Showing papers on "Transition state published in 2002"

A first-principles study of methanol decomposition on Pt(111).

Abstract: A periodic, self-consistent, Density Functional Theory study of methanol decomposition on Pt(111) is presented. The thermochemistry and activation energy barriers for all the elementary steps, starting with O[bond]H scission and proceeding via sequential hydrogen abstraction from the resulting methoxy intermediate, are presented here. The minimum energy path is represented by a one-dimensional potential energy surface connecting methanol with its final decomposition products, CO and hydrogen gas. It is found that the rate-limiting step for this decomposition pathway is the abstraction of hydroxyl hydrogen from methanol. CO is clearly identified as a strong thermodynamic sink in the reaction pathway while the methoxy, formaldehyde, and formyl intermediates are found to have low barriers to decomposition, leading to very short lifetimes for these intermediates. Stable intermediates and transition states are found to obey gas-phase coordination and bond order rules on the Pt(111) surface.

Mechanism of C-H bond activation/C-C bond formation reaction between diazo compound and alkane catalyzed by dirhodium tetracarboxylate

Abstract: The B3LYP density functional studies on the dirhodium tetracarboxylate-catalyzed C-H bond activation/C-C bond formation reaction of a diazo compound with an alkane revealed the energetics and the geometry of important intermediates and transition states in the catalytic cycle. The reaction is initiated by complexation between the rhodium catalyst and the diazo compound. Driven by the back-donation from the Rh 4d(xz) orbital to the C[bond]N sigma*-orbital, nitrogen extrusion takes place to afford a rhodium[bond]carbene complex. The carbene carbon of the complex is strongly electrophilic because of its vacant 2p orbital. The C[bond]H activation/C[bond]C formation proceeds in a single step through a three-centered hydride transfer-like transition state with a small activation energy. Only one of the two rhodium atoms works as a carbene binding site throughout the reaction, and the other rhodium atom assists the C[bond]H insertion reaction. The second Rh atom acts as a mobile ligand for the first one to enhance the electrophilicity of the carbene moiety and to facilitate the cleavage of the rhodium[bond]carbon bond. The calculations reproduce experimental data including the activation enthalpy of the nitrogen extrusion, the kinetic isotope effect of the C[bond]H insertion, and the reactivity order of the C[bond]H bond.

Isotope effects in the study of phosphoryl and sulfuryl transfer reactions.

Abstract: Phosphoryl and sulfuryl transfer reactions are essential biological processes. Multiple kinetic isotope effects have provided significant insights into the transition states of these reactions. The data are reviewed for the uncatalyzed reactions of phosphate and sulfate monoesters and for a number of enzymatic phosphoryl transfer reactions. Uncatalyzed phosphoryl and sulfuryl hydrolysis reactions are found to have very similar transition states. The phosphoryl transfer reaction catalyzed by protein-tyrosine phosphatases proceeds by a transition state very similar to that of the uncatalyzed reaction, but isotope effect data reveal an interesting interplay between the conserved arginine and enzyme dynamics involving general acid catalysis.

Detailed Kinetics and Thermochemistry of C2H5 + O2: Reaction Kinetics of the Chemically-Activated and Stabilized CH3CH2OO• Adduct

Abstract: The kinetics of the chemically activated reaction between the ethyl radical and molecular oxygen are analyzed using quantum Rice−Ramsperger−Kassel (QRRK) theory for k(E) with both a master equation analysis and a modified strong-collision approach to account for collisional deactivation. Thermodynamic properties of species and transition states are determined by ab initio methods at the G2 and CBS-Q//B3LYP/6-31G(d,p) levels of theory and isodesmic reaction analysis. Rate coefficients for reactions of the energized adducts are obtained from canonical transition state theory. The reaction of C2H5 with O2 forms an energized peroxy adduct with a calculated well depth of 35.3 kcal mol-1 at the CBS-Q//B3LYP/6-31G(d,p) level of theory. The calculated (VTST) high-pressure limit bimolecular addition reaction rate constant for C2H5 + O2 is 2.94 × 1013T-0.44. Predictions of the chemically activated branching ratios using both collisional deactivation models are similar. All of the product formation pathways of ethyl...

