Showing papers on "Transition state published in 2007"
TL;DR: In this article, the rotational symmetry number for different molecular configurations and how to apply them to transition state theory is discussed. But special care is advised in the evaluation of symmetry numbers in the following situations: (i) reaction is symmetric, (ii) if reactants and/or transition states are chiral, (iii) if the reaction has multiple conformers for reactants or transition states and, (iv) if there is an internal rotation of part of the molecular system.
Abstract: This article shows how to evaluate rotational symmetry numbers for different molecular configurations and how to apply them to transition state theory. In general, the symmetry number is given by the ratio of the reactant and transition state rotational symmetry numbers. However, special care is advised in the evaluation of symmetry numbers in the following situations: (i) if the reaction is symmetric, (ii) if reactants and/or transition states are chiral, (iii) if the reaction has multiple conformers for reactants and/or transition states and, (iv) if there is an internal rotation of part of the molecular system. All these four situations are treated systematically and analyzed in detail in the present article. We also include a large number of examples to clarify some complicated situations, and in the last section we discuss an example involving an achiral diasteroisomer.
336 citations
TL;DR: Possible "alternative" H-atom isomerizations leading to different products from the parent O2QOOH radical were included in the low-temperature chemical kinetic mechanism and were found to play a significant role.
Abstract: A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Rules for reaction rate constants are developed for the low-temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Because cyclohexane produces only one type of cyclohexyl radical, much of the low-temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical with O2 through five-, six-, and seven-membered-ring transition states. The direct elimination of cyclohexene and HO2 from RO2 is included in the treatment using a modified rate constant of Cavallotti et al. (Proc. Combust. Inst. 2007, 31, 201). Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data, are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies ...
203 citations
TL;DR: A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations and to facilitate the design of improved next-generation multiscale quantum models.
Abstract: A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations. The model, designated AM1/d-PhoT, is parametrized for H, O, and P atoms to reproduce high-level density-functional results from a recently constructed database of quantum calculations for RNA catalysis (http://theory.chem.umn.edu/Database/QCRNA), including geometries and relative energies of minima, transition states and reactive intermediates, dipole moments, proton affinities, and other relevant properties. The model is tested in the gas phase and in solution using a QM/MM potential. The results indicate that the method provides significantly higher accuracy than MNDO/ d, AM1, and PM3 methods and, for the transphosphorylation reactions, is in close agreement with the density-functional calculations at the B3LYP/6-311++G(3df,2p) level with a reduction in computational cost of 3-4 orders of magnitude. The model is expected to have considerable impact on the application of semiempirical QM/MM methods to transphosphorylation reactions in solution, enzymes, and ribozymes and to ultimately facilitate the design of improved next- generation multiscale quantum models.
139 citations
TL;DR: It is found that the U correction method plays a significant role in energetics, especially for the intermediates of the exit channels and products that are partially reduced in CeO(2)(110) surfaces.
Abstract: Reaction mechanisms for the interactions between CeO2A and (110) surfaces are investigated using periodic density functional theory (DFT) calculations. Both standard DFT and DFT + U calculations to examine the effect of the localization of Ce 4f states on the redox chemistry of H2–CeO2 interactions are described. For mechanistic studies, molecular and dissociative local minima are initially located by placing an H2 molecule at various active sites of the CeO2 surfaces. The binding energies of physisorbed species optimized using the DFT and DFT + U methods are very weak. The dissociative adsorption reactions producing hydroxylated surfaces are all exothermic; exothermicities at the DFT level range from 4.1 kcal mol � 1 for the (111) to 26.5 kcal mol � 1 for the (110) surface, while those at the DFT + U level are between 65.0 kcal mol � 1 for the (111) and 81.8 kcal mol � 1 for the (110) surface. Predicted vibrational frequencies of adsorbed OH and H2O species on the surfaces are in line with available experimental and theoretical results. Potential energy profiles are constructed by connecting molecularly adsorbed and dissociatively adsorbed intermediates on each CeO2 surface with tight transition states using the nudged elastic band (NEB) method. It is found that the U correction method plays a significant role in energetics, especially for the intermediates of the exit channels and products that are partially reduced. The surface reduction reaction on CeO2A is energetically much more favorable. Accordingly, oxygen vacancies are more easily formed on the (110) surface than on the (111) surface.
138 citations
TL;DR: The reaction force of a chemical or physical process is the negative derivative of the system's potential energy V(R) along the reaction coordinate as mentioned in this paper, which can be characterized in terms of changes in structural and/or electronic properties.
