and the transition state analogue overcome the unfavorable van der Waals interactions; thus, AZ28 shows higher binding affinity for the TSA than the germ line. However, the AZ28 is not flexible enough to accept the relatively planar transition state structure. Because the lower flexibility causes poorer antibody-hapten interaction energies, the activation free energy of the oxy-Cope rearrangement becomes larger in the mature antibody than the germ line. We show that the differences in flexibility between the germ line and the mature form and the differences in structure between TSA and the transition state are the origin of the negative correlation in AZ28-catalyzed oxy-Cope rearrangement. The mutation of residue 34 of the light chain, 34(L), affects the binding free energies through the interresidue interaction because it is the closest to the hapten among the six mutatable residues. However, it does not affect the negative correlation.     

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.     

Synthesis and Crystal Structure of Pd（ptac—C,N）（acac—O,O）

1INTRODUCTIONTherehasbeenconsiderableattentionfocusedonthestudyofpalladiumcomplexinorganicsynthesis,catalyticprocesses,chemicalreactivity,spectroscopyandstructuralanalysisandfunctionalmaterials[1].Manypalladacycleshavebeenappliedinthepreparationofliquid-crystallinecomplexes[2],andsomeofthemshowantitumoractivity.Theincreasingimportanceofsuchcyclo-organometalliccomplexleadsustoinvestigatethecyclicPdcomplexeswithenhancedchemicalandthermalstability,fromwhichdetailedspectroscopicandstructuralc…     

Using direct electrochemistry to probe rate limiting events during nitrate reductase turnover

Protein film voltammetry of NarGH catalysing nitrate reduction under steady state conditions provides information on events occurring within the enzyme during the catalytic cycle. In this discussion we have focused on exploring the ability of two simple catalytic schemes to reproduce the voltammetric response of NarGH; electron transfer to the enzyme's active site being described either by interfacial electron exchange (Scheme 1) or intramolecular electron delivery via the operation of an electron relay centre (Scheme 2). When the two electron reduced, catalytically competent active site of the enzyme is generated from the oxidised form in 'rapid', non-rate limiting steps of the catalytic cycle, the voltammetric behaviour of NarGH cannot be reproduced. Rather under all the conditions investigated, one electron reduction of the active site from a semi-reduced to a fully-reduced state is found to be crucial to progression through the enzyme's catalytic cycle. The catalytically relevant semi- and fully-reduced oxidation states of the NarGH active site are most likely to correspond to the Mo(V) and Mo(IV) states of the Mo(MGD)2 centre, respectively, although it is not possible to rule out the possibility that they correspond to molybdopterin based oxidation states as observed in other enzymes. We suggest that the rate of either conformational rearrangement within the semi-reduced active site or intramolecular electron delivery to the active site constitutes a defining feature in the catalytic cycle of NarGH and results in the napp approximately 1 appearance of the catalytic waveform.     

Computational study of the mechanism and selectivity of ruthenium-catalyzed hydroamidations of terminal alkynes

Density functional theory calculations were performed to elucidate the mechanism of the ruthenium-catalyzed hydroamidation of terminal alkynes, a powerful and sustainable method for the stereoselective synthesis of enamides. The results provide an explanation for the puzzling experimental finding that with tri-n-butylphosphine (P(Bu)₃) as the ligand, the E-configured enamides are obtained, whereas the stereoselectivity is inverted in favor of the Z-configured enamides with (dicyclohexylphosphino)methane (dcypm) ligands. Using the addition of pyrrolidinone to 1-hexyne as a model reaction, various pathways were investigated, among which a catalytic cycle turned out to be most advantageous for both ligand systems that consists of: (a) oxidative addition, (b) alkyne coordination, (c) alkyne insertion (d) vinyl-vinylidene rearrangement, (e) nucleophilic transfer and finally (f) reductive elimination. The stereoselectivity of the reaction is decided in the nucleophilic transfer step. For the P(ⁿBu)₃ ligand, the butyl moiety is oriented anti to the incoming 2-pyrolidinyl unit during the nucleophilic transfer step, whereas for the dcypm ligand, steric repulsion between the butyl and cyclohexyl groups turns it into a syn orientation. Overall, the formation of E-configured product is favorable by 4.8 kcal mol^–1 (Δ^‡ GSDL) for the catalytic cycle computed with P(Bu)₃ as ancillary ligand, whereas for the catalytic cycle computed with dcypm ligands, the Z-product is favored by 7.0 kcal mol^–1 (Δ^‡ GSDL). These calculations are in excellent agreement with experimental findings.     