Methane transformation to carbon and hydrogen on Pd(100): Pathways and energetics from density functional theory calculations

Abstract: Density functional theory with gradient corrections has been employed to study the reaction pathways and the reaction energetics for the transformations of CH4 to C and H on a Pd(100) surface. On examination of transition state structures identified in each elementary reaction, a clear relationship between the valencies of the CHx fragments and the locations of the transition states emerges. The higher the valency of the CHx fragment, the higher the coordination number of the CHx with the surface atoms. The calculated reaction energetics are in good agreement with the experiments. In addition, calculation results are also used to illustrate an interesting issue concerning the CH3 stability on Pd surfaces.

Reactivity Descriptors and Rate Constants for Electrophilic Aromatic Substitution: Acid Zeolite Catalyzed Methylation of Benzene and Toluene

Abstract: The acid zeolite catalyzed methylation of benzene and toluene with methanol to form toluene and ortho-, meta-, or para-xylene is investigated at the B3LYP/6-31G* level of calculation with a T4 cluster representing the zeolite. After geometry optimization of reactants, transition states and products, reaction rate constants, entropy of activation, activation hardness, and local hardness are calculated and used to model the reactions. In general, the ortho and para products are favored over the meta and nonsubstituted products. Through calculation of rate constants and entropy of activation comparison between different reaction mechanisms has been carried out, indicating that the direct and consecutive mechanisms are competitive at higher temperature. The activation hardness correlates well with the activation energy and local hardness is a good parameter for describing intermolecular reactivity in charge controlled reactions.

Theoretical Study of the CH3NO2 Unimolecular Decomposition Potential Energy Surface

Abstract: The complex potential energy surface for the unimolecular isomerization and dissociation of nitromethane (CH3NO2), including 10 CH3NO2 isomers, 46 interconversion transition states, and 16 major dissociation products, is probed theoretically at the G2MP2//B3LYP/6-311++G(2d,2p) level of theory. The geometries and relative energies for various stationary points are determined and are in good agreement with the available experimental values. Based on the calculated G2MP2 potential energy surface, the possible nitromethane unimolecular decomposition mechanism is discussed. It is shown that the most feasible decomposition channels for CH3NO2 are those that lead to 2CH3 + 2NO2, 2CH3O + 2NO, H2CO + HNO, and HCNO + H2O, respectively. Among them, 2CH3 and 2NO2 are produced by the direct C−N bond rupture of nitromethane, while the formation of the latter three products is initiated by CH3NO2 rearranging first to methyl nitrite or to aci-nitromethane. The C−N bond dissociation energy for nitromethane is calculated t...

Formation of Three C4H3N Isomers from the Reaction of CN (X2Σ+) with Allene, H2CCCH2 (X1A1), and Methylacetylene, CH3CCH (X1A1): A Combined Crossed Beam and Ab Initio Study

Abstract: Crossed molecular beam reactions of cyano radicals, CN (X2Σ+), with two C3H4 isomersmethylacetylene, CH3CCH (X1A1), and allene, H2CCCH2 (X1A1)have been investigated at six collision energies between 13.4 and 36.7 kJ mol-1 to elucidate the chemical reaction dynamics to form three C4H3N isomers1-cyanomethylacetylene, CH3CCCN (X1A1), cyanoallene, H2CCCH(CN) (X1A‘), and 3-cyanomethylacetylene, CH2(CN)CCH (X1A‘)under single collision conditions. The forward-convolution fitting of the laboratory angular and time-of-flight distributions combined with ab initio calculations reveal that both reactions have no entrance barrier, proceed via indirect (complex-forming) reaction dynamics, and are initiated by addition of CN(X2Σ+) to the π electron density of the unsaturated hydrocarbon at the terminal carbon atom to form long-lived CH3CCH(CN) (methylacetylene reaction) and H2CCCH2(CN) (allene reaction) intermediates. Both complexes fragment via exit transition states located 8−19 kJ mol-1 above the products to form 1-c...