Abstract: The reaction force F(R) of a chemical or physical process is the negative derivative of the system's potential energy V(R) along the reaction coordinate. The features of F(R) – its maxima, minima and zeroes – divide the process into well-defined stages which can, in general, be characterized in terms of changes in structural and/or electronic properties. This has been demonstrated for bond dissociation/formation and for reactions that have activation barriers in both forward and reverse directions. An important aspect of the reaction force is that it naturally and unambiguously divides activation energies into two components, one corresponding to the preparative structural stage of the process and the other to the first phase of the transition to products. It is shown how this can help to elucidate the effect of a solvent or a catalyst upon an activation barrier.
137 citations
TL;DR: Experimental and density functional theory show that the reaction of acetonitrile with a zerovalent nickel bis(dialkylphosphino)ethane fragment (alkyl = methyl, isopropyl) proceeds via initial exothermic formation of an eta(2)-nitrile complex, which contradicts the observation of thermal C-CN activation in THF.
Abstract: Experimental and density functional theory show that the reaction of acetonitrile with a zerovalent nickel bis(dialkylphosphino)ethane fragment (alkyl = methyl, isopropyl) proceeds via initial exothermic formation of an η2-nitrile complex. Three well-defined transition states have been found on the potential energy surface between the η2-nitrile complex and the activation products. The lowest energy transition state is an η3-acetonitrile complex, which connects the η2-nitrile to a higher energy η3-acetonitrile intermediate with an agostic C−H bond, while the other two lead to cleavage of either the C−H or the C−CN bonds. Gas-phase calculations show C−CN bond activation to be endothermic, which contradicts the observation of thermal C−CN activation in THF. Therefore, the effect of solvent was taken into consideration by using the polarizable continuum model (PCM), whereupon the activation of the C−CN bond was found to be exothermic. Furthermore the C−CN bond activation was found to be favored exclusively o...
124 citations
TL;DR: Reaction pathways during CO(2) hydrogenation catalyzed by the Ru dihydride complex (RuHHOCHO) have been studied by DFT calculations and by IR and NMR spectroscopy, and the highly ionic characters of various complexes and transition states are shown.
Abstract: Reaction pathways during CO2 hydrogenation catalyzed by the Ru dihydride complex [Ru(dmpe)2H2] (dmpe=Me2PCH2CH2PMe2) have been studied by DFT calculations and by IR and NMR spectroscopy up to 120 bar in toluene at 300 K. CO2 and formic acid readily inserted into or reacted with the complex to form formates. Two formate complexes, cis-[Ru(dmpe)2(OCHO)2] and trans-[Ru(dmpe)2H(OCHO)], were formed at low CO2 pressure (<5 bar). The latter occurred exclusively when formic acid reacted with the complex. A RuH⋅⋅⋅ HOCHO dihydrogen-bonded complex of the trans form was identified at H2 partial pressure higher than about 50 bar. The trans form of the complex is suggested to play a pivotal role in the reaction pathway. Potential-energy profiles along possible reaction paths have been investigated by static DFT calculations, and lower activation-energy profiles via the trans route were confirmed. The H2 insertion has been identified as the rate-limiting step of the overall reaction. The high energy of the transition state for H2 insertion is attributed to the elongated Ru−O bond. The H2 insertion and the subsequent formation of formic acid proceed via Ru(η2-H2)-like complexes, in which apparently formate ion and Ru+ or Ru(η2-H2)+ interact. The bond properties of involved Ru complexes were characterized by natural bond orbital analysis, and the highly ionic characters of various complexes and transition states are shown. The stability of the formate ion near the Ru center likely plays a decisive role for catalytic activity. Removal of formic acid from the dihydrogen-bonded complex (RuH⋅⋅⋅HOCHO) seems to be crucial for catalytic efficiency, since formic acid can easily react with the complex to regenerate the original formate complex. Important aspects for the design of highly active catalytic systems are discussed.
118 citations
TL;DR: The determination of kinetic isotope effects (KIEs) for different reaction pathways and steps in a complex reaction network, where KIEs may affect the overall reaction in various different ways including dominant and minority pathways or the buildup of a reaction-inhibiting adlayer, is demonstrated.
