Quantum chemical studies on substitution effects within silyl group in the silylative coupling of olefins

In this study quantum chemical calculations based on the density functional theory (DFT) have been carried out to examine the effects of methoxy substituent attached to a silicon atom on the reaction of silylative coupling of olefins. It has been shown, that substituted substrate undergoes the reaction according to the recently proposed insertion-rotation-elimination mechanism. During the rotation around C-C single bond additional stabilization by oxygen-ruthenium interaction was observed. Similarly to the (trimethylsilyl)ethene the rate determining step of the reaction is the insertion of the alkene into Ru-Si single bond. The substitution of SiMe₃ by Si(OMe)₃ decreases the energy span of the reaction by almost 3 kcal mol^-1 that is from 21 kcal mol^-1 to 18 kcal mol^-1. The decrease of the energy barrier of the reaction seems to be the result of the increase of point charge differences between the Ru and Si atoms which increases electrostatic attraction between these atoms. Moreover, for Si(OMe)₃ the rate-determining transition state is closer to the alkene interacting with the Ru centre side of the reaction.     

The Amide Route in Imine Metathesis with Imidomolybdenum Catalysts: A Model DFT Study

Gradient-corrected density-functional computations (BP86/ECP1 level) confirm the viability of the recently proposed reaction pathway for imine metathesis with imidomolybdenum(VI) species [Mo(NR)₂L_x] (e.g., L_x = Cl₂, DME; R = tBu). In addition to a Chauvin-type [2+2] addition-elimination mechanism, model calculations for the [MoCl₂(NH)₂] + NH₃ + CH₂NH system corroborate the suspected involvement of amido intermediates such as [MoCl₂(NH)(NH₂)₂] and . Several catalytic cycles are characterised that differ in the stereochemistry of the ligands about Mo. The lowest computed rate-determining barriers are only a few kcal mol^-1 higher than that obtained for the Chauvin-type mechanism in the [MoCl₂(NH)₂] + CH₂NH system via , provided the necessary H-atom transfers are catalysed efficiently by traces of base.Electronic Supplementary Material available.     

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.     

Theoretical study of the catalytic reaction mechanism of MndD

Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho-dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a catalytic mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O–O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last reaction steps. Alternative reaction paths were considered, and their calculated barriers were found to be higher than for the suggested mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Mechanistic investigation of platinum-catalysed hydroformylation of propene: A density functional study

The mechanism of hydroformylation of propene in the presence of both cis-PtH(SnCl₃)(PH₃)₂ and trans-PtH(SnCl₃)(PH₃)₂ catalysts has been investigated. A density functional study has been carried out for all of the elementary steps of the catalytic cycle, i.e. for the alkene coordination, for its insertion into the Pt-H bond, carbon monoxide activation and its subsequent insertion into the Pt-alkyl bond. Finally, the product forming step, the dihydrogen activation and aldehyde elimination have been investigated.It has been found that the regioselectivity of hydroformylation is determined in the olefin insertion step. The computed ratio of the linear regioisomer, n-butanal is predicted to be 83% when solvation corrections were employed, being in very good agreement with the experimental result. Among the elementary steps the hydrogenolysis has been found to be the slowest followed by the migratory carbon monoxide insertion step. Due to the crucial role of the trichlorostannato ligand the electronic effects of SnCl₃ has been analysed employing the charge decomposition analysis (CDA), the natural bond orbital (NBO) and the atoms in molecules (AIM) methods.     

Tungsten-dependent formaldehyde ferredoxin oxidoreductase: reaction mechanism from quantum chemical calculations

Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus is a tungsten-dependent enzyme that catalyzes the oxidation of formaldehyde to formic acid. In the present study, quantum chemical calculations are used to elucidate the reaction mechanism of this enzyme. Several possible mechanistic scenarios are investigated with a large model of the active site designed on the basis of the X-ray crystal structure of the native enzyme. Based on the calculations, we propose a new mechanism in which the formaldehyde substrate binds directly to the tungsten ion. W^VI=O then performs a nucleophilic attack on the formaldehyde carbon to form a tetrahedral intermediate. In the second step, which is calculated to be rate limiting, a proton is transferred to the second-shell Glu308 residue, coupled with a two-electron reduction of the tungsten ion. The calculated barriers for the mechanism are energetically very feasible and in relatively good agreement with experimental rate constants. Three other second-shell mechanisms, including one previously proposed based on experimental findings, are considered but ruled out because of their high barriers.     