Femtochemistry of Norrish type-I reactions: IV. Highly excited ketones--experimental.

Abstract: Femtosecond dynamics of Norrish type-I reactions of cyclic and acyclic ketones have been investigated in real time for a series of 13 compounds using femtosecond-resolved time-of-flight mass spectrometry. A general physical description of the ultrafast processes of ketones excited into a high-lying Rydberg state is presented. It accounts not only for the results that are presented herein but also for the results of previously reported studies. For highly excited ketones, we show that the Norrish type-I reaction is nonconcerted, and that the first bond breakage occurs along the effectively repulsive S_2 surface involving the C-C bond in a manner which is similar to that of ketones in the S_1 state (E. W.-G. Diau et al. ChemPhysChem 2001, 2, 273-293). The experimental results show that the wave packet motion out of the initial Franck-Condon region and down to the S_2 state can be resolved. This femtosecond (fs) internal conversion from the highly excited Rydberg state to the S_2 state proceeds through conical intersections (Rydberg-valence) that are accessed through the C=O stretching motion. In one of these conical intersections, the internal energy is guided into an asymmetric stretching mode. This explains the previously reported pronounced nonstatistical nature of the reaction. The second bond breakage involves an excited-state acyl radical and occurs on a time scale that is up to one order of magnitude longer than the first. We discuss the details regarding the ion chemistry, which determines the appearance of the mass spectra that arise from ionization on the fs time scale. The experimental results presented here, aided by the theoretical work reported in paper III, provide a unified picture of Norrish reactions on excited states and on the ground-state potential energy surfaces.

DFT study of CH4 activation by d0 Cl2LnZ (Z = H, CH3) complexes

Abstract: DFT(B3PW91) calculations of the activation of CH4 by models (Cl2LnZ) of Cp*2LnZ (Z = H, Me) have been carried out for the entire lanthanide series. Cl2LnZ appears to be a good model for Cp*2LnZ. It reproduces well the coordination around the lanthanide. The energetics of the transformation X2LnH + CH4 → X2LnCH3 + H2 are fairly close for X = Cl and Cp and the difference in behavior can be attributed to the stronger electron donating ability of Cp. Formation of the lanthanide hydride complex is calculated to be exothermic in agreement with experimental evidence. The energy profiles of the reactions Cl2LnH + CH4 → Cl2LnCH3 + H2; Cl2LnH* + CH4 → Cl2LnH + H*CH3; Cl2LnCH*3 + CH4 → Cl2LnCH3 + H–CH*3 have been calculated. The transition states for the first and third transformations are energetically accessible, in good agreement with the known experimental data. The second reaction has a transition state of very high energy indicating an unfeasible reaction. The geometry of the transition stuctures are suggestive of a proton transfer between two anionic species (Z and CH3−; Z = H− and CH3−) in the field of the lanthanide fragment.

Reaction of phenyl radicals with propyne.

Abstract: The potential energy surface (PES) for the phenyl + propyne reaction, which might contribute to the growth of polycyclic aromatic hydrocarbons (PAHs) under a wide variety of reaction conditions, is described. The PES was characterized at the B3LYP-DFT/6-31G(d) and B3LYP-DFT/6-311+G(d,p) levels of theory. The energies of the entrance transition states, a direct hydrogen-transfer channel and two addition reactions leading to chemically activated C9H9† intermediates, were also evaluated at the QCISD(T)/ 6-311G(d,p) and CCSD(T)/6-311G(d,p) levels of theory. An extensive set of unimolecular reactions was examined for these activated C9H9† intermediates, comprising 70 equilibrium structures and over 150 transition states, and product formation channels leading to substituted acetylenes and allenes such as PhCCH, PhCCCH3, and PhCHCCH2 were identified. The lowest energy pathway leads to indene, a prototype PAH molecule containing a five-membered ring. The title reaction thus is an example of possible direct forma...

