Elementary Reaction Paths Research Articles

Desorption model of volatile Ru species induced by partial chlorination on Ru(0001) under an O2/Cl2-based plasma process

Ruthenium (Ru) is known to be effectively etched by O2-based plasma with a 10%–20% amount of Cl2, while it is less etched by pure O2-based or Cl2-rich plasma. In this work, reaction paths and energy profiles on a metallic Ru surface were calculated in density functional theory (DFT) simulations to reveal the chemical role of the small amount of Cl2 in the O2-based plasma for Ru etching. We prepared three Ru(0001) surfaces with (1 × 1) adatoms in which chemisorption sites were occupied by O and Cl adatoms. Subsequently, we assumed that convex Ru moieties, which are precursors to form volatile Ru species, were formed on the surface and that they were oxidized by the irradiation of O2-rich plasma. In each Ru(0001) surface, we calculated the production and activation energies of each elementary reaction path to desorb the volatile Ru products. Compared with the surface where all chemisorption sites were covered with O, both energies decreased in locations where some chemisorption sites were replaced by Cl. Our DFT-based research showed that a small amount of Cl2 in the O2/Cl2 plasma contributes to decreasing the production and activation energy to form volatile Ru products on the Ru surface, resulting in the etching rate being increased.

Construction of elementary reaction paths of pure and mixed Argon-Xenon clusters : a parallel tempering based study

The problem of studying structural transformation for going from one isomer to another through a transition state is one of considerable interest in chemistry. In this work, we would like to examine the efficiency of the replica exchange Monte Carlo strategy or parallel tempering to search potential energy surface describing the interaction between atoms in noble gas clusters. The systems chosen are both a pure noble gas cluster as well as those formed by two different noble gas entities. Location of minimal structures as well as transition state with the path connecting these three critical points has been carried out for different sizes. To understand the working principles of the parallel tempering method, distribution of structures found in different replicas has been analyzed and insights have been given as to how parallel tempering can be use effectively to handle this problem effectively.

Investigation on the decomposition process of sodium aluminate solution by spectroscopic and theoretical calculation

This study focused on the determination of intermediate (6AlO-OH) structure and its elementary reaction path design during the decomposition process of sodium aluminate solution by combining experimental and theoretical approach. The molecular structure, Raman spectra, UV–Vis spectra, frontier molecular orbitals and molecular electrostatic potential of Al(OH)4−,[(HO)2−Al−O2−Al−(OH)2]2−, [(HO)2−Al−O2−Al−(HO)2−Al−O2−Al−OH)2]2−, 6AlO−OH were characterized by density functional theory calculation. The calculated Raman and UV–Vis spectra of 6AlO-OH agreed with experiments results, which showed that the supposed structure of 6AlO−OH was reasonable. Combined with the theoretical calculation results, a possible elementary reaction path of intermediate (6AlO-OH) formation was designed to propose the generation mechanism of intermediate.

Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

Addendum to “Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 1. Molecular Dynamics Simulations” and “Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 2. Elementary Reaction Paths”

Addendum to “Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 1. Molecular Dynamics Simulations” and “Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 2. Elementary Reaction Paths”

A generalized recipe to construct elementary or multi-step reaction paths via a stochastic formulation: Application to the conformational change in noble gas clusters

• We demonstrate a general strategy to map out reaction paths irrespective of the number of kinetic steps involved. • The objective function proposed does not need the information of gradient norm and eigenvalue of Hessian matrix explicitly. • A stochastic optimizer Simulated Annealing is used in searching reaction path. • The strategy is applied in mapping out the path for conformational changes in pure Ar clusters and Ar N Xe mixed clusters. In this paper we demonstrate a general strategy to map out reaction paths irrespective of the number of kinetic steps required to bring about the change. i.e., whether the transformation takes place in a single step or in multiple steps with the appearance of intermediates. The objective function proposed is unique and works equally well for a concerted or a multiple step pathway. As the objective function proposed does not explicitly involves the calculation of the gradient of the potential energy function or the eigenvalues of the Hessian Matrix during the iterative process, the calculation is computationally economical. To map out the reaction path, we cast the entire problem as one of optimization and the solution is done with the use of the stochastic optimizer Simulated Annealing. The formalism is tested on Argon clusters ( Ar N ) and Argon clusters singly doped with Xenon ( Ar N - 1 Xe ). The size of the systems for which the method is applied ranges from N = 7 - 25 , where N is the total number of atoms in the cluster. We also test the results obtained by us by comparing with an established gradient only method. Moreover to demonstrate that our strategy can overcome the standard problems of drag method, we apply our strategy to a two dimensional LEPS + harmonic oscillator Potential to locate the TS, in which standard drag method has been seen to encounter problems.

