Concerted Reaction Mechanism Research Articles

Lowering Energy Barriers in Surface Reactions through Concerted Reaction Mechanisms

Any technologically important chemical reaction typically involves a number of different elementary reaction steps consisting of bond-breaking and bond-making processes. Usually, one assumes that such complex chemical reactions occur in a step-wise fashion where one single bond is made or broken at a time. Using first-principles calculations based on density functional theory we show that the barriers of rate-limiting steps for technologically relevant surface reactions are significantly reduced if concerted reaction mechanisms are taken into account.

Unraveling the Reactions that Unravel Cellulose

For over 90 years, researchers have postulated mechanisms for the cleavage of cellulose's glycosidic bonds and resulting formation of levoglucosan without reaching consensus. These reactions are key primary reactions in thermal processes for the production of carbon-neutral, renewable transportation fuels. Previous literature reports have proposed a variety of mainly heterolytic and homolytic mechanisms, but there has been insufficient evidence to settle the debate. Using density functional theory (DFT) methods and implicit solvent, we compared the likelihood of forming either radical or ionic intermediates. We discovered a concerted reaction mechanism that is more favorable than previously proposed mechanisms and is in better alignment with experimental findings. This new understanding of the mechanism of cellulose thermal decomposition opens the door to accurate process modeling and educated catalyst design, which are vital steps toward producing more cost-efficient renewable energy.

Influence of Acid Strength and Confinement Effect on the Ethylene Dimerization Reaction over Solid Acid Catalysts: A Theoretical Calculation Study

The influence of both Brønsted acid strength and pore confinement effect on the ethylene dimerization reaction has been systematically studied by density functional theory (DFT) calculations. In the theoretical calculations, both stepwise and concerted reaction mechanisms are considered. It is demonstrated that the reactivity of the ethylene dimerization reaction can be significantly enhanced by increasing acid strength no matter which mechanism is included, while on the basis of activated barriers, the concerted mechanism is preferred on weak acids and two mechanisms are competitive when the acid strength increases to a medium–strong acid. Due to the pore confinement effect that can effectively stabilize the ionic transition states of the dimerization reaction, the activity of the dimerization reaction is considerably improved inside the zeolite pore. Compared with the reaction on the isolated acid sites, the transition states of the stepwise reaction are more effectively stabilized than those of the concerted reaction inside the zeolite confined pore, resulting in the former reaction being preferred when the dimerization reaction occurs inside the zeolite confinement spaces. Additionally, on the basis of the systematic investigations on the alkene dimerization reactions over zeolites with varying pore sizes (such as ZSM-22, ZSM-5, and SSZ-13), it is demonstrated that ZSM-22 and ZSM-5 zeolites are effective catalysts for the ethylene dimerization.

Mechanism of the aerobic oxidation of methanol to formic acid on Au8−: A DFT study

AbstractThe mechanism of the aerobic oxidation of methanol to formic acid catalyzed by Au8− has been systematically investigated using density functional theory with the M06 functional. The reaction pathways were examined by taking into account the full structural relaxation of the Au8−. Stepwise and concerted reaction mechanisms are proposed. The stepwise mechanism is initiated by the hydrogen abstraction of a methoxy species by a superoxo‐like anion on the gold cluster, resulting in the formation of formaldehyde. Subsequently, the formaldehyde is activated by the hydroxyl group of a hydroperoxyl‐like complex, leading to the formation of a hemiacetal intermediate. The formation of formic acid in the final step is achieved by hydrogen abstraction of the hemiacetal intermediate by atomic oxygen attached to the gold cluster. Our calculations indicate that the first step of the stepwise mechanism, that is, hydrogen abstraction of the methoxy species, is the rate‐determining step. Another possible reaction pathway involving a single‐step hydrogen abstraction, a concerted mechanism, is also discussed. This mechanism may also be responsible for the reasonable catalytic activity of aerobic oxidation of methanol on Au8− because of the low activation energy barrier. © 2012 Wiley Periodicals, Inc.