Reaction mechanism of the binuclear zinc enzyme glyoxalase II - A theoretical study

The glyoxalase system catalyzes the conversion of toxic methylglyoxal to nontoxic d-lactic acid using glutathione (GSH) as a coenzyme. Glyoxalase II (GlxII) is a binuclear Zn enzyme that catalyzes the second step of this conversion, namely the hydrolysis of S-d-lactoylglutathione, which is the product of the Glyoxalase I (GlxI) reaction. In this paper we use density functional theory method to investigate the reaction mechanism of GlxII. A model of the active site is constructed on the basis of the X-ray crystal structure of the native enzyme. Stationary points along the reaction pathway are optimized and the potential energy surface for the reaction is calculated. The calculations give strong support to the previously proposed mechanism. It is found that the bridging hydroxide is capable of performing nucleophilic attack at the substrate carbonyl to form a tetrahedral intermediate. This step is followed by a proton transfer from the bridging oxygen to Asp58 and finally C-S bond cleavage. The roles of the two zinc ions in the reaction mechanism are analyzed. Zn2 is found to stabilize the charge of tetrahedral intermediate thereby lowering the barrier for the nucleophilic attack, while Zn1 stabilizes the charge of the thiolate product, thereby facilitating the C-S bond cleavage. Finally, the energies involved in the product release and active-site regeneration are estimated and a new possible mechanism is suggested.     

Density functional theory study on the mechanism and thermochemistry of olefins addition to nickel dithiolenes

We investigated the reaction mechanism and thermochemical property of conjugated dienes or mono-olefins with nickel dithiolenes (Ni(S₂C₂R₂)₂) using density functional theory. The reactions between conjugated dienes and nickel dithiolenes are concerted reactions. The thermochemical property study shows that the introduction of electron-withdrawing groups (–CF₃ or –CN) to nickel dithiolene (Ni(S₂C₂H₂)₂) not only significantly lowers the activation energy barrier but also strongly stabilises the products. The introduction of electron-donating group (–CH₃) to butadiene has the same effect. So, we conclude that the reactions between nickel dithiolenes and conjugated dienes are electrophilic cycloaddition. Mono-olefins can add to nickel dithiolenes through interligand pathway, which is a two-step process or through intraligand pathway, which is a one-step process. The thermochemical property study shows that the activation enthalpy for the reaction of butadiene with Ni(S₂C₂(CF₃)₂)₂ is much lower than those of C4 mono-olefins with Ni(S₂C₂(CF₃)₂)₂ for both interligand addition and intraligand addition. The Gibbs free energy for the reaction of butadiene with Ni(S₂C₂(CF₃)₂)₂ is also more favourable than those of C4 mono-olefins with Ni(S₂C₂(CF₃)₂)₂. It is the very preferential pathway for Ni(S₂C₂(CF₃)₂)₂ to bind butadiene than C4 mono-olefins.     

Formation and isomerization of dicyclopenta[de,mn]anthracene. Electronic Structure Study

The formation of dicyclopenta[de,mn]anthracene (P1) and its isomerization into dicyclopenta[jk,mn]phenanthrene (P3) was investigated using density functional theory. It was shown that P1 is formed from 1,4-diethynilanthracene, but due to its instability, it undergoes further transformation. This transformation involves rearrangements of some hydrogen atoms and ring contraction/ring expansion process, yielding as a final product the isomer P3. The energies of activation for the P1→P3 intraconversion show that this reaction is competitive to the other, previously investigated isomerization of P1 into dicyclopenta[de,kl]anthracene (P2). In addition, our investigation shows that the formation of P3 from P1 is energetically more favorable than the formation of P3 from P2. Thus, the presence of the isomer P3 in the reaction mixtures could also be caused by the isomerization of the very unstable isomer P1. Figure Isomerization of 1,4-diethynilanthracene to dicyclopenta[jk,mn]phenanthrene via dicyclopenta[de,mn]anthracene Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

DFT study of the intrinsic conformations of [2Fe-2S-4(SCH3)] clusters and their influence on exchange coupling

We have determined the equilibrium conformations of the diiron(III) cluster [2Fe-2S-4(SCH₃)]²⁻ using density functional theory. The conformers have dihedral Fe-Fe-S-C angles of ∼0° and ±120°. The relative energies of the conformers can be accurately parameterized with a small number of side-chain repulsion parameters. Of the 17 conformers identified on the basis of the ideal values for the dihedrals, 10 conformers are stable in both the ferromagnetic and broken symmetry state for the cluster. The exchange coupling constants for the seven energetically lowest conformers are predicted to belong to a narrow range, 150 cm⁻¹ ? J ? 178 cm⁻¹. The cluster conformers found in proteins do not coincide with any of the intrinsic ones, due to distortion of one of the dihedral angles under the influence of the protein scaffold.     