Comparison of ReaxFF, DFTB, and DFT for Phenolic Pyrolysis. 2. Elementary Reaction Paths

Reaction paths for the loss of CO, H2, and H2O from atomistic models of phenolic resin are determined using the hybrid B3LYP approach. B3LYP energetics are confirmed using CCSD(T). The energetics along the B3LYP paths are also evaluated using the PW91 generalized gradient approximation (GGA), the more approximate self-consistent charge density functional tight binding (SCC-DFTB), and the reactive force field (ReaxFF). Compared with the CCSD(T)/cc-pVTZ level for bond and reaction energies and barrier heights, the B3LYP, PW91, DFTB(mio), DFTB(pbc), and ReaxFF have average absolute errors of 3.8, 5.1, 17.4, 13.2, and 19.6 kcal/mol, respectively. The PW91 is only slightly less accurate than the B3LYP approach, while the more approximate approaches yield somewhat larger errors. The SCC-DFTB paths are in better agreement with B3LYP than are those obtained with ReaxFF.

Automated discovery of chemically reasonable elementary reaction steps

Due to the significant human effort and chemical intuition required to locate chemical reaction pathways with quantum chemical modeling, only a small subspace of possible reactions is usually investigated for any given system. Herein, a systematic approach is proposed for locating reaction paths that bypasses the required human effort and expands the reactive search space, all while maintaining low computational cost. To achieve this, a range of intermediates are generated that represent potential single elementary steps away from a starting structure. These structures are then screened to identify those that are thermodynamically accessible, and then feasible reaction paths to the remaining structures are located. This strategy for elementary reaction path finding is independent of atomistic model whenever bond breaking and forming are properly described. The approach is demonstrated to work well for upper main group elements, but this limitation can easily be surpassed. Further extension will allow discovery of multistep reaction mechanisms in a single computation. The method is highly parallel, allowing for effective use of modern large-scale computational clusters.

Effects of a Single Water Molecule on the OH + H2O2 Reaction

The effect of a single water molecule on the reaction between H(2)O(2) and HO has been investigated by employing MP2 and CCSD(T) theoretical approaches in connection with the aug-cc-PVDZ, aug-cc-PVTZ, and aug-cc-PVQZ basis sets and extrapolation to an ∞ basis set. The reaction without water has two elementary reaction paths that differ from each other in the orientation of the hydrogen atom of the hydroxyl radical moiety. Our computed rate constant, at 298 K, is 1.56 × 10(-12) cm(3) molecule(-1) s(-1), in excellent agreement with the suggested value by the NASA/JPL evaluation. The influence of water vapor has been investigated by considering either that H(2)O(2) first forms a complex with water that reacts with hydroxyl radical or that H(2)O(2) reacts with a previously formed H(2)O·OH complex. With the addition of water, the reaction mechanism becomes much more complex, yielding four different reaction paths. Two pathways do not undergo the oxidation reaction but an exchange reaction where there is an interchange between H(2)O(2)·H(2)O and H(2)O·OH complexes. The other two pathways oxidize H(2)O(2), with a computed total rate constant of 4.09 × 10(-12) cm(3) molecule(-1) s(-1) at 298 K, 2.6 times the value of the rate constant of the unassisted reaction. However, the true effect of water vapor requires taking into account the concentration of the prereactive bimolecular complex, namely, H(2)O(2)·H(2)O. With this consideration, water can actually slow down the oxidation of H(2)O(2) by OH between 1840 and 20.5 times in the 240-425 K temperature range. This is an example that demonstrates how water could be a catalyst in an atmospheric reaction in the laboratory but is slow under atmospheric conditions.

