Intrinsic Reaction Coordinate Calculations Research Articles

Quantum chemical studies on the partial hydrogenolysis of methyl 2,3- O-diphenylmethylene-α- l-rhamnopyranoside

The potential energy surface for dioxolane ring-opening and hydride donation for the title compound has been mapped. The transition state (TS) was determined at various levels of theories and it has been proven by intrinsic reaction coordinate calculations that it connects the reactant to the product. The breaking of the O3–C acetal bond and formation of the new H–C bond seems to occur in one (rate limiting) elementary step, which is, however, rather asynchronous.

Thermodynamic and kinetic studies of hydroxyl radical reaction with bromine oxide using density functional theory

Thermodynamic properties such as enthalpies, Gibb’s free energies, entropies of BrO+OH reaction and rate coefficients were computed using density functional theory, viz. B3LYP/6-311G(2df,2pd) and mPW1PW91/6-311G(2df,2pd) level of theories. Geometries of reactants, intermediates, transitions states and products were optimized using these theories. Twelve different transitions states were identified using both the theories and confirmed by intrinsic reaction coordinate (IRC) calculations. Reaction mechanism of BrO+OH was explored using two reaction paths namely channel 1 (producing HO2+Br) and channel 2 (producing HBr+O2).Reaction channel 2 is found to be four times faster than reaction channel 1. The rate coefficient for the title reaction was computed to be k=(1.81±0.17)×10−13[exp (1532±25)/T]cm3molecule−1s−1 in the temperature range of 200 and 400K using B3LYP/6-311G(2df,2pd) level of theory. Theoretically computed enthalpy of the reaction and rate coefficients using B3LYP/6-311G(2df,2pd) level of theory were found to be in good agreement with the experimentally measured ones.

Quantum chemical analysis of carbon dioxide absorption into aqueous solutions of moderately hindered amines

Abstract Aqueous solutions of moderately hindered amines are promising absorbents for the capture of CO 2 from a gas stream because of their relatively low heats of reaction and high rates of absorption. To determine the reaction mechanisms underlying the absorption process, we performed a quantum chemical analysis of the absorption of CO 2 into aqueous amine solutions and carried out an experimental comparison of representative amines. We correlated properties such as absorption capacity and product ratio with results from free energy calculations using the conductor-like screening model for real solvents (COSMO-RS) coupled with density functional theory (DFT). Additionally, the reaction mechanisms were investigated by transition state optimizations and intrinsic reaction coordinate (IRC) calculations in an aqueous solution phase by DFT calculations using the latest continuum solvation model (SMD/IEF-PCM). The results indicated that a bicarbonate anion likely forms directly by the reaction of CO 2 , H 2 O and an amine rather than by the hydrolysis of a carbamate anion.

Theoretical study of lanthanide mono cation-mediated C–F bond activation

The potential energy surface corresponding to the reaction of lanthanide mono-cations (Ln +; Ln = Ce–Yb) with CH 3F has been investigated using density functional theory calculations. In the initial step of the C–F activation reaction, Ln + directly coordinates to the F atom of CH 3F, and forms same [Ln⋯F⋯CH 3] + type transition state structures with an accompanying electron-transfer from the Ln + to the F atom. Performing intrinsic reaction coordinate calculations from the transition states, we found that all Ln + reactions can be classified into one of two different reaction mechanisms, “harpoon-like” and “insertion–elimination”, which were experimentally proposed by Cohrnel et al. and Konayagi et al., respectively. The two mechanisms have been proposed exclusive to each other. Our results show that both reaction mechanisms are possible in Ln + reaction systems.

Ab initio molecular dynamics simulation on SiN + CH and SiC + NH reactions

The production mechanism for interstellar silicon compounds SiCN, its isomer SiNC, hydrogen cyanide HCN and its isomer HNC from the neutral–neutral reactions SiN + CH and SiC + NH was studied using ab initio molecular dynamics. Classical trajectories were calculated by the direct dynamics simulation technique at the B3LYP/6-311++G(d, p) level of theory. Reaction channels were checked by single-point energy calculations on intermediates and transition states at the B3LYP/6-311++G(3df, 3pd) level of theory and by intrinsic reaction coordinate calculations on reaction coordinates at the B3LYP/6-311++G(d, p) level of theory. More than 100 trajectories were integrated for both reactions. We confirmed that the reaction SiN + CH mostly produces SiNC and HCN, and the reaction SiC + NH mostly produces HNC and SiNH. The reaction processes were examined from the viewpoint of minimum energy path.

