Showing papers on "Transition state published in 2009"
TL;DR: It is argued that even more useful than identifying the rate-determining step is identifying the Rate-controlling transition states and the rate -controlling intermediates, the species whose energetics must be most accurately measured or calculated to achieve an accurate kinetic model for any reaction mechanism.
Abstract: For many decades, the concept of a “rate-determining step” has been of central importance in understanding chemical kinetics in multistep reaction mechanisms and using that understanding to advantage. Yet a rigorous method for identifying the rate-determining step in a reaction mechanism was only recently introduced, via the “degree of rate control” of elementary steps. By extending that idea, we argue that even more useful than identifying the rate-determining step is identifying the rate-controlling transition states and the rate-controlling intermediates. These identify a few distinct chemical species whose relative energies we could adjust to achieve a faster or slower net reaction rate. Their relative energies could be adjusted by a variety of practical approaches, such as adding or modifying a catalyst, modifying the solvent, or simply modifying a reactant’s molecular structure to affect electronic or steric control on the relative energies of the key species. Since these key species are the ones wh...
438 citations
TL;DR: In this article, first-principles calculations based on density functional theory (DFT) have been used to investigate the reaction mechanism of dry methane reforming on Ni(1.1/1) and the transition states for all the possible elementary steps are explored by the dimer method.
307 citations
TL;DR: It is concluded that the energetic difficulty of a catalytic reaction, imposed by gas-phase reactant proton affinities in transition state analogues, does not determine its sensitivity to the acid strength of solid catalysts.
Abstract: We address here the manner in which acid catalysis senses the strength of solid acids. Acid strengths for Keggin polyoxometalate (POM) clusters and zeolites, chosen because of their accurately known structures, are described rigorously by their deprotonation energies (DPE). Mechanistic interpretations of the measured dynamics of alkane isomerization and alkanol dehydration are used to obtain rate and equilibrium constants and energies for intermediates and transition states and to relate them to acid strength. n-Hexane isomerization rates were limited by isomerization of alkoxide intermediates on bifunctional metal−acid mixtures designed to maintain alkane−alkene equilibrium. Isomerization rate constants were normalized by the number of accessible protons, measured by titration with 2,6-di-tert-butylpyridine during catalysis. Equilibrium constants for alkoxides formed by protonation of n-hexene increased slightly with deprotonation energies (DPE), while isomerization rate constants decreased and activatio...
137 citations
TL;DR: In this paper, the thermal decomposition of menthyl benzoate (2-isopropyl-5-methylcyclohexyl-benzoate) was investigated at the B3LYP/6-31-G/6−31−G/G(d,p) and M05-2X/6 −31G+
133 citations
TL;DR: Significantly, experimental and computational studies question the predictability of primary EIEs in these systems based on the notion that deuterium prefers to occupy the highest frequency oscillator, and the applicability of these rules to the interactions of H-H and C-H bonds with a transition metal center is evaluated.
Abstract: Deuterium kinetic isotope effects (KIEs) serve as versatile tools to infer details about reaction mechanisms and the nature of transition states, while equilibrium isotope effects (EIEs) associated with the site preferences of hydrogen and deuterium enable researchers to study aspects of molecular structure. Researchers typically interpret primary deuterium isotope effects based on two simple guidelines: (i) the KIE for an elementary reaction is normal (kH/kD > 1) and (ii) the EIE is dictated by deuterium preferring to be located in the site corresponding to the highest frequency oscillator. In this Account, we evaluate the applicability of these rules to the interactions of H−H and C−H bonds with a transition metal center. Significantly, experimental and computational studies question the predictability of primary EIEs in these systems based on the notion that deuterium prefers to occupy the highest frequency oscillator. In particular, the EIEs for (i) formation of σ-complexes by coordination of H−H and ...
111 citations
TL;DR: Combining the dimer saddle point searching method and periodic density functional theory calculations, the potential energy surface of methanol decomposition on Cu(110) has been mapped out.
