Intrinsic Reaction Coordinate Research Articles

A reaction force perspective of a model amide bond formation reaction

A reaction force approach of amide bond formation between ammonia and formic acid is demonstrated along with each atom’s contribution to structural changes and electronic reordering of the chemical reaction. The B3LYP/6-31G(d,p) level of density functional theory based calculations were carried out to explore transition states (TSs) of stepwise and concerted amide bond formation reaction pathways. Various stages that characterize structural and electronic properties in the progress of reaction are identified from reaction force calculations on energetics of geometries obtained from intrinsic reaction coordinate (IRC) pathways. The reaction works in preparative region of the pathway are less than that in relaxation stage, reflecting favorable formation of product geometries (Formamide and water). More than 80% of the activation energy comes from structural changes in preparative region. A comparison of reaction force profiles and reaction works in preparative region of TS1 and TS2 of stepwise path and TS3 of concerted path discloses that both the stepwise and concerted mechanisms are equally competent in terms of kinetic feasibility. The atomic resolution of pathways unveils that, hydrogen and oxygen forming the water molecule contribute significantly to the negative reaction energy of product geometries. The preferential contribution of the atoms comes from enhanced negative charge of the oxygen and positive charge on hydrogen in the progress of reaction.

A molecular electron density theory study of Diels‐Alder reaction between Danishefsky's diene and (2E)‐3‐phenyl‐2‐(trifluoromethyl) acrylonitrile

AbstractThe Diels‐Alder reaction between Danishefsky's diene (DD 4) and (2E)‐3‐phenyl‐2‐(trifluoromethyl) acrylonitrile (EPTA 5) at 393 K in the presence of toluene has been studied using the molecular electron density theory at the M06‐2X/6‐31G(d,p) computational level. The calculated relative Gibbs free energies indicated that the studied reaction takes place in a complete regioselective and stereoselective manner in which the most nucleophilic center of DD 4 is attacked by the most electrophilic center of EPTA 5 passing through the stationary point of TS2n. It was shown that the TS2n affords the corresponding cycloadduct of CA2n as the unique product in excellent agreement with the experimental outcomes. On the other hand, a great destabilizing steric repulsion between methoxy moiety of DD 4 and the trifluoromethyl moiety of EPTA 5 along the exo stereoselective approach is responsible for the predominance of the endo approach over the exo one. The nucleophilic and electrophilic Parr functions at the reactive sites of the DD 4 and EPTA 5 have been used to explain the regioselectivity of the Diels‐Alder reaction. According to the electron localization function analysis of the intrinsic reaction coordinate profile of the energetically most preferred TS2n, a nonconcerted two‐stage one‐step molecular mechanism has been proposed. The mechanism indicated the formation of C1C6 single bond through coupling of C1 to C6 and subsequent C4C5 single bond through coupling of C4 to C5 at cycloadduct CA2n.

Insight into the Effects of Electrostatic Potentials on the Conversion Mechanism of the Hydrogen-Bonded Complexes and Carbon-Bonded Complexes: An Ab Initio and Quantum Theory of "Atoms in Molecules" Investigation.

Carbon bond and hydrogen bond are common noncovalent interactions; although recent advances on these interactions have been achieved in both the experimental and computational aspects, little is known about the conversion mechanism between them. Here, MP2 calculations with aug-cc-pVDZ basis set (aug-cc-pVDZ-pp for element Sn) were used to optimize the geometric configurations of the hydrogen-bonded complexes MH3F···HCN (M = C, Si, Ge, and Sn), carbon-bonded complexes HCN···MH3F (M = C, Si, Ge, and Sn), and transition states; the conversion mechanism between these two types of interactions has been carried out. The molecular electrostatic potential, especially the σ-hole, is directly related to the flatten degree of intrinsic reaction coordinate (IRC) curve. The energy barriers from the hydrogen-bonded complexes to the carbon-bonded complexes are 6.99, 7.73, 10.56, and 13.59 kJ·mol–1. The energy barriers from the carbon-bonded complexes to the hydrogen-bonded complexes are 4.65, 7.81, 9.10, and 13.04 kJ·mol–1. The breakage and formation of the bonds along the reaction paths have been discussed by the topological analysis of electronic density. The energy barriers are obviously related to the width of the structure transition region (STR). For the first derivative curve of IRC energy surface versus reaction coordinate, there is a maximum peak and a minimum peak, reflecting the structural transition states in the ring STRs.