Mechanism Insights of Ethane C–H Bond Activations by Bare [FeIII═O]+: Explicit Electronic Structure Analysis

Alkane C-H bond activation by various catalysts and enzymes has attracted considerable attention recently, but many issues are still unanswered. The conversion of ethane to ethanol and ethene by bare [Fe(III)═O](+) has been explored using density functional theory and coupled-cluster method comprehensively. Two possible reaction mechanisms are available for the entire reaction, the direct H-abstraction mechanism and the concerted mechanism. First, in the direct H-abstraction mechanism, a direct H-abstraction is encountered in the initial step, going through a collinear transition state C···H···O-Fe and then leading to the generation of an intermediate Fe-OH bound to the alkyl radical weakly. The final product of the direct H-abstraction mechanism is ethanol, which is produced by the hydroxyl group back transfer to the carbon radical. Second, in the concerted reaction mechanism, the H-abstraction process is characterized via overcoming four/five-centered transition states (6/4)TSH_c5 or (4)TSH_c4. The second step of the concerted mechanism can lead to either product ethanol or ethene. Moreover, the major product ethene can be obtained through two different pathways, the one-step pathway and the stepwise pathway. It is the first report that the former pathway starting from (6/4)IM_c to the product can be better described as a proton-coupled electron transfer (PCET). It plays an important role in the product ethene generation according to the CCSD(T) results. The spin-orbital coupling (SOC) calculations demonstrate that the title reaction should proceed via a two-state reactivity (TSR) pattern and that the spin-forbidden transition could slightly lower the rate-determining energy barrier height. This thorough theoretical study, especially the explicit electronic structure analysis, may provide important clues for understanding and studying the C-H bond activation promoted by iron-based artificial catalysts.

C and N Isotope Fractionation during Biodegradation of the Pesticide Metabolite 2,6-Dichlorobenzamide (BAM): Potential for Environmental Assessments

2,6-Dichlorobenzamide (BAM) is a metabolite of the herbicide 2,6-dichlorobenzonitrile (dichlobenil), and a prominent groundwater contaminant. Observable compound-specific isotope fractionation during BAM formation-through transformation of dichlobenil by Rhodococcus erythropolis DSM 9685-was small. In contrast, isotope fractionation during BAM degradation-with Aminobacter sp. MSH1 and ASI1, the only known bacterial strains capable of mineralizing BAM-was large, with pronounced carbon (ε(C) = -7.5‰ to -7.8‰) and nitrogen (ε(N) = -10.7‰ to -13.5‰) isotopic enrichment factors. BAM isotope values in natural samples are therefore expected to be dominated by the effects of its degradation rather than formation. Dual isotope slopes Δ (=Δδ(15)N/Δδ(13)C ≈ ε(N)/ε(C)) showed only small differences for MSH1 (1.75 ± 0.03) and ASI1 (1.45 ± 0.03) suggesting similar transformation mechanisms of BAM hydrolysis. Observations are in agreement with either a tetrahedral intermediate promoted by OH(-) or H(3)O(+) catalysis, or a concerted reaction mechanism. Therefore, owing to consistent carbon isotopic fractionation, isotope shifts of BAM can be linked to BAM biodegradation, and may even be used to quantify degradation of this persistent metabolite. In contrast, nitrogen isotope values may be rather indicative of different sources. Our results delineate a new approach to assessing the fate of BAM in the environment.

Investigation of reaction mechanisms of NO with CO on Pd1/MgO and Pd4/MgO catalysts

The stepwise and concerted reaction mechanisms of NO with CO on Pd1 atom and Pd4 cluster adsorbed on the MgO surface have been studied by using the DFT/B3LYP method with the embedded cluster model. The reaction barriers have been calculated by using the IMOMO method at the CCSD level. The results suggest that the rate-controlling step barrier of the NO dissociation on the supported Pd4 cluster for the stepwise reaction mechanism is about 57kcal/mol and lower by about 33kcal/mol than that on the single supported Pd atom. However, the concerted reaction pathways on the single supported Pd atom and four supported Pd atoms are energetically unfavorable with the barriers of about 98kcal/mol and 71kcal/mol, respectively. Compared to the concerted reaction mechanism, the stepwise reaction mechanism of NO+CO is a possible pathway of CO2 molecule formation on the supported Pd catalysts.

Products and Mechanism of Acene Dimerization. A Computational Study

The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso-carbon atoms of the central ring of acene blocks the reactivity of this ring but does not efficiently prevent dimerization through other rings.

Glycine Peptide Bond Formation Catalyzed by Faujasite

The catalysis of peptide bond formation between two glycine molecules on H-FAU zeolite was computationally studied by the M08-HX density functional. Two reaction pathways, the concerted and the stepwise mechanism, starting from three differently adsorbed reactants, amino-bound, carboxyl-bound, and hydroxyl-bound, are studied. Adsorption energies, activation energies, and reaction energies, as well as the corresponding intrinsic rate constants were calculated. A comparison of the computed energetics of the various reaction paths for glycine indicates that the catalyzed reaction proceeds preferentially via the concerted reaction mechanism of the hydroxyl-bound configuration. This involves an eight-membered ring of the transition structure instead of the four-membered ring of the others. The step from the amino-bound configuration to glycylglycine is the rate-determining step of the concerted mechanism. It has an estimated activation energy of 51.2 kcal mol(-1). Although the catalytic reaction can also occur via the stepwise reaction mechanism, this path is not favored.