Abstract: The determination of kinetic isotope effects (KIEs) for different reaction pathways and steps in a complex reaction network, where KIEs may affect the overall reaction in various different ways including dominant and minority pathways or the buildup of a reaction-inhibiting adlayer, is demonstrated for formic acid electrooxidation on a Pt film electrode by quantitative electrochemical in situ IR spectroscopic measurements under controlled mass-transport conditions. The ability to separate effects resulting from different contributions--which is not possible using purely electrochemical kinetic measurements--allows conclusions on the nature of the rate-limiting steps and their transition state in the individual reaction pathways. The potential-independent values of approximately 1.9 for the KIE of formic acid dehydration (CO(ad) formation) in the indirect pathway and approximately 3 for the CO(ad) coverage-normalized KIE of formic acid oxidation to CO2 (direct pathway) indicate that 1) C-H bond breaking is rate-limiting in both reaction steps, 2) the transition states for these reactions are different, and 3) the configurations of the transition states involve rather strong bonds to the transferred D/H species, either in the initial or in the final state, for the direct pathway and--even more pronounced--for formic acid dehydration (CO(ad) formation).
103 citations
TL;DR: The calculations provide strong support to an associative mechanism for the hydrolysis of phosphotriesters by PTE using the hybrid density functional theory method B3LYP, and demonstrate that the nucleophilicity of the bridging hydroxide is sufficient to be utilized in the Hydrolysis reaction.
Abstract: Phosphotriesterase (PTE) is a binuclear zinc enzyme that catalyzes the hydrolysis of extremely toxic organophosphate triesters. In the present work, we have investigated the reaction mechanism of PTE using the hybrid density functional theory method B3LYP. We present a potential energy surface for the reaction and provide characterization of the transition states and intermediates. We used the high resolution crystal structure to construct a model of the active site of PTE, containing the two zinc ions and their first shell ligands. The calculations provide strong support to an associative mechanism for the hydrolysis of phosphotriesters by PTE. No protonation of the leaving group was found to be necessary. In particular, the calculations demonstrate that the nucleophilicity of the bridging hydroxide is sufficient to be utilized in the hydrolysis reaction, a feature that is of importance for a number of other di-zinc enzymes.
101 citations
TL;DR: The kinetics of the reaction CO + HO2* --> CO2 + *OH was studied using a combination of ab initio electronic structure theory, transition state theory, and master equation modeling and shows that the overall rate coefficient is independent of pressure up to 500 atm for temperature ranging from 300 to 2500 K.
Abstract: The kinetics of the reaction CO + HO2• → CO2 + •OH was studied using a combination of ab initio electronic structure theory, transition state theory, and master equation modeling. The potential energy surface was examined with the CCSD(T) and CASPT2 methods. The classical energy barriers were found to be about 18 and 19 kcal/mol for CO + HO2• addition following the trans and cis paths, respectively. For the cis path, rate constant calculations were carried out with canonical transition state theory. For the trans path, master equation modeling was also employed to examine the pressure dependence. Special attention was paid to the hindered internal rotations of the HOOC•O adduct and transition states. The theoretical analysis shows that the overall rate coefficient is independent of pressure up to 500 atm for temperature ranging from 300 to 2500 K. On the basis of this analysis, we recommend the following rate expression for reaction R1 k(cm3/mol·s) = 1.57 × 105 T 2.18e-9030/T for 300 ≤ T ≤ 2500 K with the...
93 citations
TL;DR: Ab initio calculations at the level of CBS-QB3 theory have been performed to investigate the potential energy surface for the reaction of benzyl radical with molecular oxygen, and it was suggested that the dissociation of Benzyl peroxy radicals proceeded with the partial equilibrium between the benzyl+O2 and benzylperoxy radicals.
Abstract: Ab initio calculations at the level of CBS-QB3 theory have been performed to investigate the potential energy surface for the reaction of benzyl radical with molecular oxygen. The reaction is shown to proceed with an exothermic barrierless addition of O2 to the benzyl radical to form benzylperoxy radical (2). The benzylperoxy radical was found to have three dissociation channels, giving benzaldehyde (4) and OH radical through the four-centered transition states (channel B), giving benzyl hydroperoxide (5) through the six-centered transition states (channel C), and giving O2-adduct (8) through the four-centered transition states (channel D), in addition to the backward reaction forming benzyl radical and O2 (channel E). The master equation analysis suggested that the rate constant for the backward reaction (E) of C6H5CH2OO → C6H5CH2 + O2 was several orders of magnitude higher that those for the product dissociation channels (B−D) for temperatures 300−1500 K and pressures 0.1−10 atm; therefore, it was also ...
