Unimolecular Reaction Mechanism Research Articles

Copper(I) activation of C-X bonds: bimolecular vs. unimolecular reaction mechanism.

Experimental kinetic studies and DFT calculations show that the oxidative addition of aryl halides (Ar-X) to complexes [Cu(NHC)R] follow different paths depending on the nature of X. For X = Br a concerted addition leads to cis-[Cu(NHC)XRAr] from which the usual C-C coupled product Ar-R eliminates. However, for X = I trans-[Cu(NHC)IRAr] is formed instead, leading to the elimination of R-I in a metathesis reaction. This behaviour is accounted for by a change in the reaction mechanism for Ar-I, which involves two molecules of copper(I) complex, the second one stabilising the incipient iodide formed in the C-I breaking (oxidative addition) and C-I forming (reductive elimination) processes.

Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family.

The first S-adenosyl methionine (SAM) degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as a SAM hydrolase forming 5'-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha-beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography, and nuclear magnetic resonance spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis and in vitro and in vivo mutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.

Computational Study on the Kinetics and Mechanisms of Unimolecular Reactions of (Z)-(Z)-N-(λ5-phosphanylidene) Formohydrazonic Formic Anhydride: Intramolecular aza-Wittig Reaction in Competition with Mumm Rearrangement

For (Z)-(Z)-N-(λ5-phosphanylidene) formohydrazonic formic anhydride, Aza-Wittig reaction and Mumm rearrangement are studied using both density functional and coupled cluster theories. For this purpose, two different products starting from one substrate are considered that are competing with each other. The obtained products, P1 and P2, are thermodynamically favorable. The product of the aza-Wittig reaction, P1, is more stable than the product of Mumm rearrangement (P2). For the mentioned products, just one reliable pathway is separately proposed based on unimolecular reaction. Therefore, the rate constants based on RRKM theory in 300-600 K temperature range are calculated. Results show that the P1 generation pathway is a suitable path due to low energy barriers than the path P2. The first path has three steps with three transition states, TS1, TS2, and TS3. The P2 production path is a single-step reaction. In CCSD level, the computed barrier energies are 14.55, 2.196, and 10.67 kcal/mol for Aza-Wittig reaction and 42.41 kcal/mol for Mumm rearrangement in comparison with the corresponding complexes or reactants. For final products, the results of the computational study are in a good agreement with experimental predictions.

A Density Functional Theory Study on the Acid‐Catalyzed Transesterification Mechanism for Biodiesel Production from Waste Cooking Oils

AbstractThe acid‐catalyzed transesterification reaction has been one of the most effective methods to produce biodiesel, especially from waste cooking oils (WCO) with high contents of water and free fatty acids (FFA). However, in the acid‐catalyzed processes, the H+ action mechanism and the controlling step of the reaction rate have been ambiguous. To clearly understand the reaction process, the DMol3 module based on the density functional theory (DFT) was employed to investigate the acid (H+‐)‐catalyzed transesterification mechanism of methanol and oleic acid monoacylglycerol (OAM). The one step transesterification without a catalyst and the feasible paths of SN2 (substitution nucleophilic bimolecular) and SN1 (substitution nucleophilic unimolecular) reaction mechanisms with H+‐based catalysts were built as Path 1, Path 2, and Path 3, respectively. The calculated structures, thermodynamic, and kinetic data revealed that the H+‐based catalysts could effectively reduce the activation energy for the transesterification reaction, and the Path 2 based on the SN2 reaction mechanism was the optimal reaction path. A tetrahedral intermediate (IM2‐2) could be generated with the highest active energy of 15.383 kcal mol−1, implying that there was the most stable structure of IM2‐2 as the key species in the transesterification process. Hence, the increasing decomposition rate of IM2‐2 accelerated the forward reaction in H+‐based biodiesel processes. The calculated active energy of 15.383 kcal mol−1 was in good agreement with the kinetic data for the monoacylglycerol transesterification of 15.067 kcal mol−1. Our calculations should provide basic and reliable theoretical data for further understanding the mechanism of transesterification of WCO to biodiesel products in the future work.