Abstract: Combining the dimer saddle point searching method and periodic density functional theory calculations, the potential energy surface of methanol decomposition on Cu(110) has been mapped out. Each elementary step in the methanol decomposition reaction into CO and hydrogen occurs via one of three possible mechanisms: O−H, C−H, or C−O bond scission. Multiple reaction pathways for each bond scission have been identified in the present work. Reaction pathway calculations are started from an initial (reactant) state with methanol adsorbed in the most stable geometry on Cu(110). The saddle point and corresponding final state of each reaction or diffusion mechanism were determined without assuming the reaction mechanism. In this way, the reaction paths are determined without chemical intuition. The harmonic pre-exponential factor of each identified reaction is calculated from a normal-mode analysis of the stationary points. Then, using harmonic transition state theory, the rate constant of each identified reaction...
101 citations
TL;DR: Evidence supports the idea that a reaction should be viewed as going through a transition region rather than through a single point transition state, and describes this region as a chemically-active, or electronically-intensive stage of the reaction, while the ones that precede and follow it are structurally-intensive.
Abstract: The reaction force F(R) and the position-dependent reaction force constant κF(R) are defined by F(R)=-∂V(R)/∂R and κ(R)=∂2V(R)/∂R2, where V(R) is the potential energy of a reacting system along a coordinate R. The minima and maxima of F(R) provide a natural division of the process into several regions. Those in which F(R) is increasing are where the most dramatic changes in electronic properties take place, and where the system goes from activated reactants (at the force minimum) to activated products (at the force maximum). κ(R) is negative throughout such a region. We summarize evidence supporting the idea that a reaction should be viewed as going through a transition region rather than through a single point transition state. A similar conclusion has come out of transition state spectroscopy. We describe this region as a chemically-active, or electronically-intensive, stage of the reaction, while the ones that precede and follow it are structurally-intensive. Finally, we briefly address the time dependence of the reaction force and the reaction force constant.
99 citations
TL;DR: The products from the hetero-Diels-Alder reaction of acrolein with methyl vinyl ketone arise from a single transition state and trajectory studies accurately predict the selectivity.
Abstract: The products from the hetero-Diels-Alder reaction of acrolein with methyl vinyl ketone arise from a single transition state and trajectory studies accurately predict the selectivity. In an extension of the dynamic matching idea of Carpenter, the product formed is determined by the direction of motion passing through the transition state. Recrossing of the cycloaddition transition state occurs extensively and decreases formation of the minor product.
96 citations
TL;DR: In this paper, the role of step sites in the water gas shift reaction catalyzed by Cu surfaces has been studied by using the Cu(3.2.1)-stepped surface as a representative model and periodic density functional theory within a supercell approach.
96 citations
TL;DR: These features, together with the response of the system to a sequential reaction procedure, suggest that a similar type of network is at the heart of the Soai reaction.
Abstract: In a closed system an irreversible enantioselective autocatalysis coupled to a mutual inhibition reaction, corresponding to a fast and low exergonic formation of the heterochiral dimer which reverts to the monomers in the final reaction work-up, yields absolute asymmetric synthesis even in the absence of chiral polarizations. This is due to the very high chiral amplifications of the initial small statistical deviations from the ideal racemic composition. Moreover, this system is sensitive to very small chiral polarizations (energy differences between transition states below the mJ mol−1 range). This behaviour can also be observed in reversible exergonic reactions, because the racemization time scale is substantially longer than that of the transformation of the initial reagents. The effect of the presence of other reactions likely to occur (i.e. non-catalytic transformations, non-enantioselective catalysis and homodimer formation) is discussed. Even if these decrease the sensitivity of the network in several chemical scenarios, the emergence of kinetically controlled spontaneous symmetry breaking is not hindered. These features, together with the response of the system to a sequential reaction procedure, suggest that a similar type of network is at the heart of the Soai reaction.
89 citations
TL;DR: CDFT-CI can recover the correct energy for charge delocalized states by approximating the true wave function as a linear combination of localized configurations (e.g., reactant and product).
Abstract: In this work, a constrained density functional theory based configuration interaction approach (CDFT-CI) is applied to calculating transition state energies of chemical reactions that involve bond forming and breaking at the same time. At a given point along the reaction path, the configuration space is spanned by two diabaticlike configurations: reactant and product. Each configuration is constructed self-consistently with spin and charge constraints to maximally retain the identities of the reactants or the products. Finally, the total energy is obtained by diagonalizing an effective Hamiltonian constructed in the basis spanned by these two configurations. By design, this prescription does not affect the energies of the reactant or product species but will affect the energy at intermediate points along the reaction coordinate, most notably by modifying the reaction barrier height. When tested with a large set of reactions that include hydrogen transfer, heavy atom transfer, and nucleophilic substitution...