Dynamics Effects on an E2/E1cb Borderline Mechanism: Unimolecular Elimination of 2‐Aryl‐3‐chloro‐2‐R‐propanols

The mechanistic dichotomy between concerted E2 and stepwise E1cb of the base-promoted elimination of 2-aryl-3-chloro-2-R-propanols was examined computationally at the HF, M05-2X, and MP2 levels of theory. Optimizations of transition states (TSs) and reaction intermediates, and intrinsic reaction coordinates (IRC) calculations showed that there was a single reaction route for each substrate, and that the mechanism could be changed from E2 to E1cb by making a carbanion intermediate more stable through the introduction of electron-withdrawing substituents. Molecular dynamics simulations revealed that trajectories started at a single TS led directly to two product regions; the carbanion intermediate region in the E1cb mechanism, and the alkene product region in the E2 mechanism, through path bifurcation after the TS. The present system is a new example of bifurcation in reactions of closed-shell molecules. The overall reaction mechanism changes dynamically from E2 to E1cb by a gradual change in the ratio of E2 and E1cb trajectories, rather than a path switch in concurrent pathways.

Thermodynamics and Dynamic Kinetics of the Oxidation of Selenomethionine to Methionine Selenoxide: A Dft Study

In order to investigate the stability of selenomethionine (SeMet), the oxidation reaction of selenomethionine (SeMet) with an oxygen atom was studied by the density function theory (DFT) method. The structures of reactants, transition state and products were fully optimized at the B3LYP/6-311G** level. Intrinsic reaction coordinate (IRC) calculations were carried out to ensure the validity of the reaction path. The thermodynamic functions, namely entropy, enthalpy, free energy and equilibrium constant, and the reaction rate constant k in Eyring transition state theory, were also calculated. It has been shown that the SeMet oxidation process is favoured at lower temperatures, which might have implications for the storage stability of selenomethionine (SeMet) at lower temperatures.

Mechanistic Investigation on the Reaction of O− with CH3CN Using Density Functional Theory

The potential energy profile of the reaction between the atomic oxygen radical anion and acetonitrile has been mapped at the G3MP2B3 level of theory. Geometries of the reactants, products, intermediate complexes, and transition states involved in this reaction have been optimized at the (U)B3LYP/6-31+G(d,p) level, and then their accurate relative energies have been improved using the G3MP2B3 method. The potential energy profile is confirmed via intrinsic reaction coordinate calculations of transition states. Four possible production channels are examined respectively, as H+ transfer, H-atom transfer, H2+ transfer, and bi-molecular nucleophilic substitution (SN2) reaction pathways. Based on present calculations, the H2+ transfer reaction is major among these four channels, which agrees with previous experimental conclusions.

Compelling Computational Evidence for the Concerted Cyclization of the ABC Rings of Hopene from Protonated Squalene

The long-standing question of what is the nature of the cyclization of squalene to form tetracyclic and pentacyclic triterpenes has been addressed computationally. Using the DFT method with an intrinsic reaction coordinate calculation, we find that the first three rings of protonated squalene were formed without the intermediacy of mono- or bicyclic carbocations. The cyclization, calculated in the gas phase, proceeds in a highly asynchronous, concerted reaction to yield the tricyclic, tertiary carbocation with a 5-membered C ring. The fourth double bond of squalene is not properly oriented for the ring expansion of the C ring in concert with the formation of the 5-membered ring.

