Alkylation of δ-ketoesters : a mechanism change depending on conformational mobility and substituent effects on stereoselection.

Kinetic evidence shows that the two groups of a δ-ketoester can interact in the transition state of a Grignard reaction. This promotes high stereoselectivity by chiral center far from the ketonic group and produces good correlations between stereoselection and electronic effects of substituents.     

Mechanistic investigation and DFT calculation of the new reaction between S-methylisothiosemicarbazide and methyl acetoacetate

A study on the synthesis and mechanistical aspects of formation of 3-methyl-5-oxo-3-pyrazolin-1-carboxamide (MOPC) starting from S-methylisothiosemicarbazide hydrogen iodide and methyl acetoacetate was performed. In the alkaline aqueous solution, the intermediate methyl acetoacetate S-methylisothiosemicarbazone undergoes substitution of CH₃S^? anion by hydroxide anion, cyclization, carbanion formation, and elimination of methanol, thus yielding corresponding Na-enolate salt of pyrazol-5-one derivative. The structure of the compound obtained after protonation of the formed enolate salt was determined by means of spectroscopic techniques and single-crystal X-ray diffraction analysis. The mechanism of conversion of methyl acetoacetate S-methylisothiosemicarbazone into MOPC was investigated by means of the B3LYP functional, and it was found that the reaction is thermodynamically controlled.     

DFT study on mechanism of the classical Biginelli reaction

The condensation of benzaldehyde, urea, and ethyl acetoacetate according to the procedure described by Biginelli was investigated at the B3LYP/6-31G（d）, B3LYP/6-31 ＋G（d,p）, and B3LYP/6-311＋G（3df,2p）//B3LYP/6-31＋G（d,p） levels to explore the reaction mechanism. According to the mechanism proposed by Kappe, structures of five intermediates were optimized and four transition states were found. The calculation results proved that the mechanism proposed by Kappe is right.     

Relativistic DFT study on the reaction mechanism of second-row transition metal Ru with CO2

To estimate the importance of relativistic effects on the reaction mechanisms between Ru and CO2, the potential energy surfaces have been performed in the triplet and quintet electronic states using quasi-relativistic (Pauli), zero-order regularly approximated (ZORA), and nonrelativistic (NR) density functional theory (DFT) at the PW91/TZP level. The results demonstrate that there are two rival reaction mechanisms: one is an addition mechanism and the other is an insertion mechanism in the triplet state. The only mechanism in the quintet state is the insertion mechanism. The most favored reaction mechanism in Ru + CO2 is that the Ru atom in its ground state first attacks the CO bond of CO2, forming q-Ru(CO)O (5A') with the insertion mechanism, and then undergoes an intersystem crossing to t-Ru(CO)O (3A'). Then it crosses t-TS3 to produce t-ORuCO molecule. The relativistic effects are important for reactivity of the second-row transition metal to CO2. In the key step of t-Ru(CO)O via t-TS3 to t-ORuCO, relativistic effects reduce the barrier energy by 10.3 kcal/mol, which is nearly half the nonrelativistic barrier energy.     

DFT investigation on the mechanism of the deacetylation reaction catalyzed by LpxC

LpxC is a key enzyme in the biochemical synthesis of Lipid A, an important outer cell-membrane component found in a number of pathogenic bacteria. Using DFT, we have investigated the binding of the substrate within its active site as well as the deacetylation mechanism it catalyzes. The substrate is found to preferentially coordinate to the active site Zn2+ via its carbonyl oxygen between a Zn2+-bound H2O and an adjacent threonine (Thr191). Furthermore, upon substrate binding a nearby Glu78 residue is found to readily deprotonate the remaining Zn2+-bound H2O. Unlike several related metallopeptidases, the mechanism of LpxC is found to proceed via four steps; (i) initial hydroxylation of the substrates' carbonyl carbon to give a gem-diolate intermediate, (ii) protonation of the amide nitrogen by the histidine His265-H+, (iii) a barrier-less change in the active site-intermediate hydrogen-bond network and finally, (iv) C-N bond cleavage. Notably, the rate-determining step of the mechanism of LpxC is found to be the initial hydroxylation while the final C-N bond cleavage occurs with an overall barrier of 23.6 kJ mol-1. Furthermore, LpxC uses a general acid/base pair mechanism as indicated by the fact that both His265-H+ and Glu78 are accordingly involved.     