Mechanism and Kinetics of the Reaction NO3+ C2H4

The reaction of NO(3) radical with C(2)H(4) was characterized using the B3LYP, MP2, B97-1, CCSD(T), and CBS-QB3 methods in combination with various basis sets, followed by statistical kinetic analyses and direct dynamics trajectory calculations to predict product distributions and thermal rate constants. The results show that the first step of the reaction is electrophilic addition of an O atom from NO(3) to an olefinic C atom from C(2)H(4) to form an open-chain adduct. A concerted addition reaction mechanism forming a five-membered ring intermediate was investigated, but is not supported by the highly accurate CCSD(T) level of theory. Master-equation calculations for tropospheric conditions predict that the collisionally stabilized NO(3)-C(2)H(4) free-radical adduct constitutes 80-90% of the reaction yield and the remaining products consist mostly of NO(2) and oxirane; the other products are produced in very minor yields. By empirically reducing the barrier height for the initial addition step by 1 kcal mol(-1) from that predicted at the CBS-QB3 level of theory and treating the torsional modes explicitly as one-dimensional hindered internal rotations (instead of harmonic oscillators), the computed thermal rate constants (including quantum tunneling) can be brought into very good agreement with the experimental data for the overall reaction rate constant.

Enantioselective organocatalytic diels–Alder reactions: A density functional theory and kinetic isotope effects study

The mechanism and enantioselectivity of the organocatalytic Diels-Alder reaction were computationally investigated by density functional theory at the B3LYP/6-31G(d) level of theory. The uncatalyzed Diels-Alder reaction was also studied to explore the effect of the organocatalyst on this reaction in terms of energetics, selectivity, and mechanism. The catalyzed reaction showed improved endo/exo selectivity, and the free energy of activation was significantly lowered in the presence of the catalyst. Both uncatalyzed and catalyzed reactions exhibited concerted asynchronous reaction mechanism with the degree of asynchronicity being more evident in the presence of the catalyst. The Corey's experimentally derived predictive selection rules for the outcome of the organocatalytic Diels-Alder reaction were also theoretically analyzed, and an excellent agreement was found between experiment and theory.

Direct Detection of Products from the Pyrolysis of 2-Phenethyl Phenyl Ether

The pyrolysis of 2-phenethyl phenyl ether (PPE, C(6)H(5)C(2)H(4)OC(6)H(5)) in a hyperthermal nozzle (300-1350 °C) was studied to determine the importance of concerted and homolytic unimolecular decomposition pathways. Short residence times (<100 μs) and low concentrations in this reactor allowed the direct detection of the initial reaction products from thermolysis. Reactants, radicals, and most products were detected with photoionization (10.5 eV) time-of-flight mass spectrometry (PIMS). Detection of phenoxy radical, cyclopentadienyl radical, benzyl radical, and benzene suggest the formation of product by the homolytic scission of the C(6)H(5)C(2)H(4)-OC(6)H(5) and C(6)H(5)CH(2)-CH(2)OC(6)H(5) bonds. The detection of phenol and styrene suggests decomposition by a concerted reaction mechanism. Phenyl ethyl ether (PEE, C(6)H(5)OC(2)H(5)) pyrolysis was also studied using PIMS and using cryogenic matrix-isolated infrared spectroscopy (matrix-IR). The results for PEE also indicate the presence of both homolytic bond breaking and concerted decomposition reactions. Quantum mechanical calculations using CBS-QB3 were conducted, and the results were used with transition state theory (TST) to estimate the rate constants for the different reaction pathways. The results are consistent with the experimental measurements and suggest that the concerted retro-ene and Maccoll reactions are dominant at low temperatures (below 1000 °C), whereas the contribution of the C(6)H(5)C(2)H(4)-OC(6)H(5) homolytic bond scission reaction increases at higher temperatures (above 1000 °C).