Tunneling Reaction Kinetics for the Hydrogen Abstraction Reaction H + H2S → H2 + HS in the Interstellar Medium.

The hydrogen abstraction reaction between H and H2S, yielding HS and H2 as products, has been studied within the framework of interstellar surface chemistry. High-temperature rate constants below 2000 K are calculated in the gas phase and are in agreement with previously reported values. Subsequently, low-temperature rate constants down to 55 K are presented for the first time that are of interest to astrochemistry, i.e., covering both bimolecular and unimolecular reaction mechanisms. For this, a so-called implicit surface model is used. In strict terms, this is a structural gas-phase model in which the restriction of the rotation in the solid state is taken into account. The calculated kinetic isotope effects are explained in terms of the difference in activation and delocalization. All rate constants are calculated at the UCCSD(T)-F12/cc-VTZ-F12 level of theory. Finally, we show that the energetics of the reaction is affected to an only small extent by the presence of H2O or H2S molecular clusters that simulate an ice surface, calculated at the MPWB1K/def2-TZVP level of theory.

The stability of the double amino acid against decarboxylation in gas and aqueous phases

The double amino acid (DAA) molecule ((NH2)2C(COOH)2) whose existence was recently proposed is investigated regarding its stability against the unimolecular decarboxylation process in both gas and aqueous phases. The results of the ab initio CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ calculations indicate that the spontaneous detachment of carbon dioxide from DAA molecule (regardless of the reaction path chosen) should not be considered as operative despite the fact that the decarboxylation process leading to the most stable products is expected to be thermodynamically slightly favorable (by less than 2 kcal/mol in both gas and aqueous phases). The adequate unimolecular reaction mechanisms of the possible DAA decarboxylation processes are presented and discussed.

Identification of the Final Two Genes Functioning in Methanofuran Biosynthesis in Methanocaldococcus jannaschii.

All methanofuran structural variants contain a basic core structure of 4-[N-(γ-l-glutamyl)-p-(β-aminoethyl)phenoxymethyl]-(aminomethyl)furan (APMF-Glu) but have different side chains depending on the source organism. Recently, we identified four genes (MfnA, MfnB, MfnC, and MfnD) that are responsible for the biosynthesis of the methanofuran precursor γ-glutamyltyramine and 5-(aminomethyl)-3-furanmethanol-phosphate (F1-P) from tyrosine, glutamate, glyceraldehyde-3-P, and alanine in Methanocaldococcus jannaschii. How γ-glutamyltyramine and F1-P couple together to form the core structure of methanofuran was previously unknown. Here, we report the identification of two enzymes encoded by the genes mj0458 and mj0840 that catalyze the formation of F1-PP from ATP and F1-P and the condensation of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. We have annotated these enzymes as MfnE and MfnF, respectively, representing the fifth and sixth enzymes in the methanofuran biosynthetic pathway to be identified. Although MfnE was previously reported as an archaeal adenylate kinase, our present results show that MfnE is a promiscuous enzyme and that its possible physiological role is to produce F1-PP. Unlike other enzymes catalyzing coupling reactions involving pyrophosphate as the leaving group, MfnF exhibits a distinctive α/β two-layer sandwich structure. By comparing MfnF with thiamine synthase and dihydropteroate synthase, a substitution nucleophilic unimolecular (SN-1) reaction mechanism is proposed for MfnF. With the identification of MfnE and MfnF, the biosynthetic pathway for the methanofuran core structure APMF-Glu is complete. This work describes the identification of the final two enzymes responsible for catalyzing the biosynthesis of the core structure of methanofuran. The gene products of mj0458 and mj0840 catalyze the formation of F1-PP and the coupling of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. Although the chemistry of such a coupling reaction is widespread in biochemistry, we provide here the first evidence that such a mechanism is used in methanofuran biosynthesis. MfnF belongs to the hydantoinase A family (PF01968) and exhibits a unique α/β two-layer sandwich structure that is different from the enzymes catalyzing similar reactions. Our results show that MfnF catalyzes the formation of an ether bond during methanofuran biosynthesis. Therefore, this work further expands the functionality of this enzyme family.