Predicting unimolecular chemical reactions: Chemical flooding

Abstract: We present a method to predict products, transition states, and reaction paths of unimolecular chemical reactions such as dissociation or rearrangement reactions of small to medium sized molecules. The method thus provides the necessary input for established procedures to compute barrier heights and reaction rates, which conventionally have to be assumed heuristically. The method is an extension of the force field based conformational flooding procedure, but here aims at an accelerated barrier crossing of chemical reactions rather than conformational motions. Accordingly, it is now coupled to density functional molecular dynamics, such that the chemical reaction under study takes place at the picoseconds time scale set by todays computer technology. Barrier crossings are accelerated by means of an additional energy term (flooding potential) that locally destabilizes the educt conformation without affecting possible transition states or product states. The method is applied to two test systems, bicyclopropylidene and methylenecyclopropane, for which the reaction paths are predicted correctly. New details of reaction pathways are found, such as a transient concerted, but asynchronous rotation of the two methylene groups for the bicyclopropylidene→methylenespiropentane reaction. Our method can be applied to simulations in the gas phase as well as in solution and can be combined with force field simulations, e.g., in hybrid density functional/force field (QM/MM) computations.

Structural Investigations into the retro-Diels-Alder Reaction. Experimental and Theoretical Studies.

Abstract: The manifestations of the retro-Diels Alder reaction in the ground-state structures of a range of cyclopentadiene and cyclohexadiene cycloadducts 9−15 have been investigated by a combination of techniques. These include low-temperature X-ray crystallography, density functional calculations (B3LYP/6-31G(d,p)) on both the ground states and transition states, and the measurement of 13C−13C coupling constants. We have found that the carbon−carbon bonds (labeled bonds a and b), which break in the rDA, are longer in the cycloadducts 9−15 than in their corresponding saturated analogues 9s−15s, which cannot undergo the rDA reaction. The degree of carbon−carbon bond lengthening appears to be related to the reactivity of the cycloadduct, thus the more reactive benzoquinone cycloadducts 5b and 13 have longer carbon−carbon bonds. Those cycloadducts 14 and 15 which are predicted to undergo asynchronous reactions show differing degrees of carbon−carbon bond lengthening, reflecting the differing degrees of bond breaking...

A First Principles Study of Carbon−Carbon Coupling over the {0001} Surfaces of Co and Ru

Abstract: The coupling of CH (methylidyne) and CH2 (methylene), to form CHCH2 (vinyl), over Co and Ru surfaces has been studied with the nonlocal gradient-corrected density functional theory slab calculations. The results show that this reaction is slightly exothermic on Co while endothermic on Ru within a (2 × 2) surface unit cell. Transition states were isolated on both surfaces, and the reaction barriers were found to be 55.9 and 116.5 kJ/mol on Co and Ru, respectively. The structures of the transition state on the two metal surfaces are similar; both involve the formation of a multicentered bond.

The Origins of Noncovalent Catalysis of Intermolecular Diels−Alder Reactions by Cyclodextrins, Self-Assembling Capsules, Antibodies, and RNAses

Abstract: The catalysis of Diels-Alder reactions by noncovalent binding by synthetic, protein, and nucleic acid hosts has been surveyed and compared. These catalysts consist of binding cavities that form complexes containing both the diene and the dienophile; the cycloaddition reaction occurs in the cavity. The binding requires no formation of covalent bonds and is driven principally by the hydrophobic (or solvophobic) effect. A molecular mechanics and dynamics study of the cyclodextrin catalysis of a Diels-Alder reaction is used to exemplify and probe this form of catalysis. Detailed kinetic data is available for catalysis by antibodies, RNA, cyclodextrins, and Rebek's tennis ball capsules. Some of these catalysts stabilize the reactants more than the transition state and consequently will only have catalytic effect under conditions of low substrate-to-catalyst ratios. None of the hosts achieve significant specific binding of transition states that is the hallmark of enzyme catalysis.