Theoretical studies of hydrogen abstraction from H2X and CH3XH (X = O, S) by trichloromethyl radicals.

We have theoretically investigated the hydrogen abstraction reactions of H2O, H2S, CH3OH, and CH3SH by the CCl3 radical, which is of interest in atmospheric chemistry research. In this study, mechanistic and kinetic analyses for the title reactions have been performed at the W1 and the CCSD(T)/cc-pVTZ//M06-2X/cc-pVTZ level. Standard Gibbs free energies for all reaction channels at the W1 level with ZPE corrections were also calculated. Intrinsic Reaction Coordinate (IRC) calculations were performed to verify the connectivity of all the transition states with the reactants and products. All rate coefficients are computed by conventional transition state theory (CTST) with the zero-curvature tunneling (ZCT) and also Wigner's tunneling (W) correction in the temperature range from 200 K to 2000 K. The rate coefficients for each reaction channel are also evaluated by canonical variational transition state theory (CVT) with the small-curvature tunneling correction method (SCT) in the same temperature range. Three-parameter Arrhenius expressions have been obtained by fitting to the computed rate coefficients of all abstraction channels between 200 and 2000 K. The branching ratios for these reactions have been determined. This study provides the first theoretical and kinetic determination of the CCl3 rate coefficient for reactions with H2O, H2S, CH3OH, and CH3SH over a large temperature range.

Ion reactions in atmospherically-relevant clusters: mechanisms, dynamics and spectroscopic signatures.

Reactions of nitrogen oxides with seawater are of major atmospheric importance, but microscopic understanding of these processes is still largely unavailable. In this paper we explore models of reactions of N2O4 with ions in water in order to provide molecular-level understanding of the processes. Presented here are studies of N2O4 interacting with two ions, SO42- and Cl-, in small water clusters. Reactions of the asymmetric conformer of N2O4 with SO42- ions in water clusters are studied via ab initio molecular dynamics (AIMD) simulations in order to unravel the microscopic mechanism of the processes and predict the timescales of different steps. Spectroscopic signatures of the reaction are proposed. The mechanisms of chloride substitution and hydrolysis of symmetric and asymmetric N2O4 are explored via intrinsic reaction coordinate (IRC) calculations. Spectroscopic calculations for relevant species suggest possible experimental signatures for the processes. The results of these model ion-N2O4 reactions in water throw light on the molecular-level mechanisms of the reactions of nitrogen oxides with seawater.

Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices.

Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (e.g., a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called PathReducer, which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecting the series of geometries into the low-dimensional space for visualization. We investigated two options to represent molecular structures within PathReducer: aligned Cartesian coordinates and matrices of interatomic distances. We found that interatomic distance matrices better captured non-linear motions in a smaller number of dimensions. To demonstrate the utility of PathReducer, we have carried out a number of applications where we have projected molecular dynamics trajectories into a reduced dimensional space defined by an intrinsic reaction coordinate. The visualizations provided by this analysis show that dynamic paths can differ greatly from the minimum energy pathway on a potential energy surface. Viewing intrinsic reaction coordinates and trajectories in this way provides a quick way to gather qualitative information about the pathways trajectories take relative to a minimum energy path. Given that the outputs from PCA are linear combinations of the input molecular structure coordinates (i.e., Cartesian coordinates or interatomic distances), they can be easily transferred to other types of calculations that require the definition of a reduced dimensional space (e.g., biased molecular dynamics simulations).