Copper-catalyzed 1,2-addition of nucleophilic silicon to aldehydes: mechanistic insight and catalytic systems

Activation of the Si-B inter-element bond with copper(I) alkoxides produces copper-based silicon nucleophiles that react readily with aldehydes to yield α-silyl alcohols (that is, α-hydroxysilanes) after hydrolysis. Two independent protocols were developed, one employing a well-defined NHC-CuOtBu complex and one using the simple CuCN-NaOMe combination without added ligand. The mechanism of the aldehyde addition was investigated in detail by stoichiometric and catalytic experiments as well as NMR spectroscopic measurements. The primary reaction product of the addition of the Si-B reagent and the aldehyde (a boric acid ester of the α-silyl alcohol) and also the "dead-end" intermediate, formed in the competing [1,2]-Brook rearrangement, were characterized crystallographically. Based on these data, a reasonable catalytic cycle is proposed. The NHC-CuOtBu catalytic setup performs nicely at elevated temperature. A more reactive catalytic system is generated from CuCN-NaOMe, showing fast turnover at a significantly lower temperature. Both aromatic and aliphatic aldehydes are transformed into the corresponding α-silyl alcohols in good to very good yields under these mild reaction conditions.     

Propylene oxidation by palladium nitro and nitrato complexes: in situ NMR and IR studies

The mechanism of the propylene oxidation by Pd(NO_n)Cl_2 − m(CH₃CN)₂ complexes (n = 2, 3; m = 0, 1, 2) in chloroform solutions has been studied by ¹H NMR and IR spectroscopy. The main reaction products are acetone and 2-nitropropylene, with their ratio depending on the equilibrium existing in the reaction solutions between palladium complexes containing NO_n ligands bonded to a palladium atom via either an oxygen or a nitrogen atom. Reactivities of the oxygen bonded nitrato and nitrito complexes are significantly higher than that of the nitrogen bonded nitro complex. Various new organopalladium intermediates have been observed and monitored in situ. A reversible insertion of the coordinated propylene into the Pd-O or Pd-N bonds results in nitrato-, nitrito- and nitropalladation intermediates, which then decompose via a β-hydrogen elimination. Two isomers of the nitritopalladation intermediate have been detected, i.e., a palladium metallacycle and an open ring complex, with the latter being much more reactive towards the β-hydrogen elimination than the former. The decomposition of the nitrato- and nitritopalladation intermediates results in the organometallic precursor of acetone, i.e., an acetonylpalladium complex, and then in acetone itself. On the other hand, the nitropalladation intermediate originates 2-nitropropylene. In the presence of dioxygen, which re-oxidizes the nitrosyl groups, the acetone formation becomes a catalytic reaction with respect to both palladium and nitrogen.     

Peptide hydrolysis catalyzed by matrix metalloproteinase 2: a computational study

The MMP-2 reaction mechanism is investigated by using different computational methodologies. First, quantum mechanical (QM) calculations are carried out on a cluster model of the active site bound to an Ace-Gly approximately Ile-Nme peptide. Along the QM reaction path, a Zn-bound water molecule attacks the Gly carbonyl group to give a tetrahedral intermediate. The breaking of the C-N bond is completed thanks to the Glu 404 residue that shuttles a proton from the water molecule to Ile-N atom. The gas-phase QM energy barrier is quite low ( approximately 14 kcal/mol), thus suggesting that the essential catalytic machinery is included in the cluster model. A similar reaction path occurs in the MMP-2 catalytic domain bound to an octapeptide substrate according to hybrid QM and molecular mechanical (QM/MM) geometry optimizations. However, the rupture of the Gly( P 1) approximately Ile( P 1') amide bond is destabilized in the static QM/MM calculations, owing to the positioning of the Ile( P 1') side chain inside the MMP-2 S 1' pocket and to the inability of simple energy miminization methodologies to properly relax complex systems. Molecular dynamics simulations show that these steric limitations are overcome easily through structural fluctuations. The energetic effect of structural fluctuations is taken into account by combining QM energies with average MM Poisson-Boltzmann free energies, resulting in a total free energy barrier of 14.8 kcal/mol in good agreement with experimental data. The rate-determining event in the MMP-2 mechanism corresponds to a H-bond rearrangement involving the Glu 404 residue and/or the Glu 404-COOH --> N-Ile( P 1') proton transfer. Overall, the present computational results and previous experimental data complement each other well in order to provide a detailed view of the MMPs catalytic mechanism.     

Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH

In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.