Impact of Water on the OH + HOCl Reaction

The effect of a single water molecule on the OH + HOCl reaction has been investigated. The naked reaction, the reaction without water, has two elementary reaction paths, depending on how the hydroxyl radical approaches the HOCl molecule. In both cases, the reaction begins with the formation of prereactive hydrogen bond complexes before the abstraction of the hydrogen by the hydroxyl radical. When water is added, the products of the reaction do not change, and the reaction becomes quite complex yielding six different reaction paths. Interestingly, a geometrical rearrangement occurs in the prereactive hydrogen bonded region, which prepares the HOCl moiety to react with the hydroxyl radical. The rate constant for the reaction without water is computed to be 2.2 × 10(-13) cm(3) molecule(-1) s(-1) at room temperature, which is in good agreement with experimental values. The reaction between ClOH···H(2)O and OH is estimated to be slower than the naked reaction by 4-5 orders of magnitude. Although, the reaction between ClOH and the H(2)O···HO complex is also predicted to be slower, it is up to 2.2 times faster than the naked reaction at altitudes below 6 km. Another intriguing finding of this work is an interesting three-body interchange reaction that can occur, that is HOCl + HO···H(2)O → HOCl···H(2)O + OH.

Development of the reaction time accelerating molecular dynamics method for simulation of chemical reaction

We present a novel and efficient method to integrate chemical reactions into molecular dynamics to simulate chemical reaction systems. We have dubbed this method RTAMD, an acronym for reaction time accelerating molecular dynamics. The methodology we propose here requires no more than the knowledge of the empirical intermolecular potentials for the species at play as well as the elementary reaction path among them. Bond formation during the simulation is performed by changing the inter-atomic potentials from those of the non-bonded species to those of the bonded ones, and a reaction is deemed to occur by the distance separating the bond forming atoms. In this way the energy barrier for a reaction is no longer considered; the estimation of the reaction rate, however, is possible by introducing the principles of the transition state theory. The simplicity of the present scheme to simulate chemical reactions enables it to be used in large-scale MD simulations involving a large number of simultaneous chemical reactions and to evaluate kinetic parameters. In this paper, the basic theory of the method is presented and application to simple equiatomic reaction system where the reaction rates were estimated was illustrated.

Decomposition Reaction of Dioxetanone in Firefly Bioluminescence by Computer Experiment

Firefly luciferin (Ln) reacts with molecular oxygen in the presence of the enzyme luciferase (E), the Mg(+2) ion and ATP to form a four-membered cyclic peroxide, so-called dioxetanone, which has not yet been observed by spectrophotometric techniques. Subsequently, dioxetanone decomposes into carbon dioxide (CO(2)) and electronically excited oxyluciferin (Oxyln(-∗)), emitting yellow-green light. In order to clarify the characteristics of the elementary reaction path from dioxetanone to Oxyln(-∗), the potential energy curve of the singlet ground-state (S(0)-PEC) along the reaction coordinate was obtained by the intrinsic reaction coordinate (IRC) calculations using the AM1 Hamiltonian. Furthermore, the potential energy curve of the singlet excited-state (S(1)-PEC) was calculated, because dioxetanone decomposes to Oxyln(-∗) along the reaction coordinate. The S(1)-PEC relative to S(0)-PEC was estimated at each point of the reaction coordinate using the INDO/S, where only the singly-excited configuration interactions (CI) constructed from 20 occupied and 20 unoccupied molecular orbitals (MOs) were considered. As a result of these calculations, it was concluded that (1) firefly dioxetanone might not be an intermediate but rather be in an unstable transition state; (2) the S(0)-PEC has an activation barrier of 37.5 kcal/mol for dioxetanone formation and the reaction is exothermic along the S(0)-PEC; (3) the S(1)-PEC approaches the S(0)-PEC in a concave manner where dioxetanone decomposes to efficiently produce Oxyln(-∗); and (4) rupturing of an O-O bond in dioxetanone can trigger the coming and going of electrons in a "cradle" motion mediated by S(0)- and S(1)-PECs in the chemiexcitation step toward Oxyln(-∗).