Ruthenium-mediated C–C coupling reactions of alkynes – mechanistic investigations based on DFT calculations

This article describes the highlights of the reactions of the substitutionally labile neutral pseudo 14VE complexes RuCp(COD)Cl (COD = 1,5-cyclooctadiene) and the cationic complexes [RuCp(CH₃CN)₂ L]⁺ with alkynes. The ligand L is a co-ligand, whose nature turns out to be critical to the reaction’s outcome being tertiary phosphines (PR ₃ ) and the N-heterocyclic carbene 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr). A crucial role in all reactions reported is the intermediacy of electrophilic ruthenacyclopentatriene complexes, an entity featuring a biscarbene functionality. While with RuCp(COD)Cl the catalytic cylcotrimerization of alkynes is achieved, [RuCp(CH₃CN)₂(L)]⁺ complexes are catalytically inactive for this process. These compounds undergo selective head-to-tail coupling of two alkynes. However, addition of a third alkyne is precluded due to an unusual migratory insertion of the PR ₃ and the N-heterocyclic carbene, respectively, into the Ru–C carbon double bond of a ruthenacyclopentatriene intermediate to afford stable allyl carbenes. With parent acetylene, on the other hand, an unusual C–C coupling process takes place involving three acetylene molecules and migration of the NHC ligand to give formal [2 + 2 + 1] cycloaddition products. Conceivable mechanisms for all these reactions are established by means of DFT/B3LYP calculations. Correspondence: Karl Kirchner, Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, A-1060 Vienna, Austria.     

DFT and ab initio study on the reaction mechanism of CH2SH + O2

The mechanism for the CH₂SH + O₂ reaction was investigated by DFT and ab initio chemistry methods. The geometries of all possible stationary points were optimized at the B3LYP/6-311+G(d,p) level, and the single point energy was calculated at the CCSD(T)/cc-pVXZ(X = D and T), G3MP2 and BMC-CCSD levels. The results indicate that the oxidation of CH₂SH by O₂ to form HSCH₂OO is a barrierless process. The most favorable channel is the rearrangement of the initial adduct HSCH₂OO (IM1) to form another intermediate H₂C(S)OOH (IM3) via a five-center transition state, and then the C–O bond fission in IM3 leads to a complex CH₂S. . .HO₂ (MC1), which finally gives out to the major product CH₂S + HO₂. Due to high barriers, other products including cis- and trans-HC(O)SH + HO could be negligible. The direct abstraction channel was also determined to yield CH₂S + HO₂, with the barrier height of 22.3, 18.1 and 15.0 kcal/mol at G3MP2, CCSD(T)/cc-pVTZ and BMC-CCSD levels, respectively, it is not competitive with the addition channel, in which all stationary points are lower than reactant energetically. The other channels to produce cis- and trans-CHSH + HO₂ are also of no importance.     

Regioselective addition of Ti enolates to conjugated enones: New insights into the mechanism based on experimental and DFT investigation

The regioselective addition mechanism of the Ti(IV) enolates derived from α-diazo-β-keto carbonyl compounds and α-diazo-β-keto phosphonates to conjugated enones has been studied on the basis of a hypothetical bridging chloride-controlled theory, by density functional theory (DFT), and experimentally. The DFT results indicate that, for the Ti(IV) enolate 3 derived from α-diazo-β-keto carbonyl compounds, the free energy of the bridging chloride-controlled 1,2-addition transition state is 2.4 kcal/mol higher than that of 1,4-addition, and the calculated enthalpies of 1,2-addition is 4.36 kcal/mol more than that of 1,4-addition. For the Ti(IV) enolate 4 derived from α-diazo-β-keto phosphonates, in contrary, the free energy of the bridging chloride-controlled 1,2-addition transition state is 1.1 kcal/mol lower than that of 1,4-addition, and the calculated enthalpy of 1,2-addition is 3.46 kcal/mol less than that of 1,4-addition. Our findings demonstrate that the nucleophilic addition of these Ti(IV) enolates to conjugated enones was carried out not only kinetically but also irreversibly for the first time.     