TL;DR: This work suggests that the vibrational distribution at the first conical intersection and the interactions among the states as the reaction proceeds between the two transition states are the origin of the population of the chemiluminescent (n,sigma*) states.
Abstract: The unimolecular chemiluminescent decomposition of unsubstituted dioxetanone was studied at the complete active space self-consistent field level of theory combined with the multistate second-order multiconfigurational perturbation theory energy correction. The calculations revealed interesting features. Two transition states, two conical intersections, and one intermediate stable biradical structure along the lowest energy reaction path were identified. It was noted that the conical intersections are found at or in very close proximity to the transition states. The first and second transition states correspond to O-O and C-C cleavages, respectively. In particular, a planar structure is supported by the (1)(sigma,sigma*) state during the O-O dissociation up to the first transition state and conical intersection. At this point the (1)(sigma,sigma*) state dissociation path bifurcates, corresponding to a torsion of the O-C-C-O angle. Simultaneously, the (1)(n,sigma*) state becomes lower in energy while still favoring a planar structure. As the lowest-energy reaction path proceeds toward the second transition state and conical intersection, the (1)(n,sigma*), (3)(n,sigma*), and (1)(sigma,sigma*) states are close in energy. This work suggests that the vibrational distribution at the first conical intersection and the interactions among the states as the reaction proceeds between the two transition states are the origin of the population of the chemiluminescent (n,sigma*) states.
TL;DR: The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free‐energy calculations.
Abstract: We describe a method for the systematic improvement of reaction coordinates in quantum mechanical/molecular mechanical (QM/MM) calculations of reaction free-energy profiles. In umbrella-sampling free-energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (approximately 10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations.
TL;DR: In this paper, the authors analyze midpoint species along the reaction coordinate for hydrogen transfer in the reaction R′−H−M−R−→ R−H+M+R−R+R −H−+M −R′ with Bader's AIM analysis.
TL;DR: Six archetypal DGT reactions using density functional theory (DFT) at the OLYP/TZ2P level are explored using the activation strain model of chemical reactivity and an alternative fragmentation and a valence bond model are used for analyzing the character of the transition states.
Abstract: Double group transfer (DGT) reactions, such as the bimolecular automerization of ethane plus ethene, are known to have high reaction barriers despite the fact that their cyclic transition states have a pronounced in-plane aromatic character, as indicated by NMR spectroscopic parameters. To arrive at a way of understanding this somewhat paradoxical and incompletely understood phenomenon of high-energy aromatic transition states, we have explored six archetypal DGT reactions using density functional theory (DFT) at the OLYP/TZ2P level. The main trends in reactivity are rationalized using the activation strain model of chemical reactivity. In this model, the shape of the reaction profile DeltaE(zeta) and the height of the overall reaction barrier DeltaE( not equal)=DeltaE(zeta=zeta(TS)) is interpreted in terms of the strain energy DeltaE(strain)(zeta) associated with deforming the reactants along the reaction coordinate zeta plus the interaction energy DeltaE(int)(zeta) between these deformed reactants: DeltaE(zeta)=DeltaE(strain)(zeta)+DeltaE(int)(zeta). We also use an alternative fragmentation and a valence bond model for analyzing the character of the transition states.
01 Jan 2009
TL;DR: In this paper, the C7H7 potential energy surface was studied from first principles to determine the benzyl radical decomposition mechanism, which is in agreement with the literature evidences reporting that benzyl decomposes to hydrogen and a C 7H6 species.