Kinetics of Decomposition and Isomerization of Methylcyclohexane: Starting Point for Studying Monoalkylated Cyclohexanes Combustion

Monoalkylated cyclohexanes are one of the typical constituents existing in practical fuels, especially in jet fuel. As the first step to study the combustion chemistry of monoalkylated cyclohexanes, the unimolecular reactions of methylcyclohexane (MCH) were investigated by combined theoretical calculations and experimental measurements for MCH pyrolysis and flames in the present work. The temperature- and pressure-dependent kinetics of unimolecular reactions of MCH including its dissociation and isomerization channels were computed by high-level quantum chemical calculations and Rice–Ramsperger–Kassel–Marcus/master equation simulations, which also reveal the competition relationship between the two channels. The theoretical predictions were examined by the experimental observations including species identification measured by photoionization efficiency spectra. The presented unimolecular reaction mechanism and corresponding temperature- and pressure-dependent rate constants provide a useful reference for further exploring combustion chemistry of cyclohexanes by kinetic modeling.

Theoretic studies on the kinetics and mechanism of multi-channel gas-phase unimolecular reactions of 1-chloropropane and 2-chloropropane

The potential energy surfaces of the gas-phase unimolecular decomposition reactions of 1-chloropropane and 2-chloropropane are investigated by various quantum chemical methods including CCSD(T), CCSD, GBS-QB3, C3B3, MP4, MP2, and B3LYP. Modified strong collision/RRKM theory was used to calculate the unimolecular rate constants as a function of pressure and temperature. It is found that the major reaction pathway is the HCl elimination. It is predicted that bond dissociation reactions have negligible contribution to the overall rate constant. The computed rate constants are compared with the available experimental data.

Effect of S Replacement on the Mechanism of Unimolecular Reactions for Ground‐state Thioacetic Acid: A Theoretical Study

AbstractThe potential energy surfaces of nine molecular reactions for the ground‐state CH3C(O)SH and CH3C(S)OH have been investigated with a B3LYP method in conjugation with 6‐31G∗︁∗︁, cc‐pVDZ, aug‐cc‐pVDZ, and cc‐pVTZ basis sets. The present calculations predict that thioacetic acid mainly exists as a CH3C(O)SH tautomer, and both tautomers predominately adopt syn conformations, which reproduces the experimental observations. By comparison of the reactivity difference among CH3C(O)SH, CH3C(S)OH, and CH3C(O)OH, it can be concluded that the replacement of atom O by S in –OH group of CH3C(O)OH has a big effect on the molecular decompositions only when –SH takes part in the reaction as one group, while the CO or CS group has minor contribution to the reactivity difference.

Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of E(a) = 79.7 kcal/mol and log A/s(-1) = 14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.

Influence of spatial distribution of active centers on the kinetics of model heterogeneous catalytic processes

The kinetics of two model catalytic processes, one with a unimolecular and the other with a bimolecular Langmuir–Hinshelwood surface reaction mechanism was investigated using dynamic Monte Carlo simulations. The catalytic processes proceeded on the surfaces with heterogeneous surface centers and the influence of the arrangement of the centers active in the surface reaction on dynamics of processes was considered. The conditions in which the spatial distribution of active centers is important were found qualitatively and among them the surface diffusion of reactant particles with a rate comparable with other processes was the most important. The influence of the arrangement of active centers on the ratio of the two model processes was investigated and explained. In the case of the unimolecular surface reaction mechanism, increasing the ordering in the arrangement of active centers decreased turnover number. In the systems with the bimolecular reaction mechanism the highest turnover number values were observed for the surfaces with moderate order in the arrangement of active centers. The mean fraction of active centers neighboring an average active center n A–A was proposed as a measure of the order of active centers arrangement.