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions

This study describes the framework of the quantum mechanical (QM)/Monte Carlo (MC)/free-energy perturbation (FEP) method, a FEP method based on MC simulations using quantum chemical calculations. Because a series of structures generated by interpolating internal coordinates between transition state and reactant did not produce smooth free-energy profiles, we used structures from the intrinsic reaction coordinate calculations. This method was first applied to the Diels-Alder reaction between methyl vinyl ketone and cyclopentadiene and produced ΔG( sol)‡ values of 20.1 and 21.4 kcal mol(-1) in aqueous and methanol solutions, respectively. They are very consistent with the experimentally observed values. The other two applications were the free-energy surfaces for the Cope elimination of N,N-dimethyl-3-phenylbutan-2-amine oxide in aqueous, dimethyl sulfoxide, and tetrahydrofuran solutions, and the Kemp decarboxylation of 6-hydroxybenzo-isoxazole-3-carboxylic acid in aqueous, dimethyl sulfoxide, and CH(3) CN solutions. The calculated activation free energies differed by less than 1.8 kcal mol(-1) from the experimental values for these reactions. Although we used droplet models for the QM/MC/FEP simulations, the calculated results for three reactions are very close to the experimental data. It was confirmed that most of the interactions between the solute and solvents can be described using small numbers of solvent molecules. This is because a few solvent molecules can produce large portions of the solute-solvent interaction energies at the reaction centers. When we confirmed the dependency on the droplet sizes of solvents, the QM/MC/FEP for a large droplet with 106 water molecules produced a ΔG (sol)‡ value similar to the experimental values, as well as that for a small droplet with 34 molecules.

QUANTUM CHEMITRY STUDY ON STRUCTURES, ACTIVITIES AND REACTIONS OF ONIUM-BORONIUM DICATIONS

This paper provides information about theoretical investigations of structures of onium-boronium dications X+BH3+, X+BH5+; (X= NH3, PH3, H2O, H2S) and some reactions of them in thermodynamic control and kinetic control. Two kinds of reactions studied are complexation of onium-boronium dications X+BH3+ with H2 leading to X+BH5+ and deprotonation of X+BH5+ to give X+BH4. The similar studies with boronium ion analog BH4+ and BH6+ is carried out and results obtained pointed out that the eletrophility of onium-boronium dications is more stronger than that of boronium ion: onium-boronium dications X+BH3+, X+BH5+ are superelectrophiles. The structures of onium-boronium dications and boronium ions are optimized by using ab initio methods at the MP2/6-311+G** level of Gaussian 03W, revision B.04 and represented with Gaussview 3.0. Frequency calculation is performed to assure the obtained structures corresponding to minimun energies and have no any imaginary frequency. The transition structures are calculated and verified due to Intrinsic Reaction Coordinate Calculations. The properties of structures, as MP2 energy, Gibbs free energy, activation energy are also examined.

Quantum Chemistry of C3H6O Molecules: Structure and Stability, Isomerization Pathways, and Chirality Changing Mechanisms

Electronic structure calculations were carried out to study the various isomers of formula C(3)H(6)O, as a part of our current quantum chemical and dynamical approaches to intra- and intermolecular kinetics for the C(n)H(2n)O (n = 1, 2, 3) molecules. The usefulness of the GRRM (global reaction route mapping) program developed by Ohno and Maeda in predicting the structure of all isomers and of the transition states connecting them is fully exploited. All the isomers are identified as local minima on the MP2/CC-PVDZ potential energy surface. Acetone is the most stable isomer. In increasing order of stability the others are propanal, 2-propenol, 1-propenol, allyl alcohol, methyl vinyl ether, cyclopropanol, propylene oxide, and oxetane. Various isomerization paths connecting them are identified. All the transition states are fully characterized using intrinsic reaction coordinate calculations. The isomerization reactions may proceed through a single step or involve an intermediate species which is either a carbene or a diradical. Special attention is devoted to propylene oxide, a favorite molecule in current photochemical and stereodynamical studies because of its chiral nature. It is a rigid molecule, and chirality switching is found to be supported by its isomers. Two different chirality switching mechanisms which are assisted by propanal and allyl alcohol are presented.