Multireference Character of 1,3-Dipolar Cycloaddition of Ozone with Ethylene and Acrylonitrile

In the present study, the concerted and stepwise reaction mechanisms for 1,3-dipole cycloaddition of ozone with ethylene (1) and acrylonitrile (2) are investigated. The stationary points are optimized by using four hybrid R(U)DFT methods. A geometry optimization method based on an approximate spin projection (AP-opt method) is applied to eliminate a spin contamination from the broken-symmetry (BS) solution. The AP-opt method reveals that a diradical intermediate for the stepwise pathway is spurious due to the spin contamination. The revised reaction profile with no diradical intermediate supports the stereospecificity. On the basis of the experimental data, the RCCSD(T) method outperforms AP-UCCSD(T), AP-UBD(T), and MkMRCCSD(4e,4o) for the systems, indicating that the RCCSD(T) method can describe the diradical character of ozone within a framework of single reference wave function. The subsequent single point energy calculations show that the highly synchronous transition state is much more favorable than the asynchronous one for 1. In the case of 2, there is not much difference between two transition states because of its asymmetric structure and charge separations in the transition states.

The Participation of 2H‐Pyran‐2‐ones in [4+2] Cycloadditions: An Experimental and Computational Study

AbstractExperimental and computational DFT studies of the Diels–Alder (DA) reaction mechanism for the series of 2H‐pyran‐2‐ones 1 and non‐symmetrically substituted alkynes 2, 10, and 11 were undertaken. Several 2H‐pyran‐2‐ones 1 were treated with N,N‐diethylpropynamine (2). The results point toward a polar and asynchronous two‐step mechanism that is in line with the characteristics of a polar Diels–Alder (P‐DA) reaction mechanism.5 Unexpected formation of minor products 4a–d during the reaction of 1 with 2 can be rationalized by considering the easily passable torsion barrier around the newly formed C–C bond that enables two different cyclization modes. The charge transfer (CT) and global reactivity indices analyses demonstrated that in these reactions 2H‐pyran‐2‐ones act as electrophiles and N,N‐diethylpropynamine (2) acts as a nucleophile reaction partner. The introduction of electron‐withdrawing carboxylic substituents on the dienophiles 10 and 11 shifts the DA reaction with 2H‐pyran‐2‐ones to a less polar and more synchronous concerted reaction mechanism. Calculated CT as well as values of the global electrophilicity and nucleophilicity N indexes revealed that 2H‐pyran‐2‐ones act in this case as nucleophiles and reacting dienophiles 10 and 11 as electrophiles. The results are consistent with the experimental data and kinetic analyses, thus providing valuable insights into 2H‐pyran‐2‐one chemistry and paving the way for an efficient synthesis of highly functionalized benzene derivatives as well as broadening the mechanistic understanding of these highly versatile reactions.

SOLVENT AND SUBSTITUENT EFFECTS ON THE INTRAMOLECULAR AMIDE HYDROLYSIS OF N-METHYLMALEAMIC ACID

Intramolecular amide hydrolysis of N-methylmaleamic acid is revisited at the B3LYP/6-311G(2df, p)//B3LYP/6-31G(d, p) + ZVPE level, including solvent effects at the CPCM-B3LYP/6-311G(2df, p)//Onsager-B3LYP/6-31G(d, p) + ZPVE level. The concerted reaction mechanism is energetically favorable over stepwise reaction mechanisms in both the gas phase and solution. The calculated reaction barriers are significantly lower in solution than in the gas phase. In addition, it is concluded that the substituents of the four N-methylmaleamic acid derivatives considered herein have a significant effect on the gas-phase reaction barriers but a smaller, or little, effect on the barriers in solution.

Stable Carbon Isotope Fractionation of 1,2-Dichloropropane during Dichloroelimination by Dehalococcoides Populations

The isotope fractionation of 1,2-dichloropropane (1,2-D) during dichloroelimination to propene by Dehalococcoides populations was explored in laboratory experiments in order to provide data for the characterization of the fate of 1,2-D in heterogeneous subsurface systems. Compound specific stable carbon isotope analysis (CSIA) was used to determine the bulk enrichment factors (epsilonbulk), reactive position specific enrichment factors (epsilonreactive), and apparent kinetic isotope effect (AKIE) values for 1,2-D dichloroelimination in two distinct Dehalococcoides-containing cultures. The epsilonbulk factors calculated in the two cultures were statistically identical, -10.8 +/- 0.9 and -11.3 +/- 0.8 per thousand, even though the cultures were derived from geographically distinct locations. AKIE values for 1,2-D dichloroelimination assuming stepwise and concerted reaction mechanisms were approximately 1.033 and 1.017, respectively. These values are within the range of previously reported values for dichloroelimination reactions and were equivalent to values reported for biotic 1,2-dichloroethane and abiotic 1,1,2,2,-tetrachloroethane and pentachloroethane dichloroelimination reactions.