Abstract: The C7H7 potential energy surface was studied from first principles to determine the benzyl radical decomposition mechanism. The investigated high temperature reaction pathway involves 15 accessible energy wells connected by 25 transition states. The analysis of the potential energy surface, performed determining kinetic constants of each elementary reaction using conventional transition state theory, evidenced that the reaction mechanism has as rate determining step the isomerization of the 1,3-cyclopentadiene, 5-vinyl radical to the 2-cyclopentene,5-ethenylidene radical and that the fastest reaction channel is dissociation to fulvenallene and hydrogen. This is in agreement with the literature evidences reporting that benzyl decomposes to hydrogen and a C7H6 species. The benzyl high-pressure decomposition rate constant estimated assuming equilibrium between the rate determining step transition state and benzyl is k1(T) = 1.44 × 1013T0.453exp(−38400/T) s−1, in good agreement with the literature data. As fulvenallene reactivity is mostly unknown, we investigated its reaction with hydrogen, which has been proposed in the literature as a possible decomposition route. The reaction proceeds fast both backward to form again benzyl and, if hydrogen adds to allene, forward toward the decomposition into the cyclopentadienyl radical and acetylene with high-pressure kinetic constants k2(T) = 8.82 × 108T1.20exp(1016/T) and k3(T) = 1.06 × 108T1.35exp(1716/T) cm3/mol/s, respectively. The computed rate constants were then inserted in a detailed kinetic mechanism and used to simulate shock tube literature experiments.
TL;DR: A theoretical study of the mechanism of the isomerization reaction HOC(+) --> HCO(+) is presented and it has been found that the evolution of changes in REF along the intrinsic reaction coordinate can be explained in terms of bond orders.
Abstract: A theoretical study of the mechanism of the isomerization reaction HOC+→HCO+ is presented. The mechanism was studied in terms of reaction force, chemical potential, reaction electronic flux (REF), and bond orders. It has been found that the evolution of changes in REF along the intrinsic reaction coordinate can be explained in terms of bond orders. The energetic lowering of the hydrogen assisted (catalyzed) reaction has been identified as being due to the stabilization of the H3+ transition state complex and the stepwise bond dissociation and formation of the H–O and H–C bonds, respectively.
TL;DR: The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computationally and shows that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from theOxirane than for the thiolate obtaining from the thiiranes.
Abstract: The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computation- ally. The inhibition mechanism involves C-H deprotonation with concomitant opening of the three- membered heterocycle. SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine the reaction of these two inhibitors in the active site of MMP2. The calculationsshowthatthereactionbarrierfortransformationofSB-3CTis1.6kcal/mollowerthanitsoxirane analogue, and the ring-opening reaction energy of SB-3CT is 8.0 kcal/mol more exothermic than that of its oxirane analogue. Calculations also show that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane than for the thiolate obtained from the thiirane. A six-step partial charge fitting procedure is introduced for the QM/MM calculations to update atomic partial charges of the quantum mechanics region and to ensure consistent electrostatic energies for reactants, transition states, and products.
TL;DR: The investigations present an important step toward a systematic investigation of phenyl radical reactions under single collision conditions similar to those found in combustion flames and in high-temperature interstellar environments.
Abstract: Polycyclic aromatic hydrocarbons (PAHs)organic compounds that consist of fused benzene ringsand their hydrogen-deficient precursors have attracted extensive interest from combustion scientists, organic chemists, astronomers, and planetary scientists. On Earth, PAHs are toxic combustion products and a source of air pollution. In the interstellar medium, research suggests that PAHs play a role in unidentified infrared emission bands, diffuse interstellar bands, and the synthesis of precursor molecules to life. To build clean combustion devices and to understand the astrochemical evolution of the interstellar medium, it will be critical to understand the elementary reaction mechanisms under single collision conditions by which these molecules form in the gas phase. Until recently, this work had been hampered by the difficulty in preparing a large concentration of phenyl radicals, but the phenyl radical represents one of the most important radical species to trigger PAH formation in high-temperature environments. However, we have developed a method for producing these radical species and have undertaken a systematic experimental investigation. In this Account, we report on the chemical dynamics of the phenyl radical (C(6)H(5)) reactions with the unsaturated hydrocarbons acetylene (C(2)H(2)), ethylene (C(2)H(4)), methylacetylene (CH(3)CCH), allene (H(2)CCCH(2)), propylene (CH(3)CHCH(2)), and benzene (C(6)H(6)) utilizing the crossed molecular beams approach. For nonsymmetric reactants such as methylacetylene and propylene, steric effects and the larger cones of acceptance drive the addition of the phenyl radical to the nonsubstituted carbon atom of the hydrocarbon reactant. Reaction intermediates decomposed via atomic hydrogen loss pathways. In the phenyl-propylene system, the longer lifetime of the reaction intermediate yielded a more efficient energy randomization compared with the phenyl-methylacetylene system. Therefore, two reaction channels were open: hydrogen losses from the vinyl and from the methyl groups. All fragmentation pathways involved tight exit transition states. In the range of collision energies investigated, the reactions are dictated by phenyl radical addition-hydrogen atom elimination pathways. We did not observe ring closure processes with the benzene ring. Our investigations present an important step toward a systematic investigation of phenyl radical reactions under single collision conditions similar to those found in combustion flames and in high-temperature interstellar environments. Future experiments at lower collision energies may enhance the lifetimes of the reaction intermediates, which could open up competing ring closure channels to form bicyclic reaction products.