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TL;DR: A theoretical study of the gas-phase unimolecular decomposition of cyclobutane, cyclopentane and cyclohexane by means of quantum chemical calculations shows that the rotational barriers between the conformers are of importance in decomposition rate of the largest biradicals.
Abstract: This work reports a theoretical study of the gas phase unimolecular decomposition of cyclobutane, cyclopentane and cyclohexane by means of quantum chemical calculations. A biradical mechanism has been envisaged for each cycloalkane, and the main routes for the decomposition of the biradicals formed have been investigated at the CBS-QB3 level of theory. Thermochemical data (\delta H^0_f, S^0, C^0_p) for all the involved species have been obtained by means of isodesmic reactions. The contribution of hindered rotors has also been included. Activation barriers of each reaction have been analyzed to assess the 1 energetically most favorable pathways for the decomposition of biradicals. Rate constants have been derived for all elementary reactions using transition state theory at 1 atm and temperatures ranging from 600 to 2000 K. Global rate constant for the decomposition of the cyclic alkanes in molecular products have been calculated. Comparison between calculated and experimental results allowed to validate the theoretical approach. An important result is that the rotational barriers between the conformers, which are usually neglected, are of importance in decomposition rate of the largest biradicals. Ring strain energies (RSE) in transition states for ring opening have been estimated and show that the main part of RSE contained in the cyclic reactants is removed upon the activation process.
TL;DR: It is demonstrated how methylphenyl radical formation is important in the combustion and pyrolysis of other alkyl-substituted aromatic compounds such as xylene and trimethylbenzene and how reactions leading to the important unsaturated oxygenated intermediates identified in this study, and the further reactions of these intermediates, are not included in current aromatic oxidation mechanisms.
Abstract: Aromatic compounds such as toluene and xylene are major components of many fuels. Accurate kinetic mechanisms for the combustion of toluene are, however, incomplete, as they do not accurately model experimental results such as strain rates and ignition times and consistently underpredict conversion. Current kinetic mechanisms for toluene combustion neglect the reactions of the methylphenyl radicals, and we believe that this is responsible, in part, for the shortcomings of these models. We also demonstrate how methylphenyl radical formation is important in the combustion and pyrolysis of other alkyl-substituted aromatic compounds such as xylene and trimethylbenzene. We have studied the oxidation reactions of the methylphenyl radicals with O2 using computational ab initio and density functional theory methods. A detailed reaction submechanism is presented for the 2-methylphenyl radical + O2 system, with 16 intermediates and products. For each species, enthalpies of formation are calculated using the computational methods G3 and G3B3, with isodesmic work reactions used to minimize computational errors. Transition states are calculated at the G3B3 level, yielding high-pressure limit elementary rate constants as a function of temperature. For the barrierless methylphenyl + O2 and methylphenoxy + O association reactions, rate constants are determined from variational transition state theory. Multichannel, multifrequency quantum Rice-Ramsperger-Kassel (qRRK) theory, with master equation analysis for falloff, provides rate constants as a function of temperature and pressure from 800 to 2400 K and 1 x 10(-4) to 1 x 10(3) atm. Analysis of our results shows that the dominant pathways for reaction of the three isomeric methylphenyl radicals is formation of methyloxepinoxy radicals and subsequent ring opening to methyl-dioxo-hexadienyl radicals. The next most important reaction pathway involves formation of methylphenoxy radicals + O in a chain branching process. At lower temperatures, the formation of stabilized methylphenylperoxy radicals becomes significant. A further important reaction channel is available only to the 2-methylphenyl isomer, where 6-methylene-2,4-cyclohexadiene-1-one (ortho-quinone methide, o-QM) is produced via an intramolecular hydrogen transfer from the methyl group to the peroxy radical in 2-methylphenylperoxy, with subsequent loss of OH. The decomposition of o-QM to benzene + CO reveals a potentially important new pathway for the conversion of toluene to benzene during combustion. A number of the important products of toluene combustion proposed in this study are known to be precursors of polyaromatic hydrocarbons that are involved in soot formation. Reactions leading to the important unsaturated oxygenated intermediates identified in this study, and the further reactions of these intermediates, are not included in current aromatic oxidation mechanisms.
TL;DR: The ability of uranium monoxide cations, UO+ and UO2+, to activate the O-H bond of H2O was studied by using two different approaches of the density functional theory, using relativistic small-core pseudopotentials and B3LYP hybrid functional.
