Reaction mechanisms density functional theory calculations

Cheng, J., Gong, X.-Q., Hu, P Lok, C. M Ellis, P and French, S. 2008. A quantitative determination of reaction mechanisms from density functional theory calculations Fischer-Tropsch synthesis on flat and stepped cobalt surfaces. J. Catal. 254 285-95. 

Due to the historical importance of the initial stages of silicon oxidation to microelectronics fabrication, there has been a great deal of interest in the reaction of the water oxidant on the Si(100)-2 x 1 surface. A number of studies have shown that water adsorbs in a dissociated state consisting of OH(a) and H(a) species adsorbed on the Si surface dimer at room temperature [60-69]. More recent studies have closely investigated the mechanism of water oxidation. A series of density functional theory calculations (DFT) calculations by Konecny and Doren indicated that water first molecularly adsorbs through one of its lone pairs in a weakly bound precursor state, then transfers a proton to form OH(a) and H(a) species on the surface dimer [43]. The pathway to proton transfer is found to be unactivated with respect to the entrance channel, which suggests that OH(a) and H(a) are the dominant surface species at room temperature, in agreement with the previous experimental work [60-69]. 

A detailed sequence for N02 storage on BaO has been proposed after experimental observations and density-functional theory calculations by Broqvist et al. (2004). It involves the formation of nitrites, followed by the formation of nitrite-nitrate and nitrate-nitrate pairs on the surface, the latter being most stable. The Ba-nitrites-nitrates (N02-Ba0-N02) are then transformed to Ba(N03)2 via redox reaction, including consumption of N02 and release of NO. Thus, the overall reaction for the N02 storage on BaO with this disproportion mechanism can be written as... 

FIGURE 17. Postulated mechanism for Q reaction with methane based on Density Functional Theory calculations. (Siegbahn and Crabtree, 1997). 

An AuCl,-catalyzed intramolecular reaction between 2-methylfuran and a terminal alkyne to produce a phenol was the key step in the synthesis of jungianol and cpr-jungianol <03CEJ4339>. This reaction could also be catalyzed by PtClj. Based on density functional theory calculations and on the trapping of certain interme ates die mechanism was proposed to involve the cyclopropyl platinacarbene complex shown below as a key intermediate <03JA5757>. 

Perakyla M. A model study of the enzyme-catalyzed cytosine methylation using ab initio quantum mechanical and density functional theory calculations pKa of the cytosine N3 in the intermediates and transition states of the reaction. J. Amer. Chem. Soc. 1998 120 12895-12902. 

Dialkoxotitanacyclopropane derivatives Ti(CH2CR)(OPr1)2 react with esters to afford cycopropanols via a Kulinkovich hydroxycyclopropanation reaction, an efficient, fast, exothermic, and irreversible organic synthetic method. A detailed mechanism for this process has been explored with density functional theory calculations.286... 

The role of CI2 and monochloroacetic acid in the selective chlorination is a difficult problem to understand from the experimental studies. There are several possible orientations for the reactant, product and promoter molecules inside the complex structure of zeolite-L. In this context, it is pertinent to note that molecular modelling techniques are contributing in considerable amount to understand the reaction mechanisms. Molecular modelling includes force field based calculations [3] such as energy minimisation, Monte Carlo, and molecular dynamics calculations and quantum chemical calculations [4 ] such as EHMO, CNDO/INDO, MOPAC, Hartree-Fock and density functional theory calculations. In this study, we have attempted to apply the combination of molecular graphics, force field calculations and quantum chemical calculations to understand the mechanism of selective chlorination of DCB to TCB over zeolite K-L promoted by monochloroacetic acid. 

In the mechanism put forth by Siegbahn/" " depicted in Figure 26, successive S-state advancements via PCET path B leads to the formation of a /i-oxyl radical. The mechanism is based largely upon density functional theory calculations. The role of Ca is to polarize the Mn—O bonds and direct the placement of the radical. The O—O bond-forming step is as yet unclear in the density functional theory (DFT) calculations, but it appears to involve reaction of the oxyl radical with outer-sphere H2O to form a hydroperoxide species that is oxidized to O2. 