Cobalt-mediated cyclic and linear 2:1 cooligomerization of alkynes with alkenes: a DFT study

The mechanism of the cobalt-mediated [2 + 2 + 2] cycloaddition of two alkynes to one alkene to give CpCo-complexed 1,3-cyclohexadienes (cyclic oligomerization) has been studied by means of DFT computations. In contrast to the mechanism of alkyne cyclotrimerization, in which final alkyne inclusion into the common cobaltacyclopentadiene features a direct "collapse" pathway to the complexed arene, alkene incorporation proceeds via insertion into a Co-C sigma-bond rather than inter- or intramolecular [4 + 2] cycloaddition. The resulting seven-membered metallacycle 7 is a key intermediate which leads to either CpCo-complexed cyclohexadiene 5 or hexatriene 13. The latter transformation, particularly favorable for ethene, accounts, in part, for the linear oligomerization observed occasionally in these reactions. With aromatic double bonds, a C-H activation mechanism by the cobaltacyclopentadiene seems more advantageous in hexatriene product formation. Detailed investigations of high- and low-spin potential energy surfaces are presented. The reactivity of triplet cobalt species was found kinetically disfavored over that of their singlet counterparts. Moreover, it could not account for the formation of CpCo-complexed hexatrienes. However, triplet cobalt complexes cannot be ruled out since all unsaturated species appearing in this study were found to exhibit triplet ground states. Consequently, a reaction pathway that involves a mixing of both spin-state energy surfaces is also described (two-state reactivity). Support for such a pathway comes from the location of several low-lying minimum-energy crossing points (MECPs) of the two surfaces.     

DFT and experimental study on denitration mechanism over VPO/TiO2 catalyst

Research on Chemical Intermediates - A titanium dioxide supported VPO(VPO/TiO2) catalyst for NH3-SCR de-NOx was prepared. The NH3-SCR catalytic activity of VPO/TiO2 was tested and a corresponding...     

Dienophile twisting and substituent effects influence reaction rates of intramolecular Diels-Alder cycloadditions: a DFT study

Intramolecular cycloadditions of 5-vinyl-1,3-cyclohexadienes were studied with B3LYP/6-31G(d) density functional calculations. The one-atom tether dictates that the Z substituent becomes exo and the E substituent becomes endo in the TS. The geometry of the cycloaddition TS is typical of a pericyclic transformation except unusual twisting of the dienophile places the endo substituent in a relatively steric-free position and the exo substituent in a highly crowded position. The experimental rate differences between isomeric pairs of vinylcyclohexadienes can be explained by comparing reactant destabilization when a bulky group occupies the Z position of the starting alkene and transition state stabilization when a bulky group is endo in the cycloaddition TS.     

DFT study into the reaction mechanism of CO methanation over pure MoS2

Mo‐based catalysts are commonly used in the direct methanation of CO; however, no integrated mechanism has been proposed due to limits in characterizing the nano‐sized active structures of MoS₂. Thus, we report our investigation into the mechanism of CO methanation over pure MoS₂ through density functional theory simulations, considering that only MoS₂ edge sites exhibit catalytic activity. Simulations revealed the presence of (010) and (110) surfaces on the MoS₂ edges. Both surfaces are reconstructed by the redistribution of surface sulfur atoms upon exposure to H₂/H₂S, and after sulfur coverage redistribution, S vacancies are generated for CO hydrogenation. The reaction mechanisms on both surfaces are discussed, with the S‐edge being better suited to CO methanation than Mo‐edge on the (010) surface. The rate‐controlling step differs between surfaces, and corresponds to the initial activation reaction, which was achieved more easily on the (110) surface.     

DFT investigation of the mechanism of CH2CO + O(3P) reaction

A detailed theoretical survey of the potential energy surface (PES) for the CH₂CO + O(³P) reaction is carried out at the QCISD(T)/6‐311+G(3df,2p)//B3LYP/6‐311+G(d,p) level. The geometries, vibrational frequencies, and energies of all stationary points involved in the reaction are calculated at the B3LYP/6‐311+G(d,p) level. More accurate energy information is provided by single‐point calculations at the QCISD(T)/6‐311+G(3df,2p) level. Relationships of the reactants, transition states, intermediates, and products are confirmed by the intrinsic reaction coordinate (IRC) calculations. The results suggest that P1(CH₂+CO₂) is the most important product. This study presents highlights of the mechanism of the title reaction. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DFT study on reaction mechanism of di-tert-butylphenol to di-tert-butylhydroxybenzoic acid

Structural Chemistry - Experimental studies on the Kolbe–Schmitt reaction and its side reactions have made great progresses; however, the relative theoretical studies fall behind. In order to...     