EStokTP: Electronic Structure to Temperature- and Pressure-Dependent Rate Constants-A Code for Automatically Predicting the Thermal Kinetics of Reactions.

A priori rate predictions for gas phase reactions have undergone a gradual but dramatic transformation, with current predictions often rivaling the accuracy of the best available experimental data. The utility of such kinetic predictions would be greatly magnified if they could more readily be implemented for large numbers of systems. Here, we report the development of a new computational environment, namely, EStokTP, that reduces the human effort involved in the rate prediction for single channel reactions essentially to the specification of the methodology to be employed. The code can also be used to obtain all the necessary master equation building blocks for more complex reactions. In general, the prediction of rate constants involves two steps, with the first consisting of a set of electronic structure calculations and the second in the application of some form of kinetic solver, such as a transition state theory (TST)-based master equation solver. EStokTP provides a fully integrated treatment of both steps through calls to external codes to perform first the electronic structure and then the master equation calculations. It focuses on generating, extracting, and organizing the necessary structural properties from a sequence of calls to electronic structure codes, with robust automatic failure recovery options to limit human intervention. The code implements one or multidimensional hindered rotor treatments of internal torsional modes (with automated projection from the Hessian and with optional vibrationally adiabatic corrections), Eckart and multidimensional tunneling models (such as small curvature theory), and variational treatments (based on intrinsic reaction coordinate following). This focus on a robust implementation of high-level TST methods allows the code to be used in high accuracy studies of large sets of reactions, as illustrated here through sample studies of a few hundred reactions. At present, the following reaction types are implemented in EStokTP: abstraction, addition, isomerization, and beta-decomposition. Preliminary protocols for treating barrierless reactions and multiple-well and/or multiple-channel potential energy surfaces are also illustrated.

Designing Reactions with Post-Transition-State Bifurcations: Asynchronous Nitrene Insertions into C–C σ Bonds

Summary Discoveries of chemical reactions with potential energy surfaces with post-transition-state bifurcations are increasing in frequency. Although such potential energy surface features are often discovered accidentally, we demonstrate here that they can be designed rationally. We describe a process for designing such reactions and apply it to the design of a nitrene addition/alkyl-shift reaction with a post-transition state bifurcation. We examine substituent effects on this reaction and propose a dynamics-based model for selectivity control.

Unraveling the sequence of the electronic flow along the water-assisted ring-opening reaction in mutagen MX

The ring-opening reaction of 3-chloro-4-(dichloromethyl)-5-hydroxy-5H-furan-2-one (mutagen X or MX) remains an intriguing subject of both theoretical and experimental interest. This relies on the fact of uncertainty concerning which structure acts as the real mutagen. Challenging the current accepted idea of a direct tautomeric process transforming the furanone ring to the oxobutenoic acid chain structure, a water-assisted process via a six-membered transition structure (TS) is revealed to proceed with activation energy of 24.5 kcal/mol (i.e., 26.8 kcal/mol lower than the conventional tautomeric process). An analysis based on the application of catastrophe theory to the evolution of the electron localization function topology along the intrinsic reaction coordinate reveals that the process can be explained, using a Lewis-like chemical language, as a result of the electronic activation of the furanone specie by the water molecule: on the activation pathway (i.e., before TS is reached), the electronic perturbation introduced by the water reagent is first observed on the valence shell of the ring oxygen and then on that of the hydroxylic one. Thereafter, the release of the hydroxylic hydrogen and the breaking of the C–O bond in the furanone ring follow the electronic rearrangement. On the de-activation pathway, the water molecule first captures the hydroxylic proton. Then, a hydronium-like structure transfers a proton to the oxygen of the furanone moiety contributing to stabilize the open ring structure. The above description of such a favorable ring-opening process become thus associated with nine topological structural stability domains, featuring the following sequence of catastrophes: C5H3O3Cl3 + H2O: 10-C†F†[FU]UC[C†C†]CC-0: C5H3O3Cl3 + H2O.