Thermochemical and Kinetic Analysis of the Acetyl Radical (CH3C•O) + O2 Reaction System

Abstract: Thermochemical properties for reactants, intermediates, products, and transition states important in the acetyl radical (CH3C•(O)) + O2 reaction system are analyzed with density functional and ab initio calculations, to evaluate reaction paths and kinetics in both oxidation and pyrolysis. Enthalpies of formation (Δ ) are determined using isodesmic reaction analysis at the CBSQ composite and density functional levels. Entropies ( ) and heat capacities ( (T)) are determined using geometric parameters and vibrational frequencies obtained at the HF/6-31G(d‘) level of theory. Internal rotor contributions are included in S and Cp(T) values. The acetyl radical adds to O2 to form a CH3C(O)OO• peroxy radical with a 35 kcal/mol well depth. The peroxy radical can undergo dissociation back to reactants, decompose to products, CH2CO + HO2 via concerted HO2 elimination (Ea = 34.58 kcal/mol), or isomerize via hydrogen shift (Ea = 26.42) to form a C•H2C(O)OOH isomer. This C•H2C(O)OOH isomer can undergo β scission to prod...

N2O and NO2 formation on Pt(111): A density functional theory study

Abstract: Catalytic formation of N2O and NO2 were studied employing density functional theory with generalized gradient approximations, in order to investigate the microscopic reaction pathways of these catalytic processes on a Pt(111) surface. Transition states and reaction barriers for the addition of chemisorbed N or chemisorbed O to NO(ads) producing N2O and NO2, respectively, were calculated. The N2O transition state involves bond formation across the hcp hollow site with an associated reaction barrier of 1.78 eV. NO2 formation favors a fcc hollow site transition state with a barrier of 1.52 eV. The mechanisms for both reactions are compared to CO oxidation on the same surface. The activation of the chemisorbed NO and the chemisorbed N or O from the energetically stable initial state to the transition state are both significant contributors to the overall reaction barrier Ea, in contrast to CO oxidation in which the activation of the O(ads) is much greater than CO(ads) activation.

Mechanistic Study of β-Substituent Effects on the Mechanism of Ketone Reduction by SmI2

Abstract: The rate constants for the reduction of 2-butanone, methylacetoacetate, N, N-dimethylacetoacetamide, and a series of 4‘- and 2‘-substituted acetophenone derivatives by SmI2 were determined in dry THF using stopped-flow absorption decay experiments. Activation parameters for the electron-transfer processes in each series of compounds were determined by a temperature-dependence study over a range of 30 to 50 °C. Two types of reaction pathways are possible for these electron-transfer processes. One proceeds through coordination (Scheme 1) while the other involves chelation (Scheme 2). The results described herein unequivocally show that both coordination and chelation provide highly ordered transition states for the electron-transfer process but the presence of a chelation pathway dramatically increases the rate of the reduction of these substrates by SmI2. The ability of various functional groups to promote a chelated reaction pathway plays a crucial role in determining the rate of the reaction. Among the 2...

Rate-Equilibrium Relationships in Hydride Transfer Reactions: The Role of Intrinsic Barriers

Abstract: A literature survey on the kinetics of hydride abstractions from CH-groups by carbocations reveals a general phenomenon: Variation of the hydride acceptor affects the rates of hydride transfer to a considerably greater extent than an equal change of the thermodynamic driving force caused by variation of the hydride donor. The origin of this relationship was investigated by quantum chemical calculations on various levels of ab initio and DFT theory for the transfer of an allylic hydrogen from 1-mono- and 1,1-disubstituted propenes (XYCCH−CH3) to the 3-position of 1-mono- and 1,1-disubstituted allyl cations (XYCCH−CH2+). The discussion is based on the results of the MP2/6-31+G(d,p)//RHF/6-31+G(d,p) calculations. Electron-releasing substituents X and Y in the hydride donors increase the exothermicity of the reaction, while electron-releasing substituents in the hydride acceptors decrease exothermicity. In line with Hammond's postulate, increasing exothermicity shifts the transition states on the reaction co...