H-bonded complexes between acetylacetone and two molecules of methanol: HF and DFT level study

Five stable H-bonded complexes (supersystems) between acetylacetone and two methanol molecules were investigated at the B3LYP and HF levels of theory using the 6-311G** and 6-11++G** basis sets. The most stable complex was found as the one with the highest relative bonding and interaction energies. All vibrational frequencies resulting from calculations with the 6-311++G** basis set were compared with the recorded IR spectrum of acetylacetone/methanol mixture in a molar ratio 1:2.     

Growth of the metal framework in linear ruthenium and osmium carbonyls

Formation of the linear chain ruthenium and osmium carbonyls by successive linkage of mononuclear [M(CO)₄Cl₂] units and by opening trinuclear clusters [M₃(CO)₁₂] and [FeM₂(CO)₁₂] (M = Ru, Os) with chlorine gas have been studied by computational DFT methods. Energetically the formation of dinuclear [M₂(CO)₈Cl₂] from [M(CO)₄Cl₂] units is the most demanding step. The following chain growth by adding new mononuclear units proceeds more easily with nearly constant energy per step. Cluster opening by chlorine gas to obtain trinuclear [M₃(CO)₁₂Cl₂] is a facile reaction for both ruthenium and osmium clusters as well as for mixed metal clusters. Mixed metal clusters [FeOs₂(CO)₁₂] and [FeRu₂(CO)₁₂] open preferably between iron-osmium or iron-ruthenium bonds producing linear trinuclear Fe-M-M-type of compound. In the case of mixed metal Os-Ru clusters, the cleavage of Os-Ru bond is not clearly preferred. Fragmentation of the cluster to shorter units cis(Cl)-[M(CO)₄Cl₂] or [M₂(CO)₈Cl₂] with equatorial chlorides is highly favorable and competes with the cluster opening. No preferences on the bond type (Os-Ru, Os-Os, or Ru-Ru) that are broken can be found in the case of mixed metal Os-Ru clusters.     

Ternary uranyl hydroxo acetate complexes: A computational study of structure, energetics, and stability constants

We studied computationally uranyl monohydroxo monoacetate complexes in aqueous solution using a scalar relativistic all-electron density functional method. Such ternary uranyl complexes may serve as models of ternary uranyl humate complexes which are important for the speciation of uranyl in the environment. As for simple uranyl monocarboxylate complexes, we calculated bidentate coordination to be slightly preferred due to entropy and solvation effects. Compared to uranyl acetate, uranyl hydroxo acetate exhibits an elongated uranyl bond and a short U-OH bond of ∼214 pm. The latter may provide a signature for direct identification of such ternary complexes by EXAFS. As expected from the lower charge of uranyl monohydroxide, complexation by acetate is less exoenergetic than acetate complexation of uranyl. In contrast, experimental complexation constants of uranyl humate and uranyl hydroxo humate are quite similar. Thus, one may question the interpretation of experimental results that assign simple ternary complexes as result of uranyl humate complexation at neutral pH.     

Mechanism of the cobalt-catalyzed carbonylation of ethyl diazoacetate

Carbonyl cobalt complexes serve as catalysts or catalyst precursors for the facile and selective transformation of primary diazoalkanes into the corresponding ketene. The mechanism of this carbonylation reaction has been elucidated in the case of ethyl diazoacetate as model diazoalkane using octacarbonyl dicobalt as the catalyst precursor. Dinuclear cobalt complexes having ethoxycarbonylcarbene ligand(s) in bridging position(s) have been identified as active intermediary of the catalytic cycles and their relevant chemical properties have been explored. Key step of the carbonylation is the formation of the highly reactive ethoxycarbonylketene by intramolecular coupling of a carbonyl ligand with the ethoxycarbonylcarbene ligand. DFT calculations reveal that the ketene formation takes place via a rapid coupling of the carbene ligand with one terminal CO followed by coordination of an external carbon monoxide and by a facile intramolecular rearrangement and ketene elimination. The ethoxycarbonylketene can be in situ trapped by OH, NH, or CH acid compounds or by N-substituted imines. In the presence of ethanol diethyl malonate is the only product of the catalytic carbonylation of ethyl diazoacetate. On the bases of the kinetics of the composing steps of the catalytic cycles, localization of the rate-determining step(s) under various reaction conditions has been made.     