A theoretical study of styrene and sulfenyl chloride reaction mechanism

The classical description of sulfenyl halides additions to olefins proposes the formation of an episulfonium ion intermediate during the reaction path. However, a careful analysis of experiments performed in the past suggests that there should not be a single mechanistic picture of sulfenyl halide additions to substituted olefins. Our work is the first theoretical study of detailed insights into the mechanism of methylsulfenchloride addition to styrene. The reaction potential energy profile has been calculated by means of the B3LYP functional with the 6-31++G(d, p) basis set. Mixing of the molecular orbital shapes of reaction stationary points has been described. The addition proceeds as a single step reaction from the methylsulfenchloride and styrene reactants via the concerted transition state (TS) to the final product along the reaction path estimated by the calculation of the intrinsic reaction coordinate. The reaction intermediate was not detected by calculations. The polar solvent has a significant effect on the decrease of reaction activation energy barriers. The large charge separation of the S–Cl bond in TS implies that the addition reaction should proceed through the ionic TS.

Theoretical investigation of the mechanism for the reductive dehalogenation of methyl halides mediated by the CoI-based compounds cobalamin and cobaloxime.

Theoretical calculations focusing on the cleavage of the C-X bond in methyl halides (CH3X; X = Cl, Br, I) as mediated by CoI-based systems have been carried out using the hybrid functional ωB97-XD together with the basis set 6-311++G(2d,2p). A total of seven CoI-based compounds were evaluated: cob[I]alamin (CoICbl) in its base-on form and cobaloxime (CoICbx) with either no ligand or different ligands (either pyridine (PYR), tributylphosphine (TBP), dimethyl sulfide (DMS), cyclohexylisocyanide (CI), or 5,6-dimethylbenzimidazole (DMB)) at the lower axial position. For the large CoICbl system, an ONIOM scheme was employed, where the high layer was described at the DFT level and the low layer was computed using the semi-empirical method PM6. A full DFT model was employed for the CoICbx cases. An SN2-like mechanism was evaluated in all cases. The intrinsic reaction coordinate profiles suggested early transition states with activation energies of ≈ 12kcal/mol, ≈ 10kcal/mol, and ≈ 5kcal/mol for C-Cl, C-Br, and C-I cleavage, respectively, which is consistent with the leaving group abilities of these halides. The evolutions of the atomic charges in and the bond orders of Co-C and C-X were computed, and the results confirmed the existence of early transition states (δBav≈ 40%), where the polarization Cδ+-Xδ- (%Ev ≈ 43%) is the determining factor in the reaction process. Finally, a comparison of all the determined parameters showed that the reaction in the DMB-CoICbx system resembles the process that occurs in the larger CoICbl, suggesting that the former system could be a reliable model for the study of reductive dehalogenation mediated by vitamin B12, which is key to the anaerobic microbiological treatment of halocarbon contaminants.

Density functional theory study of the oxidation reaction in the gas and aqueous phase of allyl methyl disulfide with hydroxyl radical

An in silico analysis of the oxidation mechanism of allyl methyl disulfide (AMDS) by hydroxyl radical was achieved at DFT level using B3LYP, CAM-B3LYP, M06-2X, and BMK functionals and 6-311++G(3df,2p) triple-zeta basis set. The calculations were carried out in both gas and aqueous phases using the SMD model (density-based solvation model). Three potential reactions were proposed according to results of Fukui function; in reactions 1 and 2, the hydroxyl radical attacks the sulfur atom breaking the disulfide bond and the reaction 3 is a hydrogen atom subtraction reaction. The respective structures of transition states (TSs) were found. Intrinsic reaction coordinate (IRC) calculations were performed for the three reactions, and their rates and equilibrium constants were calculated. When the solvent effect is taken into account, the four DFT functionals employed designate R3 (a subtraction reaction) as the fastest reaction. Thus, we elucidated the thermodynamic and kinetic feasibility of the proposed oxidation reactions.