TL;DR: In this article, a non-catalytic conversion of gaseous NO into N2 was investigated using density functional theory, transition state theory and a kinetic Monte-Carlo (kMC) simulation.
TL;DR: Computational results are in good agreement with experimental observations and reveal reaction mechanisms for neutral iron oxide clusters taking methanol to formaldehyde through various reaction intermediates.
Abstract: Reactions of neutral iron oxide clusters (Fe(m)O(n), m=1-2, n=0-5) with methanol (CH(3)OH) in a fast flow reactor are investigated by time of flight mass spectrometry. Detection of the neutral iron oxide cluster distribution and reaction intermediates and products is accomplished through single photon ionization by a 118 nm (10.5 eV) VUV laser. Partially deuterated methanol (CD(3)OH) is employed to distinguish reaction products and reaction mechanisms. Three major reactions are identified experimentally: CH(3)OH association with FeO; methanol dehydrogenation on FeO(1,2) and Fe(2)O(2-5); and (CH(2)O)Fe formation. Density functional theory calculations are carried out to identify reaction products, and to explore the geometric and electronic structures of the iron oxide clusters, reaction intermediates, and transition states, and to evaluate reaction pathways. Neutral formaldehyde is calculated to be formed on FeO(1,2) and Fe(2)O(2-5) clusters. Hydrogen transfer from methanol to iron oxide clusters occurs first from the O-H moiety of methanol, and is followed by a hydrogen transfer from the C-H moiety of methanol. Computational results are in good agreement with experimental observations and reveal reaction mechanisms for neutral iron oxide clusters taking methanol to formaldehyde through various reaction intermediates. Based on the experimental results and the calculated reaction mechanisms and pathways, complete catalytic cycles are suggested for the heterogeneous reaction of CH(3)OH to CH(2)O facilitated by an iron oxide catalyst.
TL;DR: The substring strategy used in combination with the modified-GSM has been demonstrated to be an efficient transition state-finding strategy for a wide range of types of reactions.
Abstract: Efficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of the transition state structure in order to converge, particularly for complex reaction systems. The growing string method (GSM) [B. Peters et al., J. Chem. Phys. 120, 7877 (2004)] does not require an initial guess of the transition state; however, the calculation is still computationally intensive due to repeated calls to the quantum mechanics code. Recent modifications to the GSM [A. Goodrow et al., J. Chem. Phys. 129, 174109 (2008)] have reduced the total computational time for converging to a transition state by a factor of 2 to 3. In this work, three transition state-finding strategies have been developed to complement the speedup of the modified-GSM: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy. The hybrid strategy initiates the string calculation at a low level of theory (HF/STO-3G), which is then refined at a higher level of theory (B3LYP/6-31G(*)). The energy-weighted strategy spaces points along the reaction pathway based on the energy at those points, leading to a higher density of points where the energy is highest and finer resolution of the transition state. The substring strategy is similar to the hybrid strategy, but only a portion of the low-level string is refined using a higher level of theory. These three strategies have been used with the modified-GSM and are compared in three reactions: alanine dipeptide isomerization, H-abstraction in methanol oxidation on VO(x)/SiO(2) catalysts, and C-H bond activation in the oxidative carbonylation of toluene to p-toluic acid on Rh(CO)(2)(TFA)(3) catalysts. In each of these examples, the substring strategy was proved most effective by obtaining a better estimate of the transition state structure and reducing the total computational time by a factor of 2 to 3 compared to the modified-GSM. The applicability of the substring strategy has been extended to three additional examples: cyclopropane rearrangement to propylene, isomerization of methylcyclopropane to four different stereoisomers, and the bimolecular Diels-Alder condensation of 1,3-butadiene and ethylene to cyclohexene. Thus, the substring strategy used in combination with the modified-GSM has been demonstrated to be an efficient transition state-finding strategy for a wide range of types of reactions.