On the role of the axial ligand in heme proteins: a theoretical study

We present a systematic investigation of how the axial ligand in heme proteins influences the geometry, electronic structure, and spin states of the active site, and the energies of the reaction cycles. Using the density functional B3LYP method and medium-sized basis sets, we have compared models with His, His+Asp, Cys, Tyr, and Tyr+Arg as found in myoglobin and hemoglobin, peroxidases, cytochrome P450, and heme catalases, respectively. We have studied 12 reactants and intermediates of the reaction cycles of these enzymes, including complexes with H(2)O, OH(-), O(2-), CH(3)OH, O(2), H(2)O(2), and HO(2)(-) in various formal oxidation states of the iron ion (II to V). The results show that His gives ~0.6 V higher reduction potentials than the other ligands. In particular, it is harder to reduce and protonate the O(2) complex with His than with the other ligands, in accordance with the O(2) carrier function of globins and the oxidative chemistry of the other proteins. For most properties, the trend Cys相似文献   

Quantum chemical study of the structure and properties of citrinin

Detailed structures and electronic properties of three tautomeric forms of the toxin citrinin were investigated using several quantum calculation methods. Energetic preference of the predominant p- and o-quinone methide tautomeric forms is dependent on the method of calculation. A previously unstudied carboxylic acid enol tautomer was calculated to be surprisingly stable in vacuo, being within 2.5 kcal mol^? 1 at the B3LYP/6-311++G(2d,2p) level of theory. Despite differences in bond nature and connectivity of tautomers, the natural bond orbital analysis revealed that tautomeric forms share similar natural charges and natural electron configurations. Calculated bond lengths corresponded with experimentally observed values and assignments for the calculated infrared vibrational frequencies are reported.     

Reactions of triphenylphosphane-substituted ethoxycarbonylcarbene-bridged dicobalt carbonyl complexes with carbon monoxide or CO: An experimental and theoretical study

In CH₂Cl₂ solution and under a carbon monoxide atmosphere the cobalt complexes [μ₂-{ethoxycarbonyl(methylene)}-μ₂-(carbonyl)-bis(triphenylphosphanedicarbonyl-cobalt) (Co-Co)] (4) and [μ₂-{ethoxycarbonyl(methylene)}-μ₂-(carbonyl)-(tricarbonyl-cobalt)-(triphenylphosphanedicarbonyl-cobalt) (Co-Co)] (3) are in equilibrium. The equilibrium constant K = [3][PPh₃]/[4][CO] at 10 °C is 1.03 ± 0.11. The bridging and terminal CO ligands in complex 3 or 4 exchange with external ¹³CO simultaneously. In accord with that variable-temperature ¹³C NMR spectra reveal fluxional behavior for both complexes. The overall rate constant of ¹³CO-exchange for 3 at 10 °C is 17 × 10⁻³ s⁻¹ and for 4 at 10 °C is 26 × 10³ s⁻¹. In the case of complex 4 the concentration of PPh₃ has practically no influence on the rate of the ¹³CO-exchange reaction and on the rate of the reaction with CO. The coupling of the μ₂-ethoxycarbonylcarbene ligand and one of the coordinated carbon monoxide is at least one order of magnitude slower than the ¹³CO-exchange reactions, and is faster in complex 4 than in complex 3. The partial pressure of carbon monoxide has practically no effect on the coupling reaction.     

A tetrameric allyl complex of sodium, and computational modeling of the Na-allyl chemical shift

Transmetallation of Li[A′] (A′ = [1,3-(SiMe₃)₂C₃H₃]⁻) with sodium tert-butoxide produces the corresponding sodium salt, which crystallizes from THF/toluene in the form of a cyclic tetramer, {Na[A′](thf)}₄. The Na atoms are in a square planar arrangement, bridged with π-bound allyl ligands; the Na-C distances range from 2.591(3)-2.896(3) Å, with an average of 2.70 Å. The geometries of several model organosodium complexes containing cyclopentadienyl and allyl ligands were optimized with density functional theory methods. The optimized structures were used with the gauge-including atomic orbital (GIAO) method to calculate their ²³Na NMR magnetic shielding values. Unlike the case with NaCp, the chemical shift of unsubstituted Na(C₃H₅) is very sensitive to the presence of coordinated THF (causing a 20 ppm upfield shift); silyl substitution has an even larger effect (30 ppm upfield shift). The observed ²³Na shift of δ −3.3 ppm for Na[A′] in THF-d₈, however, cannot be reliably distinguished from that calculated for the [Na(thf)₄]⁺ cation alone.     

New coupling mechanism of the silane coupling agents in the TATB-based PBX

Behaviours of the silane coupling agents in 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)-based polymer bonded explosives (PBXs) were investigated using dissipative particle dynamics simulations. A new and extraordinary coupling mechanism of the silane coupling agent in TATB-based PBXs was revealed, in which the binding between the binders and TATB was improved by making the TATB's affinitive structure units of binders assembling at the interface, whereas the TATB's unaffinitive structure units are bonded together by the silane coupling agent shrinking into the binders. This is quite different from the traditional view, i.e. the coupling agent usually stays at the interface.