Elementary reaction path on polychlorinated biphenyls formation from polychlorinated benzenes in heterogeneous phase using ab initio molecular orbital calculation.

We have investigated the elementary reaction path on the 3,3',4,4',5,5'-hexachlorinated biphenyl (HxCB) formation from two 1,2,3,5-tetrachlorobenzenes (TCBz) and the catalytic role of copper on this formation using ab initio molecular orbital calculation. The elementary reaction path on the 3,3',4,4',5,5'-HxCB formation from two 1,2,3,5-TCBzs has been shown to occur as follows: Step 1--the dissociation of Cl atom substituted at 5-position in 1,2,3,5-TCBz, Step 2--the association between Cl atom substituted at 5-position in another 1,2,3,5-TCBz and the Cl radical formed in Step 1, Step 3-the elimination of Cl2 molecule from the intermediate species formed in Step 2, and Step 4--the 3,3',4,4',5,5'-HxCB formation from the direct condensation of two 1,2,3-trichlorophenyl radicals formed in Step 1 and Step 3. The geometric factor, which decides the reactivity of this formation, is the C-Cl bond strength of 1,2,3,5-TCBz. The catalytic roles of copper are to stabilize the total energy in the adsorption of 1,2,3,5-TCBz onto the copper surface and to weaken the C-Cl bond strength due to the charge transfer from the 1,2,3,5-TCBz to the copper surface. Moreover, we have achieved the prediction of the minimum energy path on the formation of non- and mono-ortho polychlorinated biphenyls congeners for which TEFs have been determined.

Analysis of Tertiary Butyl Radical + O2, Isobutene + HO2, Isobutene + OH, and Isobutene−OH Adducts + O2: A Detailed Tertiary Butyl Oxidation Mechanism

The reaction systems tert-butyl radical + O2, isobutene + HO2, isobutene + OH, and isobutene−OH adducts + O2, which are important to understanding the oxidation chemistry of tertiary butyl radical (C3C•), are analyzed. Thermochemical parameters are determined by ab initio−Mφller−Plesset (MP2(full)/6-31g(d)), complete basis set model chemistry (CBS-4 and CBS-q with MP2(full)/6-31g(d) and B3LYP/6-31g(d) optimized geometries), density functional (B3LYP/6-31g(d)), semiempirical MOPAC (PM3) molecular orbital calculations, and by group additivity estimation. Thermochemical kinetic parameters are developed for each elementary reaction path in these complex systems, and a chemical activation kinetic analysis using quantum Rice−Ramsperger−Kassel (QRRK) theory for k(E) and master equation analysis for falloff is used to calculate rate constants as a function of pressure and temperature. An elementary reaction mechanism is constructed to model experimental data for oxidation of tert-butyl radical. Calculations for loss of tert-butyl precursor, 2,2,3,3-tetramethylbutane (C3CCC3), and production of isobutene and 2,2-dimethyloxirane from the mechanism are compared with experimental data reported in the literature. Reaction of tert-butyl radical (C3C•) with O2 forms an energized tert-butyl peroxy adduct C3COO•* which can dissociate back to reactants, dissociate to isobutene + HO2, or isomerize to tert-butyl hydroperoxide (C3•COOH). This isomer can dissociate to either isobutene + HO2 or 2,2-dimethyloxirane + OH, before it is stabilized. In the tert-butyl radical + O2 reaction system, dissociation of the [C3COO•]* adduct to isobutene + HO2 via HO2 molecular elimination is faster than the hydrogen shift to C3•COOH by a factor of 86:1 at 773 K and 60 Torr. The reaction barrier (reaction enthalpy difference between TS4 and C3•COOH) for the C3•COOH reaction to 2,2-dimethyloxirane + OH is calculated as 17.98 (19.06) kcal/mol at the CBS-q//MP2(full)/6-31g(d) level but is evaluated as 15.58 (18.06) kcal/mol by fitting experimental data. Data in parentheses are thermodynamic properties based on CBS-q//B3LYP/6-31g(d) calculation. Barriers for reactions of HO2 + isobutene → C3•COOH (HO2 addition at CD/C2 carbon atom of isobutene, CD = carbon double bond) and HO2 + isobutene → C2C•COOH (HO2 addition at CD/H2 carbon atom of isobutene) are respectively determined as 7.74 (7.38) and 10.69 (10.82) kcal/mol. 2,2-Dimethyloxirane is formed primarily by HO2 addition to isobutene. OH addition to isobutene results in adducts which further react with O2 to form acetone, formaldehyde, and the OH radical (Waddington mechanism) with these pathways also analyzed.