TL;DR: In this article, the authors investigated the coordination-insertion mechanisms of scandium-alkoxide initiated ring-opening polymerizations of 3-caprolactone (CL), trimethylene carbonate (TMC), and (S,S)-lactide (LLA) using density functional theory calculations.
01 Jan 2009
TL;DR: The thermal cracking patterns from the decomposition and isomerization of octyl-1 radicals have been determined from the pyrolysis of n -octyl iodide in single pulse shock tube experiments at temperatures in the 850-1000 k range and pressures near 2 bar as discussed by the authors.
Abstract: The thermal cracking patterns from the decomposition and isomerization of octyl-1 radicals have been determined from the pyrolysis of n -octyl iodide in single pulse shock tube experiments at temperatures in the 850–1000 K range and pressures near 2 bar. Rate constants for the six beta bond scission and five of the six isomerization processes have been derived over all combustion conditions [0.1–100 bar, 700–1900 K]. Comparisons are made with previous studies on the decomposition of other primary radicals. Results are consistent with similar types of reactions having equal rate constants. The larger size of the octyl radicals makes contributions from secondary to secondary radical isomerization increasingly important. The results confirm that the 1–3 H-transfer process (involving a seven member cyclic transition state) have rate constants that are within a factor of 2 of those for the 1–4 process (six member cyclic transition state) It appears that rate constants for 1–2 H-transfer isomerization, involving an eight member cyclic transition state is unimportant in comparison to contributions from other isomerization processes. The strain energy does not appear to play an important role for these larger transition states. The implications of these results to larger fuel radicals will be discussed.
TL;DR: The stereoselectivity-determining oxidative addition step in the Suzuki-Miyaura cross-coupling of alpha-bromo sulfoxides is analyzed computationally through DFT calculations on a model system defined by Pd(PMe(3))(2) and CH(3)SOCH( 2)Br.
Abstract: The stereoselectivity-determining oxidative addition step in the Suzuki−Miyaura cross-coupling of α-bromo sulfoxides is analyzed computationally through DFT calculations on a model system defined by Pd(PMe3)2 and CH3SOCH2Br. Both monophospine and bisphosphine complexes have been considered, different reaction pathways being characterized through location of the corresponding transition states. The lowest energy transition states correspond to nucleophilic substitution mechanisms, which imply inversion of configuration at the carbon, in good agreement with experimental data on the process. The energy-lowering and stereodirecting role of the sulfinyl substituent is explained through its attractive interactions with the palladium center, which are only possible in the most favored mechanisms.
TL;DR: Distortion/interaction and absolutely localized energy decomposition analyses provide new insights into why the (3 + 2) pathway is highly preferred over the (2 + 1) pathway, the origin of rate enhancement from ligated base, and reactivity differences between OsO (4), ReO(4)(-), TcO(-), and MnO( 4)(-).
Abstract: The reaction pathways (including the transition states) of ethylene addition to osmium tetroxide (OsO4, and amine ligated), rhenate (ReO4−), technetate (TcO4−), and permanganate (MnO4−) have been studied by qualitative and quantitative analyses. Distortion/interaction and absolutely localized energy decomposition analyses provide new insights into why the (3 + 2) pathway is highly preferred over the (2 + 2) pathway, the origin of rate enhancement from ligated base, and reactivity differences between OsO4, ReO4−, TcO4−, and MnO4−. The (2 + 2) transition state has a much larger barrier than the (3 + 2) transition state because (1) the Os−O bond is stretched significantly resulting in a larger distortion energy (ΔEd⧧) value and (2) the transition state interaction energy (ΔEi⧧) is destabilizing due to large exchange repulsions overwhelming stabilizing charge-transfer terms. Base ligation lowers osmium tetroxide and ethylene distortion energies due to the ground-state O−Os−O angle being predistorted from 110°...