Cr(CO)3‐Activated Diels–Alder Reaction on Single‐Wall Carbon Nanotubes: A DFT Investigation

Breaking barriers: In agreement with experimental evidence, it was found by means of high-level DFT calculations that the Cr(CO)(3) metal fragment considerably reduces the reaction energy barrier-for both the concerted and stepwise reaction mechanisms (see graphic)-of the Diels-Alder reaction of butadiene on (5,5) carbon nanotubes.The reaction mechanism and the effect of Cr(CO)(3) on the Diels-Alder reaction of butadiene on (5,5) carbon nanotube sidewalls have been investigated by high-level DFT calculations. We investigated both concerted and stepwise reaction pathways on closed-shell and open-shell potential-energy surfaces. In agreement with recent experimental evidence, we found the Cr(CO)(3) metal fragment to considerably reduce the reaction energy barrier, both for the concerted and stepwise reaction mechanisms. The latter mechanism, previously found to be higher in energy with traditional substrates, appears to compete with the concerted mechanism on the carbon nanotube sidewalls. An analysis of the frontier molecular orbitals on the pristine and Cr(CO)(3)-complexed carbon nanotubes allowed us to identify the reason for this inverted reactivity pattern and the role of the transition metal on the addition of the diene.

A DFT study on the (2 + 3) cycloaddition reactions of 2‐nitropropene‐1 with Z‐C, N‐diarylnitrones

AbstractB3LYP/6‐31G* calculations for competing (2 + 3)‐cycloaddition pathways for 2‐nitropropene‐1 (1) to Z‐C, N‐diarylnitrones (2a–e) suggest a concerted reaction mechanism. However, the results point to the strongly asymmetric nature of transition complexes. Increasing polarity of the reaction environment and presence of electron‐donating substituents in the nitrone phenyl rings contribute to the higher asymmetry of these structures. Copyright © 2009 John Wiley &amp; Sons, Ltd.

A direct dynamics study of protonated alcohol dehydration and the Diels-Alder reaction

The dynamics of dehydration of the protonated (R)-3,3-dimethylbutan-2-ol (pinacolyl alcohol), [(CH3)3C-CH(OH2)CH3]+, and of ethene + 1,3-butadiene cycloaddition were studied with the Born-Oppenheimer molecular dynamics (BOMD) technique for direct dynamics using the AM1 method. More than 10,000 trajectories were generated, most of them related to the unexplored simulated annealing/fragmentation approach. The AM1 potential energy surface (PES) for the protonated pinacolyl alcohol presents two transition states related to the [(CH3)3C-CHCH3]+hhhOH2 intermediate complex and to CH3 migration leading to the [(CH3)2C-CH(CH)3]2+hhhOH2 product complex. Direct dynamics yielded negligible trajectories involving these complexes, since the momentum acquired by the H2O fragment led to a complete dissociation. Thus, rearrangement of the secondary carbocation [(CH3)3C-CHCH3]+ was practically inexistent during the dynamics. Despite the concerted path (H2O dissociation and CH3 migration) not being an IRC (intrinsic reaction coordinate) path in AM1-PES, a statistically significant number of trajectories involved this path. As for the Diels-Alder reaction, even when started from a symmetric transition state using the spin restricted AM1 wavefunction, the dynamics yielded a significant number of trajectories that followed asymmetric, i.e.non-IRC, paths toward cyclohexene, independent of the initialization approach. It is noteworthy that all these asymmetric path trajectories led to a concerted reaction mechanism.

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations.

Sir2 enzymes catalyze the NAD+-dependent protein deacetylation and play critical roles in epigenetics, cell death, and lifespan regulation. In spite of a current flurry of experimental studies, the catalytic mechanism for this unique and important class of enzymes remains elusive. Employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized the initial step of the Sir2Tm-catalyzed reaction, which is also the most controversial portion of its mechanism. Our results indicate that the nicotinamide cleavage reaction employs a highly dissociative and concerted displacement mechanism: the cleavage of the glycosidic bond is facilitated by the nucleophilic participation of the acetyl-lysine, and the dissociative transition state has a significant oxocarbenium ion character. During this step of the reaction, the Sir2Tm enzyme strongly stabilizes the covalent O-alkylamidate intermediate whereas its effect on the transition state is quite minimal. In addition, functional roles of key residues and motifs have been elucidated. This work further demonstrates the feasibility and applicability of the state-of-the-art ab initio QM/MM molecular dynamics approach in simulating enzyme reactions.