A New Formulation of the Lindemann Mechanism of Unimolecular Reactions

AbstractA new formulation of the Lindemann mechanism of unimolecular reactions in gaseous phase is presented, without the use of steady state hypothesis. It is hereby shown that the nature of applicability of steady state hypothesis in the regime of high reactant gas pressure is different from that in the regime of low gas pressure. In the former case it is an equilibrium approximation, while in the latter case it is a highly reactive intermediate approximation in no connection with a steady state. Furthermore for the latter case it is shown that in the classical formulation of Lindemann mechanism the use of steady state hypothesis is an ad hoc assumption. A highly reactive intermediate in the sense that its concentration is very small during the whole course of reaction is a necessary condition for the applicability of very reactive intermediate approximation. When the two distinctive nature of the applicability of steady state hypothesis is mixed‐up, wrong or useless conclusion may be arrived at. The only possible case of realizing a true steady state in a complex reaction is pointed out.

B3LYP and CCSD(T) Studies of the Mechanisms of Unimolecular Reactions of HXCS (X = H and F)

The potential energy surface for the decomposition of singlet HXCS (X = H and F) has been explored by B3LYP and CCSD(T) calculations. Five different types of reaction are proposed: (A) 1,1-HX elimination, (B) 1,2-H shift, (C) 1,2-X shift, (D) H• and XCS• radical formation, and (E) X• and HCS• radical formation. These results show interesting trends for the HXCS isomers. Our theoretical investigations suggest that the doubly bonded species HXCS is the lowest energy structure among the isomers from both kinetic and thermodynamic viewpoints. We also report theoretical predictions of molecular parameters and vibrational IR spectra of the monohalogen substituted thioformaldehyde, which should be useful for future experimental observations.

Formation of (SiN2SiC) Five-Membered Rings by Intramolecular Insertion into the Si−N Bond: A Quantum Chemical Study

The formation of the diazadisilacyclopentane 2 in a ring expansion reaction is the first example of an SiR2CH2 insertion into the nitrogen-silicon single-bond accompanied by migration of a hydrogen atom from a carbon to a nitrogen atom [J. Organomet. Chem. 1994, 482, 285]. Density functional calculations support the experimental findings and suggest a reaction mechanism which includes two four-center transition states and an intermediate silahydrazone (3b). The reaction enthalpy ∆RH° (298 K) of the isomerization reaction converting the three-membered ring (Me3SiN)2SiH2 (1b) into the diazadisilacyclopentane Me2Si(NHNSiMe3CH2)SiH2 (2b) is calculated to be -23 kcal mol-1. Another intermediate of the system shows an unexpected electronic structure with a lone electron pair at the SiH2 silicon atom. The transition states and the unimolecular reaction mechanism are discussed in detail. The calculated geometry for the product 2b is in very good agreement with X-ray structure data.

The role of nucleophile--electrophile interactions in the unimolecular and bimolecular gas-phase ion chemistry of peptides and related systems.

This account describes the experimental tools (multi-stage mass spectrometric experiments, isotopic and structural labelling, kinetics and theoretical modelling) and physical organic concepts (influence of charge, the intermediacy of ion-molecule complexes, etc.) that can be used to unravel the mechanisms of gas-phase unimolecular and bimolecular ionic reactions of peptides. The role that nucleophile-electrophile interactions play in charge-directed reactions is highlighted for both unimolecular fragmentations (examples are illustrated for protonated sulfur-containing amino acids and peptides) and bimolecular ion-molecule reactions which cleave peptide bonds.