A DFT study of the mechanism of palladium-catalyzed alkoxycarbonylation and aminocarbonylation of alkynes: Hydride versus amine pathways

A DFT study on the palladium-bisphosphine catalyzed alkoxycarbonylation and aminocarbonylation of alkyne (propyne) is reported. The theoretical study explores the feasibility and the regioselectivity control of two independent mechanisms: the first is based on the active intermediate [Pd(II)(P₂)(H)]⁺ (where P₂ = PH₂CH₂CH₂CH₂CH₂PH₂) for the alkoxycarbonylation reaction, and the second is based on the active species [Pd(II)(P₂)(NR₂)]⁺ for the aminocarbonylation reaction. The study explains the role of solvent in increasing the yield and in controlling the selectivity of reaction to produce selectively the trans isomer in the alkoxycarbonylation reaction (hydride cycle) and the gem isomer in the aminocarbonylation reaction (amine cycle). In hydride cycle, the regioselectivity is mainly determined by the stability of the complex [Pd(II)(P₂)(COC₃H₅)(CH₃CN)]⁺; however, for the amine cycle, the regioselectivity is determined by the stability of the complex [Pd(II)(P₂)(C₃H₅CON(CH₃)₂)]⁺. The calculations reveal that ligand simplification is not valid in addressing the regioselectivity behavior of alkoxycarbonylation and aminocarbonylation reactions. The kinetic data for the formation of the two key complexes show no difference between the gem and trans isomers which predict the regioselectivity to be a thermodynamically controlled process.     

Multiple electronic state mechanism for carboryne reaction with benzene: A DFT study

The multiple electronic state mechanisms of the reaction of carboryne with benzene were investigated by M11 calculations. Mechanisms leading to [4 + 2] cycloaddition product P_{4 + 2} , [2 + 2] cycloaddition product P _{2 + 2} , C? C insert product P _C‐Cins and C? H insert product P _C‐Hins were considered. The barrier/stability to structural characteristics correlations revealed that, 1) [2 + 2] addition is a two‐step mechanism which exhibits three electronic state reactivity, and both the addition steps are controlled by the barriers on open‐shell singlet (OSS) potential energy surface (PES); 2) [4 + 2] product P _{4 + 2} is a kinetic product on the experimental condition, and other products should be obtained under more harsher condition. The theoretical results well explain the experimental facts.     

Insights into the reaction mechanism between propadienylidene and ethylene: a DFT study

The reaction mechanism between propadienylidene and ethylene has been systematically investigated employing the B3LYP/6-311++G** and MP2/cc-pVTZ levels of theory to better understand the reactivity of propadienylidene with unsaturated hydrocarbons. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Two important initial reaction complexes characterized by three- and four-membered ring structures have been located firstly. After that, three different products possessing three-, four-, and five-membered ring characters have been obtained through three reaction pathways. In the first reaction pathway, a three-membered ring alkyne compound has been obtained. As for the second reaction pathway, it is a diffusion-controlled reaction, resulting in the formation of the four-membered ring conjugated diene compound. A five-membered conjugated diene compound has been obtained in the third reaction pathway, which is the most stable product in the available products thermodynamically. On the other hand, the second reaction pathway is the most favorable reaction to proceed kinetically.     

Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study

Human homogentisate dioxygenase is an Fe(II)-dependent enzyme responsible for aromatic ring cleavage. The mechanism of its catalytic reaction has been investigated with the hybrid density functional method B3LYP. A relatively big model of the active site was first used to determine the substrate binding mode. It was found that binding of the substrate dianion with a vacant position trans to Glu341 is most favorable. The model was then truncated to include only the most relevant parts of the active-site residues involved in iron coordination and substrate binding. Thus, methylimidazole was used to model His292, His335, His365, and His371, while propionate modeled Glu341. The computational results suggest that the catalytic reaction of homogentisate dioxygenases involves three major chemical steps: formation of the peroxo intermediate, homolytic cleavage of the O-O bond leading to an arene oxide radical, and finally, cleavage of the six-membered ring. Calculated barriers for alternative reaction paths are markedly higher than for the proposed mechanism, and thus the computational results successfully explain the product specificity of the enzyme. Interestingly, the results indicate that the type of ring scission, intra or extra with respect to the substituents coordinating to iron, is controlled by the barrier heights for the decay of the arene oxide radical intermediate.