Abstract: The ability of uranium monoxide cations, UO+ and UO2+, to activate the O-H bond of H2O was studied by using two different approaches of the density functional theory. First, relativistic small-core pseudopotentials were used together with B3LYP hybrid functional. In addition, frozen-core PW91-PW91 calculations were performed within the ZORA approximation. A close description of the reaction mechanisms leading to two different reaction products is presented, including all the involved minima and transition states. Different possible spin states were considered as well as the effect of spin-orbit interactions on the transition state barrier heights. The nature of the chemical bonding of the key minima and transition states was studied by using topological methodologies (ELF, AIM). The obtained results are compared with experimental data, as well as with previous studies on the reaction of the bare uranium cations with water, to analyze the influence of the oxo-ligand in reactivity.
TL;DR: Computational examinations of the efficacy of model d6 transition metal complexes of the form [(Tab)M(PH3)2X]q for the activation of benzene C-H bonds and the potential for their incorporation into catalytic functionalization cycles are presented.
Abstract: Recent reports of 1,2-addition of C-H bonds across Ru-X (X = amido, hydroxo) bonds of TpRu(PMe3)X fragments {Tp = hydridotris(pyrazolyl)borate} suggest opportunities for the development of new catalytic cycles for hydrocarbon functionalization In order to enhance understanding of these transformations, computational examinations of the efficacy of model d6 transition metal complexes of the form [(Tab)M(PH3)2X]q (Tab = tris-azo-borate; X = OH, NH2; q = -1 to +2; M = TcI, Re(I), Ru(II), Co(III), Ir(III), Ni(IV), Pt(IV)) for the activation of benzene C-H bonds, as well as the potential for their incorporation into catalytic functionalization cycles, are presented For the benzene C-H activation reaction steps, kite-shaped transition states were located and found to have relatively little metal-hydrogen interaction The C-H activation process is best described as a metal-mediated proton transfer in which the metal center and ligand X function as an activating electrophile and intramolecular base, respectively While the metal plays a primary role in controlling the kinetics and thermodynamics of the reaction coordinate for C-H activation/functionalization, the ligand X also influences the energetics On the basis of three thermodynamic criteria characterizing salient energetic aspects of the proposed catalytic cycle and the detailed computational studies reported herein, late transition metal complexes (eg, Pt, Co, etc) in the d6 electron configuration {especially the TabCo(PH3)2(OH)+ complex and related Co(III) systems} are predicted to be the most promising for further catalyst investigation
TL;DR: The results provide strong support for a model in which electrostatic interactions between the bimetallo Zn2+ site and a nonbridging phosphate ester oxygen atom make a significant contribution to the large rate enhancement observed for AP-catalyzed phosphate monoester hydrolysis.
Abstract: Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts, with the alterations presumably arising from interactions with active-site functional groups. In particular, the phosphate monoester hydrolysis reaction catalyzed by Escherichia coli alkaline phosphatase (AP) has been the subject of intensive scrutiny. Recent linear free energy relationship (LFER) studies suggest that AP catalyzes phosphate monoester hydrolysis through a loose transition state, similar to that in solution. To gain further insight into the nature of the transition state and active-site interactions, we have determined kinetic isotope effects (KIEs) for AP-catalyzed hydrolysis reactions with several phosphate monoester substrates. The LFER and KIE data together provide a consistent picture for the nature of the transition state for AP-catalyzed phosphate monoester hydrolysis and support previous models suggesting that the enzym...
TL;DR: In this paper, the authors used kinetic isotope effects (KIEs) to explore the origin of the 109-fold greater catalytic proficiency by AP for phosphate monoester hydrolysis relative to sulfate monoesters, showing that the lower charge density of this oxygen atom on a transferred sulfuryl group accounts for a large fraction of the decreased stabilization of the transition state for its reaction relative to phosphoryl transfer.