The decomposition of nitrous oxide at 1.5 ⩽ P ⩽ 10.5 atm and 1103 ⩽ T ⩽ 1173 K

AbstractReaction experiments on mixtures of N2O/H2O/N2 were performed in a variable pressure flow reactor over temperature, pressure, and residence time ranges of 1103–1173 K, 1.5–10.5 atm, and 0.2–0.8 s, respectively. Mixtures of approximately 1% N2O in N2 were studied with the addition of varying amounts of water vapor, from background to 3580 ppm. Experimentally measured profiles of N2O, O2, NO, NO2, H2O, and temperature were compared with predictions from detailed kinetic modeling calculations to assess the validity of a reaction mechanism developed from currently available literature thermochemical and rate constant parameters. Sensitivity and reaction flux analyses were performed to determine key elementary reaction path processes and rates.Reaction rate constants for the uni‐molecular reaction, N2O → N2 + O, were determined at various pressures in order to match overall experimental and numerical decomposition rates of N2O. The numerical model included a newly determined rate constant for N2O + OH → HO2 + N2 with an upper limit of 5.66 × 108 cm3 mol−1 sec−1 at 1123 K. This is considerably smaller than presently reported in the literature. The experimentally observed rate of N2O decomposition was found to be slightly dependent on added water concentration. The rate constant determined for the elementary decomposition is strongly dependent on the choice of rate constants for the N2O + O ⇔ N2 + O2 and N2O + O ⇔ NO + NO reactions. In the absence of accurate data at the temperatures of this work, and based on these and other experiments in this laboratory, we presently recommend rate constants from the review of Baulch et al. The basis for this recommendation is discussed, including the impact on the rate constants derived for elementary nitrous oxide decomposition. The uncertainties in the rate constants as reported here are ±30%.The present mechanism was applied to previously reported high‐pressure shock tube data and yields a high‐pressure limit rate constant a factor of three larger than previously reported at these temperatures. The following expressions for the elementary decomposition reaction are recommended: k = 9.13 × 1014 exp (−57, 690/RT) cm3 mol−1 s−1 and k∞ = 7.91 × 1010 exp(−56020/RT) s−1. Simple Lindemann fits utilizing these parameters reproduce the pressure dependent rate constants measured here within ±25%. © 1995 John Wiley & Sons, Inc.

Reaction of N on a Ni(110) surface with H atoms

The p(2×3) Ni(110)-N surface structure was produced by the reaction of NO with highly excess H2 (1:150) on a Ni(110) surface at 650 K. The N atoms on Ni(110) surface were inactive for the hydrogenation with H2. They, however, reacted with H atoms in the presence of H2, and the formation of NH species was detected by high resolution electron energy loss spectroscopy (HREELS). In the temperature range between 300 K and 450 K, the amount of N on Ni(110) surface decreased by reacting with H atoms in the zero order kinetics with respect to the amount of N and the decreasing rate did not depend on the temperature. When the temperature is higher than a critical temperature of 500 K, however, the amount of N on the Ni(110) surface does not decrease even if the surface is exposed to H atoms. This critical temperature corresponds to the decomposition temperature of the NH species on Ni(110) surface determined by the HREELS. One one hand, the NH species were produced by the reaction, hydrogenation, of N with H atoms on the Ni(110) suface. On the other hand, it was reported that NH2 species were preferentially formed by the decomposition, dehydrogenation, of NH3 on the Ni(110) surface. Taking these facts into account, it was deduced that there is a rather high activation barrier in an elementary reaction path from NH to NH2 on the Ni(110) surface.