Theoretical studies on the mechanism of chlorination reaction of trichlorogermyl acrylic acid

The mechanism of the chlorination reaction of trichlorogermyl acrylic acid has been studied systematically using quantum chemistry methods. Geometries of reactants, transition states and products have been optimized at the B3LYP/6-311G(d,p) level. Vibrational frequencies, IR intensities and relative energies for various stationary points have been determined. The reaction pathways have been identified by intrinsic reaction coordinate (IRC) calculations. Theoretical analysis provides conclusive evidence that the process proceeds through two and three pathways for the first and second reaction steps, respectively.

Ab initio studies on the decomposition kinetics of CF3OCF2O radical

The present study deals with the decomposition of CF(3)OCF(2)O radical formed from a hydrofluoroether, CF(3)OCHF(2) (HFE-125), in the atmosphere. The study is performed using ab initio quantum mechanical methods. Two plausible pathways of decomposition of the titled species have been considered, one involving C-O bond scission and the other occurring via F atom elimination. The geometries of the reactant, products and transition states involved in the decomposition pathways are optimized and characterized at DFT (B3LYP) level of theory using 6-311G(d,p) basis set. Single point energy calculations have been performed at G2M(CC,MP2) level of theory. Out of the two prominent decomposition channels considered, the C-O bond scission is found to be dominant involving a barrier height of 15.3 kcal mol(-1) whereas the F-elimination path proceeds with a barrier of 26.1 kcal mol(-1). The thermal rate constants for the above two decomposition pathways are evaluated using canonical transition state theory (CTST) and these are found to be 1.78 × 10(6) s(-1) and 2.83 × 10(-7) s(-1) for C-O bond scission and F-elimination respectively at 298 K and 1 atm pressure. Transition states are searched on the potential energy surfaces involved during the decomposition channels and each of the transition states is characterized. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation.

THEORETICAL MECHANISTIC STUDY ON THE RADICAL-NEUTRAL REACTION OF CH(X2Π) WITH CH2CO

A theoretical survey on the potential energy surface for the CH (X2Π) + CH2CO reaction has been carried out. The geometries and energies of all stationary points involved in the reaction are calculated at the UB3LYP/6-311+G(d, p) level. And the more accurate energy information is provided by single point calculations at the UCCSD(T)/6-311++G(2d, 2p) level. Relationships of the reactants, transition states, intermediates, and products are confirmed by the intrinsic reaction coordinate (IRC) calculations. Our calculations demonstrate that this reaction is most likely initiated by carbon-to-olefinic carbon attack manners. The results suggest that P1 (C2H3 + CO) is the most important product through two competitive channels R → IM1 → TS1/P1 → P1 (C2H3 + CO) and R → IM1 → TS1/6 → IM6 → TS6/P1 → P1 (C2H3 + CO) . This study presents highlights of the mechanism of the title reaction, which is in good agreement with experimental results.

Kinetics of OH radical reaction with CF3CHFCH2F (HFC-245eb) between 200 and 400K: G3MP2, G3B3 and transition state theory calculations

The rate coefficients of hydroxyl radical (OH) reaction with CF 3 CHFCH 2 F (HFC-245eb) were computed using G3MP2 and G3B3 theories between 200 and 400 K. Nine different transition states were identified for the title reaction and confirmed by intrinsic reaction coordinate (IRC) calculations. The contributions of all the individual hydrogen atoms in different rotamers for the title reaction were computed and compared with the results obtained by experimental methods and structure activity relationships (SAR). The rate coefficients for the title reaction were computed to be k = (1.57 ± 0.14) × 10 −13 exp[−(690 ± 26)/ T ] cm 3 molecule −1 s −1 at G3MP2, and k = (0.97 ± 0.13) × 10 −13 exp[−(513 ± 39)/ T ] cm 3 molecule −1 s −1 at G3B3 theories. Theoretically calculated rate coefficients are found to be in good agreement with the experimental results. The tropospheric lifetime of CF 3 CHFCH 2 F because of its reaction with OH radicals are computed to be 2.52 and 2.14 years at G3MP2 and G3B3 level of theories, respectively.