Abstract: The catalytic promiscuity of E. coli alkaline phosphatase (AP) and many other enzymes provides a unique opportunity to dissect the origin of enzymatic rate enhancements via a comparative approach. Here, we use kinetic isotope effects (KIEs) to explore the origin of the 109-fold greater catalytic proficiency by AP for phosphate monoester hydrolysis relative to sulfate monoester hydrolysis. The primary 18O KIEs for the leaving group oxygen atoms in the AP-catalyzed hydrolysis of p-nitrophenyl phosphate (pNPP) and p-nitrophenylsulfate (pNPS) decrease relative to the values observed for nonenzymatic hydrolysis reactions. Prior linear free energy relationship results suggest that the transition states for AP-catalyzed reactions of phosphate and sulfate esters are "loose" and indistinguishable from that in solution, suggesting that the decreased primary KIEs do not reflect a change in the nature of the transition state but rather a strong interaction of the leaving group oxygen atom with an active site Zn2+ ion. Furthermore, the primary KIEs for the two reactions are identical within error, suggesting that the differential catalysis of these reactions cannot be attributed to differential stabilization of the leaving group. In contrast, AP perturbs the KIE for the nonbridging oxygen atoms in the reaction of pNPP but not pNPS, suggesting a differential interaction with the transferred group in the transition state. These and prior results are consistent with a strong electrostatic interaction between the active site bimetallo Zn2+ cluster and one of the nonbridging oxygen atoms on the transferred group. We suggest that the lower charge density of this oxygen atom on a transferred sulfuryl group accounts for a large fraction of the decreased stabilization of the transition state for its reaction relative to phosphoryl transfer.
01 Jan 2007
TL;DR: In this paper, the authors investigated the kinetics of pyrolysis and oxidation of a simple naphthene, namely cyclo-hexane, through detailed kinetic modeling.
Abstract: Naphthenes are chemical species that are always present in liquid hydrocarbon fuels and their pyrolysis and oxidation can play an important role in real liquid fuel combustion. In spite of its practical relevance, the chemical kinetics of naphthene pyrolysis and oxidation is not yet thoroughly investigated and there is not a general agreement on the role and rate of several elementary reactions involved. In this paper, the kinetics of the pyrolysis and oxidation of a simple naphthene, namely cyclo -hexane, has been investigated through detailed kinetic modeling. Ab initio calculations were performed to estimate the kinetic parameters of some primary reactions following the oxygen attack to the cyclo -hexane radical. In fact, due to the complex behavior induced by the ring structure of cyclo -hexane, such data were difficult to determine through thermo-chemical methods. Density functional theory (B3LYP/6-31g(d, p)) was adopted to determine structure and vibrational frequencies of transition states and reaction intermediates, while energies were evaluated using the G2MP2 approach. The kinetic parameters of the investigated primary reactions were then introduced in a general detailed kinetic model consisting of elementary reactions whose kinetic constants were taken from the literature. The so obtained kinetic model was used to simulate ignition delay times and species concentrations measured in various experiments reported in the literature. The agreement between experimental data and theoretical predictions shows the validity of the chosen approach and supports the correctness of the proposed kinetic model.
TL;DR: The reactions of cyclopentadiene with α-keto-β,γ-unsaturated phosphonates or with nitroalkenes proceed through an unsymmetrical bis-pericyclic transition state to give both Diels−Alder and hetero-Diels+Alder cycloadducts.
Abstract: The reactions of cyclopentadiene with α-keto-β,γ-unsaturated phosphonates or with nitroalkenes proceed through an unsymmetrical bis-pericyclic transition state to give both Diels−Alder and hetero-Diels−Alder cycloadducts. The change in periselectivity of the Lewis acid catalyzed reactions can be qualitatively rationalized by the change in the potential energy surface (PES) landscapes, which ultimately affects the branching ratio of these bis-pericyclic reactions.
TL;DR: The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods and the participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways.
Abstract: The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.
TL;DR: The development of a new synthetic approach to acrylates based on the formation of alkyl esters of acrylic acids with fast elimination of acrylate is studied.
Abstract: The development of a new synthetic approach to acrylates based on the formation of alkyl esters of acrylic acids has been studied. A preformed Pd-COOMe moiety is used as a model system to investigate the insertion of an olefin into the Pd--C bond. The fast elimination of acrylate is observed. Density functional calculations support the experimental findings and allow the characterization of transition states along the reaction pathway. The first example of olefin/CO(2) coupling with facile release of ethyl acrylate is also presented.
TL;DR: It is reported that oxidative cleavage reactions can be used to form oxocarbenium ions that react with pendent epoxides to form bicyclic epoxonium ions as an entry to the formation of cyclic oligoether compounds.