Density functional studies on the mechanisms of unimolecular reactions of HXCSe (X=H, F, Cl, and Br)

Reaction pathways for the decomposition of HXCSe (X=H, F, Cl, and Br) on the singlet state potential energy surface have been studied using the B3LYP/6-311G* level of theory. Predicted molecular parameters (equilibrium geometries, dipole moments, atomic charges, and rotational constants) and vibrational IR spectra agree very well with the available experimental data. Five different reaction mechanisms are proposed: (A) 1,1-HX elimination, (B) 1,2-H shift, (C) 1,2-X shift, (D) H and XCSe radical formation, and (E) X and HCSe radical formation. From a consideration of the effect of halogen substitution, the following conclusions emerge: our theoretical findings suggest that selenocarbonyl molecules should be both kinetically and thermodynamically stable with respect to the unimolecular decomposition reactions given above. We also report theoretical predictions of molecular parameters and vibrational IR spectra of some monohalogen substituted selenoformaldehydes, which should be useful for further experimental observations.

NO adsorption and dissociation on Co{1010}

Nitric oxide adsorption and dissociation on Co{101̄0} have been studied using reflection absorption infrared spectroscopy (RAIRS), low energy electron diffraction (LEED) and thermal programmed desorption (TPD). At 100 K, NO is found to absorb molecularly on the Co{101̄0} surface with an estimated 0.5 ML coverage at saturation. At low coverages, three adsorption sites, on-top, twofold and threefold, are occupied, while from moderate coverage to saturation, bridge-bonded NO becomes dominant. A sharp c(2×4) LEED pattern is observed at saturation, and a corresponding surface structure is proposed for the pattern. For all precoverages of NO, dissociation is complete on heating the surface, but the temperature at which dissociation occurs depends critically on NO coverage and on the presence of the dissociation products. TPD spectra indicate that no species other than N 2 desorbs below 630 K; c(2×6) and p(2×3) LEED patterns are observed after annealing to 600 K, and removal of O adatoms by H 2 shows that these are due to N adsorption. A first-order unimolecular reaction mechanism is proposed for NO dissociation on Co{101̄0}, with a strong dependence of the activation energy for surface dissociation on both NO coverage and the coverage of the dissociation products, N and O.

Ab initio and RRKM studies of the unimolecular reactions of CH2XCHFO (X=H, F) radicals

The unimolecular reaction mechanism of the CH2XCHFO (X = H, F) radicals was studied using the ab initio G2(MP2, SVP) theory. Three kinds of reaction pathways, namely bond scission, three-center elimination of HF and isomerization, were examined. Both the energy-specific rate constant [k(E)] and the thermal rate constant [k(T, P)] were evaluated using the RRKM theory and the ab initio data. These theoretical calculations support the proposal that the C–C bond scissions dominate the decomposition of CH2XCHFO (X = H, F). The major products of the unimolecular reactions should be CH2X and CHFO. Furthermore, it is concluded that the lifetimes of CH3CHFO and CH2FCHFO are both very short in the atmosphere.

The mechanism of energy transfer in H 2O–H 2O collisions – a molecular dynamics simulation

Earlier work on the activation-deactivation mechanism of gas phase unimolecular reactions is extended to the study of the detailed energy transfer mechanism in collisions of water molecules. Molecular dynamics simulations of binary collisions between a reactant water molecule at high internal energy with medium molecules at various selected initial temperatures are compared with results from approximate statistical theory. Energy transfer is related to (i) interaction strength, (ii) hard atom–atom encounters, (iii) multiple minima in the center of mass separation, (iv) collision lifetime and (v) anharmonicity of the intramolecular potential function. The observed trends are interpreted within the framework of the partially ergodic multiple encounter theory (PEMET) of collisional energy transfer. By comparison with typical stable molecule collisions the water–water collisions are more efficient as a reflection of the strong hydrogen bonding interactions. A good agreement between PEMET and molecular dynamics simulations over a wide range of interaction strengths and initial reactant energies is shown, indicating the possibility of a priori use of the PEMET model.