The origin of diastereofacial control in allylboration reactions using tartrate ester derived allylboronates: attractive interactions between the Lewis acid coordinated aldehyde carbonyl group and an ester carbonyl oxygen.

Abstract: Transition-state structures for the allylboration reaction between the tartrate ester and tartramide modified allylboronates and acetaldehyde are located at the B3LYP/6-31G* level of theory. An attractive interaction between the boron-activated aldehyde and the ester or amide carbonyl oxygen lone pair is found to play a major role in the favored transition states 11a and 13. This attractive interaction appears to be electrostatic in origin. However, an n → π* charge-transfer type of interaction has not been ruled out. The distance (2.77 A) between the aldehydic hydrogen and the carbonyl oxygen in transition state 13 is beyond the sum of van der Waals radii. The formyl C−H···O bond angle (109°) in this transition structure deviates far from linearity. Therefore, hydrogen-bonding interactions between the formyl C−H and the amide carbonyl oxygen are considered negligible. The distance (3.81 A) between the aldehydic oxygen and the amide carbonyl oxygen in the diastereomeric, disfavored transition state 14 is ...

Insertion Reaction of Mn+ Bare Metal Cation into the N−H and C−H Bonds of Ammonia and Methane

Abstract: The Potential Energy Surfaces of the dehydrogenation reaction of NH3 and CH4 molecules by the first-row transition metal cations Mn+ (7S, 5S) were investigated employing the Density Functional (B3LYP) and the CCSD(T) levels of theory. A close description of the reaction paths leading to three dissociation products was given, including several minima and key transition states. The reactions proceed to give dehydrogenation products by oxidative addition of the metal cation into one of the H−X bonds (X = N,C) and formation of the H−M+−XHn-1, hydrido intermediates, which in these cases are also confirmed to represent stable minima along the quintet surface. Because the spin state of the reactants is different from that of intermediates and products an intersystem crossing is proposed to occur. The binding energies of reaction products were calculated and compared with available experimental data to calibrate the quality of our approach.

Selectivity of Surface Defects for the Activation of Supported Metal Atoms: Acetylene Cyclotrimerization on Pd1/MgO

Abstract: We report on the results of density functional cluster model calculations on thermodynamical and kinetical aspects of the acetylene cyclotrimerization reaction occurring on single Pd atoms deposited with soft-landing techniques on MgO(100) thin films. The different elementary steps of the reaction as well as the transition states involved have been investigated in detail for Pd atoms adsorbed on different sites of MgO to understand the role of the substrate in this reaction. The analysis of the complete reaction path indicates that only basic defect sites such as neutral and charged oxygen vacancies (F and F+ centers) located at the MgO terraces can activate supported Pd atoms for this process.

Activation of Methane by Neutral Transition Metal Oxides (ScO, NiO, and PdO): A Theoretical Study

Abstract: Density functional B3LYP calculations have been employed to investigate potential energy surfaces for the reactions of scandium, nickel, and palladium oxides with methane. The results show that NiO and PdO are reactive toward methane and can form molecular complexes with CH4 bound by 9−10 kcal/mol without a barrier. At elevated temperatures, the dominant reaction channel is direct abstraction of a hydrogen atom by the oxides from CH4 with a barrier of ∼16 kcal/mol leading to MOH (M = Ni, Pd) and free methyl radical. A minor reaction channel is an insertion into a C−H bond to produce CH3MOH molecules via transition states lying 19−20 kcal/mol above the initial reactants. For instance, for PdO, the rate constant of the hydrogen abstraction channel evaluated using the transition state theory for the 300−1000 K temperature range, kmethyl = 7.12 × 10-11 exp(−17 329/RT) cm3 s-1 molecule-1, is 2−3 orders of magnitude higher than the insertion rate constant and the branching ratio for the PdOH + CH3 products is 9...