Abstract: In this manuscript we report that oxidative cleavage reactions can be used to form oxocarbenium ions that react with pendent epoxides to form bicyclic epoxonium ions as an entry to the formation of cyclic oligoether compounds. Bicyclic epoxonium ion structure was shown to have a dramatic impact on the ratio of exo- to endo-cyclization reactions, with bicyclo[4.1.0] intermediates showing a strong preference for endo-closures and bicyclo[3.1.0] intermediates showing a preference for exo-closures. Computational studies on the structures and energetics of the transition states using the B3LYP/6-31G(d) method provide substantial insight into the origins of this selectivity.
TL;DR: Analysis of the transition state geometries revealed that the structural rigidity of catalysts, improved transition state organization as well as other weak interactions influence the relative stabilities of diastereomeric transition states and help contribute to the overall stereoselectivity in the aldol reaction.
Abstract: Density functional theory has been employed in investigating the efficiency of a series of bicyclic analogues of proline as stereoselective organocatalysts for the aldol reaction. Three classes of conformationally restricted proline analogues, as part of either a [2.2.1] or [2.1.1] bicyclic framework, have been studied. Transition states for the stereoselective C–C bond formation between enamines derived from [2.2.1] and [2.1.1] bicyclic amino acids and p-nitrobenzaldehyde, leading to enantiomeric products, have been identified. Analysis of the transition state geometries revealed that the structural rigidity of catalysts, improved transition state organization as well as other weak interactions influence the relative stabilities of diastereomeric transition states and help contribute to the overall stereoselectivity in the aldol reaction. These bicyclic catalysts are predicted to be substantially more effective in improving the enantiomeric excess than the widely used organocatalyst proline. Enantiomeric excesses in the range 82–95% are predicted for these bicyclic catalysts when a sterically unbiased substrate such as p-nitrobenzaldehyde is employed for the asymmetric aldol reaction. More interestingly, introduction of substituents, as simple as a methyl group, at the ortho position of the aryl aldehyde bring about an increase in the enantiomeric excess to values greater than 98%. The reasons behind the vital energy separation between diastereomeric transition states has been rationalized with the help of a number of weak interactions such as intramolecular hydrogen bonding and Coulombic interactions operating on the transition states. These predictions could have wider implications for the rational design of improved organocatalysts for stereoselective carbon–carbon bond-forming reactions.
TL;DR: The accurate QCISD(T) computations predict that for the model system considered, the Dissociative trans pathway is favored over the dissociative cis pathway and also over the associative reaction mechanism.
Abstract: The accurate quantum mechanical description of homogeneous catalysis involving transition-metal complexes is a complicated and computationally demanding task. Hence, in this study the performance of different quantum chemical approaches with respect to the ruthenium catalyzed olefin metathesis of ethylene and RuCl2(PH3)2CH2 as a model system is investigated. All intermediates and transition states that are relevant for the rate determining steps of competing reaction mechanisms (associative and two dissociative pathways) are considered. Results from density functional theory calculations employing B-P86, B97-D, B3-LYP, TPSSh, and B2-PLYP functionals, as well as from MP2 and SCS-MP2 perturbation theory are compared to reference values (relative and reaction energies) obtained at the QCISD(T) level of theory. In particular, the applicability of AO basis sets of increasing size ranging from double-ζ to quadruple-ζ quality is evaluated for representative methods. For some reaction steps, large basis set effects on the order of 10 kcal mol−1 (50% of Δ E) are observed. Double-ζ type basis sets yield very unreliable results while properly polarized triple-ζ sets provide reaction energies quite close to the basis set limit. The performance of recommended methods is B2-PLYP>TPSSh>B-86≈B97-D>SCS-MP2. The often used standard approaches B3-LYP and MP2 provide overall the largest errors. The accurate QCISD(T) computations predict in conclusion (and in agreement with a recent other study) that for the model system considered, the dissociative trans pathway is favored over the dissociative cis pathway and also over the associative reaction mechanism. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
TL;DR: In this paper, a diamine, di(3-methylpiperidine)methane (B), has been found with a higher catalytic activity than DMAN despite its lower proton affinity, demonstrating that both steric ability to abstract the protons and ability to return the proton to the oxoanion intermediate are important in explaining the catalytic results.
TL;DR: In this article, a combination of the DFT method with the computational description of environmental effects by solvent was applied to a theoretical study of the hydrogen transfer to imines by [2,3,4,5-Ph4(η5-C4COH)Ru(CO)2H] within a molecular model that closely mimics the authentic reaction conditions.
TL;DR: It is shown that the cation and protic solvent, each of which has been considered to retard the SN2 reactivity of the nucleophile, can accelerate the reaction tremendously when they interact with the fluoride ion in an intricate, combined fashion.