Our approach starts with and extends a mechanism initially proposed by Carpenter [175] who reported a computational study showing several very important new reaction pathways for the reaction of vinyl and phenyl radicals with molecular oxygen using semi-empirical calculations. Mebel et al. [33] extended the work of Carpenter on vinyl with Density Functional Theory calculations, B3LYP/6-311g(d,p), for structures and energies as well as G2M calculations to verify the energetics. 

Abstract The oxidative functionalization of olefins is an important reaction for organic synthesis as well as for the industrial production of bulk chemicals. Various processes have been explored, among them also metal-catalyzed methods using strong oxidants like osmium tetroxide. Especially, the asymmetric dihydroxylation of olefins by osmium(Vlll) complexes has proven to be a valuable reaction for the synthetic chemist. A large number of experimental studies had been conducted, but the mechanisms of the various osmium-catalyzed reactions remained a controversial issue. This changed when density functional theory calculations became available and computational studies helped to unravel the open mechanistic questions. This mini review will focus on recent mechanistic studies on osmium-mediated oxidation reactions of alkenes. 

Tripkovic V, Skulason E, Siahrostami S, Norskov JK, Rossmeisl J. The oxygen reduction reaction mechanism on Pt(lll) from density functional theory calculations. Electrochim Acta 2010 55 7975-81. 

Equation (24.1) was used to estimate isomer shifts of ferrate(VII) and ferrate(VIII) as — 1. 18 and — 1.40 mm s , relative to a-Fe, respectively [102]. More recently, density function theory calculations were performed on ferrates ranging from +4 to +8 oxidation states of iron [102]. Figure 24.9 depicts relationship of isomer shift with Fe O bond length and electron density on the iron nucleus An increase in Fe—O bond distance with decrease in oxidation states of iron from ferrate(VIII) to ferrate(IV) was determined. A positive linearity between isomer shift and bond distance of ferrate was found (Fig. 24.9). Conversely, values of isomer shifts showed a negative relationship with po (Fig- 24.9). An increase in the Po with increase of the oxidation state of iron was expected. The relationship of Eq. (24.1) was used to understand the mechanism of decomposition and formation reactions of solid ferrates under different conditions, which are described below. 

Besides a g-factor and aminoxyl nitrogen coupling constant dependent on the species trapped, the ESR spectra also showed different patterns due to hyperfine splitting characteristic of the radical scavenged. This last important feature was investigated by means of density functional theory calculations. The overall summary of the ESR characteristics of various ARs produced in nitrones has been completed [19, 72]. In these studies, the various aspects and features of application of the spin trap method in invetigations of the mechanism of chemical reactions are considered. 

Interestingly, the stereoselectivity of reactions of cyclohexanone vith iso-butyraldehyde and benzaldehyde vere first predicted by using density functional theory calculations on models based on Houk s calculated transition state of the Hajos-Parrish-Eder-Sauer-Wiechert reaction [125]. The transition states of inter- and intramolecular aldol reactions are almost super-imposable and readily explain the observed enantiofacial selectivity. Relative transition state energies vere then used to predict the diastereo- and enan-tioselectivity of the proline-catalyzed reactions of cyclohexanone vith iso-butyraldehyde and benzaldehyde. The predictions are compared vith the experimental results in Scheme 4.30. The good agreement clearly validates the theoretical studies, and provides support for the proposed mechanism. Additional density functional theory calculation also support a similar mechanism [126, 127]. 

Because of the complexity of the pathway, the sensitivity of the reagents involved, the heterogeneous nature of the reaction, and the limitations of modern experimental techniques and instrumentation, it is not surprising that a compelling picture of the mechanism of the Simmons-Smith reaction has yet to emerge. In recent years, the application of computational techniques to the study of the mechanism has become important. Enabling theoretical advances, namely the implementation of density functional theory, have finally made this complex system amenable to calculation. These studies not only provide support for earlier conclusions regarding the reaction mechanism, but they have also opened new mechanistic possibilities to view. 

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