Ab initio calculations to the reactions of HF and HCl with Si(OH)4 and (HO)3SiOSi(OH)3: Modeling of SiO2 etching reactions

AbstractThe local mechanisms of dissociative chemisorption and reactive etching are investigated by molecular models modeling SiOH groups and SiOSi bridges at SiO2 surfaces. The elementary reaction paths for the reactions of HF and HCl with SiO bonds of the models, Si(OH)4 and (HO)3SiOSi(OH)3, are calculated by the Hartree–Fock method. The local transition‐state structures are nearly plane quadrangles with neighboring pentacoordinated silicon and tricoordinated oxygen atoms. For the reaction and activation energies, the electron correlation is considered by the Møller–Plesset perturbation theory. The results agree with experimental findings. © 1994 John Wiley & Sons, Inc.

The Effect of Phthalate Ion and Acetate Ion on the Rate of the Reaction between Nickel(II) and Cobalt(II)-Nitrilotriacetate Complexes

Abstract A kinetic study of the substitution reactions of nickel(II) ions and cobalt(II)-nitrilotriacetate complexes in phthalate and in acetate buffer has been carried out using a procedure previously reported. The reaction was made to proceed through both hydrated nickel(II) ions and monophthalatonickel(II) complexes or monoacetatonickel(II) complexes. The rate constants for eight elementary reaction paths, four of which involve the hydrated nickel(II) ions, while the others involve the monophthalatonickel(II) complexes (the monoacetatonickel(II) complexes in the case of the measurements in acetate media), were determined at an ionic strength of 0.2 at 25°C. The values obtained indicate that all the reactions proceeding through the monophthalatonickel(II) complexes are slower than the corresponding reactions proceeding through hydrated nickel(II) ions; however, all the reactions proceeding through monoacetatonickel(II) complexes are faster than the corresponding reactions proceeding through hydrated nickel(II) ions. Thus, the kinetic reactivity is in the order of: NiOAc+>Ni2+>NiPh, where Ph2− indicates a bivalent phthalate anion.

The Effect of Acetate Ion on the Rate of the Reaction between Cobalt(II) and Manganese(II)-Ethylenediaminetetraacetate Complexes

Abstract The kinetics of the substitution reactions of cobalt(II) ions and manganese(II)-ethylene-diaminetetraacetate complexes have been studied in acetate buffer solutions at 25°C and at ionic strength of 0.2. The reaction was treated as to proceed through both hydrated metal ions and monoacetato complexes. The rate constants for six elementary reaction paths, three of which involve hydrated cobalt(II) ions and the others, monoacetatocobalt(II) complexes, were determined. The values obtained indicate that all the reactions proceeding through monoacetatocobalt(II) complexes are about three times faster than the corresponding reactions proceeding through hydrated cobalt(II) ions.

The Kinetics of Substitution Reactions Involving Metal Complexes. XII. The Reactions between Copper(II) Ions and Zinc(II)-nitrilotriacetate Complexes

Abstract The kinetic study of the substitution reaction of copper(II) ions and zinc(II)-nitrilotriacetate complexes in acetate buffer solutions has been carried out with the same procedure as reported previously. The reaction was treated as to proceed through both hydrated metal ions and monoacetato complexes. The rate constants for eight elementary reaction paths, of which four involve the hydrated copper(II) ions and the others the monoacetatocopper(II) complexes, were determined at ionic strength 0.23 at 0°C. The values obtained indicate that all the reactions proceeding through hydrated copper(II) ions are faster than the corresponding reactions proceeding through monoacetatocopper(II) complexes.