Ab initio studies on the reactivity of the CF3OCH2O radical: Thermal decomposition vs. reaction with O2

Hydrofluoroethers are being considered as potential candidates for third generation refrigerants. The present investigation involves the ab initio quantum mechanical study of the decomposition mechanism of CF(3)OCH(2)O radical formed from a hydrofluoroether, CF(3)OCH(3) (HFE-143a) in the atmosphere. The geometries of the reactant, products and transition states involved in the decomposition pathways are optimized and characterized at the DFT (B3LYP) level of theory using 6-311G(d,p) basis set. Energy calculations have been performed at the G2(MP2) and G2M(CC,MP2) level of theory. Two prominent decomposition channels, C-O bond scission and reaction with atmospheric O(2) have been considered for detailed investigation. Studies performed at the G2(MP2) level reveals that the decomposition channel involving C-O bond scission occurs with a barrier height of 23.8 kcal mol(-1) whereas the oxidative pathway occurring with O(2) proceeds with an energy barrier of 7.2 kcal mol(-1). On the other hand the corresponding values at G2M(CC,MP2) are 24.5 and 5.9 kcal mol(-1) respectively. Using canonical transition state theory (CTST) rate constants for the two pathways considered are calculated at 298 K and 1 atm pressure and found to be 5.9 x 10(-6) s(-1) and 2.3 x 10(-5) s(-1) respectively. The present study concludes that reaction with O(2) is the dominant path for the consumption of CF(3)OCH(2)O in the atmosphere. Transition states are searched and characterized on the potential energy surfaces involved in both of the reaction channels. The existence of transition state on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation.

Static and dynamic reaction pathways involved in the reaction of O − and CH 3F

The static and dynamic reaction pathways involved in the reaction between O − and CH 3F have been investigated. A special attention has been paid to the S N2 reaction channel, that the intrinsic reaction coordinate (IRC) calculation, one-dimensional relaxed potential energy scan, and Born–Oppenheimer molecular dynamics (BOMD) simulations have been performed, respectively. Both the forward IRC calculation and the relaxed potential energy scan from the [O⋯CH 3⋯F] − barrier show that the static reaction products are HF and CH 2O −. However, the BOMD simulations initiated at this S N2 barrier reveal two major dynamic reaction processes, which correspond to the products of HF + CH 2O − and the S N2 reaction products of F − + CH 3O, respectively. Although only 104 dynamic trajectories are calculated, the HF + CH 2O − production channel seems to be more dominant than the S N2 pathway. However, the electron detachment process of CH 2O − potentially causes its vanishing in experiments as an anionic product.

Rearrangement of Dewar Benzene Derivatives Studied by DFT

Skeletal rearrangement of a series of substituted Dewar benzenes to biaryl products was studied with DFT methods. Excellent agreement of calculated free energies of activation with experimental kinetic data was achieved. Two different transition states were proposed to be involved in the rearrangement. The reaction path was studied both by static intrinsic reaction coordinate (IRC) calculations and first-principles Car-Parrinello and Born-Oppenheimer molecular dynamics. All approaches confirmed the suggested reaction mechanism.

Dynamic path bifurcation for the Beckmann reaction: observation and implication

The reaction of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles instead of amides when the cations have reasonable stability. The reactions of oxime derivatives of 1-substituted-phenyl-2-propanones and 3-substituted-phenyl-2-butanones in aqueous solvents gave both rearrangement and fragmentation products, the ratio of which was dependent on substituents. Transition state (TS) optimizations and intrinsic reaction coordinate (IRC) calculations for the reaction of 1-phenyl-2-propanone oximes showed that there is a single TS for each substituted compound. The IRC path from the TS either led to a rearrangement product or a fragmentation product depending on the substituent; the IRC path changes from rearrangement to fragmentation when substituent X becomes more electron donating. Ab initio dynamics simulations were found to follow the IRC path for X = p-NH2 and p-MeO giving fragmentation products, and almost so for X = p-NO2 giving the rearrangement products. However, in a borderline case where X is less donating than p-MeO or less withdrawing than p-NO2, the trajectories did not follow the minimum energy path on the potential energy surface, but gave both rearrangement and fragmentation products directly from the single TS. This is a novel example of path bifurcation for a closed shell anionic reaction. It was concluded that a reactivity-selectivity argument based on the traditional TS theory may not always be applicable even to a well-known textbook organic reaction.