TL;DR: It is determined that proteolysis reaction is exothermic and proceeds quickly as the barrier in the rate-limiting step falls widely within the range of values expected for an enzymatic catalysis, both in vacuum and in protein medium.
Abstract: The possible mechanism by which the insulin-degrading enzyme (IDE) zinc-binding protease carries out its catalytic function toward two peptides of different length, simulating a portion of B chain of insulin, was investigated on an enzymatic model consisting of 130 /159 atoms, using the density functional theory method and the hybrid exchange−correlation functional B3LYP in gas phase and in the protein environment. Based on the geometry and relative stabilities of minima and transition states on the potential energy profiles, we determined that proteolysis reaction is exothermic and proceeds quickly as the barrier in the rate-limiting step falls widely within the range of values expected for an enzymatic catalysis, both in vacuum and in protein medium.
TL;DR: Theoretic information measures of the Shan- non type are employed to describe the course of the sim- plest hydrogen abstraction and the identity SN2 exchange chemical reactions as mentioned in this paper, and the transition state is detected and the bond breaking/forming regions are revealed.
Abstract: Theoretic-information measures of the Shan- non type are employed to describe the course of the sim- plest hydrogen abstraction and the identity SN2 exchange chemical reactions. For these elementary chemical pro- cesses, the transition state is detected and the bond breaking/forming regions are revealed. A plausibility argument of the former is provided and verified numeri- cally. It is shown that the information entropy profiles posses much more chemically meaningful structure than the profile of the total energy for these chemical reactions. Our results support the concept of a continuum of transient of Zewail and Polanyi for the transition state rather than a single state, which is also in agreement with reaction force analyses. This is performed by following the intrinsic reaction coordinate (IRC) path calculated at the MP2 level of theory from which Shannon entropies in position and momentum spaces at the QCISD(T)/6-311??G(3df,2p) level are determined. Several selected descriptors of the density are utilized to support the observations, such as the molecular electrostatic potential, the hardness, the dipole moment along with geometrical parameters.
TL;DR: A comparative density functional theory study of proline 1, beta-proline 5b, and 11 in the latter reaction revealed the origin of the improved enantioselectivity of 11 over 5b.
Abstract: 7-Azabicyclo[2.2.1]heptane-2-carboxylic acid 11 was prepared in enantiopure form, and its catalytic potential in the direct aldol reaction between acetone and 4-nitrobenzaldehyde was assessed. The bicyclic system was found to be more selective than its monocyclic analogue β-proline 5b. A comparative density functional theory study of proline 1, β-proline 5b, and 11 in the latter reaction revealed the origin of the improved enantioselectivity of 11 over 5b. The geometry of the carboxylic acid group in the transition states, which depended critically on pyrrolidine ring conformation, was found to play a key role.
TL;DR: In this article, the authors investigated the reaction mechanisms of carbonyl oxide with formic acid using the B3LYP/6-311G(d,p) and CBS-QB3 theoretical methods.
Abstract: The reaction mechanisms of carbonyl oxide with formic acid are investigated using the B3LYP/6-311G(d,p) and CBS-QB3 theoretical methods. The investigation encompasses the eight complexes formed between carbonyl oxide and formic acid, the initial transition states responsible for the formation of these transitory products including hydroxylated ozonide and hydroperoxymethyl formate, the cleavages of the transitory intermediates and the interconversion between the transitory products and between syn-formic acid anhydride and anti-formic acid anhydride. The calculated results predict that the binding energy of the most stable complex in the eight complexes is −11.0 kcal/mol, which indicates that the formed pre-complexes are of special important for the reaction carbonyl oxide with formic acid. In addition, the barrier heights of the transition states that lead to the hydroxylated ozonide and hydroperoxymethyl formate are −0.5 kcal/mol, −1.3 kcal/mol, respectively, at the CBS-QB3 level of theory, which shows that the two reaction channels contribute to the transitory product formation. In addition, under some circumstances, the cleavages of transitory products result in the formation of the anti-formic acid anhydride, which is in well agreement with experimental predictions. It is noted that splits of hydroxylated ozonide are responsible for the formation of formic acid.