Abstract: We study the effects of protic solvent (water, methanol, ethanol, and tert-butyl alcohol) and cation (Na+, K+, Cs+) on the unsymmetrical SN2 reaction X- + RY → RX + Y- (X = F, Br; R = CH3,C3H7;Y = Cl, OMs). We describe a series of calculations for the SN2 reaction mechanism under the influence of cation and protic solvent, presenting the structures of pre- and postreaction complexes and transition states and the magnitude of the activation barrier. An interesting mechanism is proposed, in which the protic solvent molecules that are shielded from the nucleophile by the intervening cation act as a Lewis base to reduce the unfavorable Coulombic influence of the cation on the nucleophile. We predict that the reaction barrier for the SN2 reaction is significantly lowered by the cooperative effects of cation and protic solvent. We show that the cation and protic solvent, each of which has been considered to retard the SN2 reactivity of the nucleophile, can accelerate the reaction tremendously when they interact...
TL;DR: A novel, yet simple, method to quantify both aromatic and antiaromatic qualities on the same linear scale, by using the experimentally measured or theoretically computed enthalpy of hydrogenation reaction of the compound examined.
Abstract: Chemical structures and transition states are often influenced by aromatic stabilization or antiaromatic destabilizing effects, which are not easy to characterize theoretically The exact description and precise quantification of the aromatic characteristics of ring structures is difficult and requires special theoretical investigation The present paper suggests a novel, yet simple, method to quantify both aromatic and antiaromatic qualities on the same linear scale, by using the experimentally measured or theoretically computed enthalpy of hydrogenation reaction of the compound examined [ΔHH2(examined)] A reference hydrogenation reaction is also considered on a corresponding nonaromatic reference compound [ΔHH2(reference)] to cancel all secondary structure destabilization factors, such as ring strain or double bond strain From these data the relative enthalpy of hydrogenation may easily be calculated: ΔΔHH2 = ΔHH2(examined) − ΔHH2(reference) In the present work concept, the ΔΔHH2 value of benzene de
TL;DR: Clearly, a bridging hydroxide is not an optimal linker to promote cooperative catalysis between Eu(III) centers in macrocycles with multiple polyaminocarboxylate pendent groups.
Abstract: The complex between Eu(III) and 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N‘-diacetic acid (L4) was characterized by pH potentiometric titration and 1H NMR spectroscopy. The conversion of the monomer to a dimeric complex is observed as the pH is increased from 7 to 10 in a reaction that releases one mol/HO- per dimer formed. The dimeric complex undergoes a further ionization with a pKa of 10.7. Kinetic parameters are reported for the cleavage of the simple phosphodiester 2-hydroxypropyl-4-nitrophenyl phosphate catalyzed by both the monomeric and the dimeric Eu(III) complexes. These data show that the monomer and dimer stabilize their bound reaction transition states with similar free energies of 7.1 and 7.6 kcal/mol, respectively. Clearly, a bridging hydroxide is not an optimal linker to promote cooperative catalysis between Eu(III) centers in macrocycles with multiple polyaminocarboxylate pendent groups.
TL;DR: The kinetics for the previously proposed 114-reaction mechanism for the chemical vapor deposition (CVD) process that leads from methyltrichlorosilane (MTS) to silicon carbide (SiC) are examined and 41 reactions are predicted to proceed with no intervening barrier.
Abstract: The kinetics for the previously proposed 114-reaction mechanism for the chemical vapor deposition (CVD) process that leads from methyltrichlorosilane (MTS) to silicon carbide (SiC) are examined. Among the 114 reactions, 41 are predicted to proceed with no intervening barrier. For the remaining 73 reactions, transition states and their corresponding barrier heights have been explored using second-order perturbation theory (MP2) with the aug-cc-pVDZ basis set. Final energies for the reaction barriers were obtained using both MP2 with the aug-cc-pVTZ basis set and coupled cluster theory (CCSD(T)) with the aug-cc-pVDZ basis set. CCSD(T)/aug-cc-pVTZ energies were estimated by assuming additivity of basis set and correlation effects. Partition functions for the computation of thermodynamic properties of the transition states were calculated with MP2/aug-cc-pVDZ. Forward and reverse Gibbs free energy barriers were obtained at 11 temperatures ranging from 0 to 2000 K. Important reaction pathways are illustrated at 0 and 1400 K.