On the electron flow sequence driving the hydrometallation of acetylene by lithium hydride.

The sequence of the electronic flow driving the hydrometallation of acetylene by lithium hydride (and that of the opposite β-hydride elimination reaction from the alkenyl metal intermediate), was examined within the perspective provided by the bonding evolution theory (BET). The analysis was based on the application of catastrophe theory to the changes of the electron localization function topology along the intrinsic reaction coordinate. The description of the electronic processes occurring on the process was represented in terms of topological structural stability domains (SSDs) and the associated elementary bifurcation catastrophes. Within such a framework of representation, the "evolution" of the system through the different SSDs reveals the key chemical events driving the transformation, including the large polarization effect as a consequence of Pauli repulsion between ions of the positive cationic metal on the hydride domain, the activation of the CC triple bond to attack the cationic center, and the agostic stabilizing interactions involving the hardest cationic metal, followed by the attack of the hydride center. These results contribute to emphasizing the intrinsic value and usefulness of using topological-based approaches and associated tools to increase our knowledge and understanding of the subtleties underlying the electronic flow as nuclei evolve along the reaction coordinate, providing detailed and complementary insights in comparison to other interpretative tool such those based on orbital-based representations, concerning the intimate nature of the electronic rearrangement of key mechanistic processes in chemistry. Graphical abstract The sequence of the electron flow (indicated by letters a and b) along the intrinsic reaction path for the hydrometallation of acetylene by lithium hydride to yield ethenyl lithium via a four-membered transition structure (TS), as determined within the bonding evolution theory to provide the key chemical events driven the changes in the key bonding patterns. Blue arrow Main event on the side HC ≡ CH + LiH → TS, red arrow the TS → HLiC=CH2 pathway, green arrows relative motion of nuclei along the imaginary frequency at the position of TS on the intrinsic reaction coordinate.

New Insight into the Chloroacetanilide Herbicide Degradation Mechanism through a Nucleophilic Attack of Hydrogen Sulfide.

The nucleophilic attack of hydrogen sulfide (HS−) on six different chloroacetanilide herbicides was evaluated theoretically using the dispersion-corrected hybrid functional wB97XD and the 6-311++G(2d,2p) Pople basis sets. The six evaluated substrates were propachlor (A), alachlor (B), metolachlor (C), tioacetanilide (D), β-anilide (E), and methylene (F). Three possible mechanisms were considered: (a) bimolecular nucleophilic substitution (SN2) reaction mechanism, (b) oxygen assistance, and (c) nitrogen assistance. Mechanisms based on O- and N-assistance were discarded due to a very high activation barrier in comparison with the corresponding SN2 mechanism, with the exception of compound F. The N-assistance mechanism for compound F had a free activation energy of 23.52 kcal/mol, which was close to the value for the corresponding SN2 mechanism (23.94 kcal/mol), as these two mechanisms could occur in parallel reactions with almost 50% of each one. In compounds A to D, an important electron-withdrawing effect of the C=O and C=S groups was seen, and consequently, the activation free energies in these SN2 reactions were smaller, with a value of approximately 18 kcal/mol. Instead, compounds E and F, which have a CH2 group in the β-position, presented a higher activation free energy (≈22 kcal/mol). Good agreement was found between experimental and theoretical values for all cases, and a reaction force analysis was performed on the intrinsic reaction coordinate profile in order to gain more details about the reaction mechanism. Finally, from the natural bond orbital (NBO) analysis, it was possible to evaluate the electronic reorganization through the reaction pathway where all the transition states were early in nature in the reaction coordinate (δBav < 50%); the transition states corresponding to compounds A to D turned out to be more synchronous than those for compounds E and F.

CPCET versus HAT: A Direct Theoretical Method for Distinguishing X–H Bond‐Activation Mechanisms

AbstractProton‐coupled electron transfer (PCET) events play a key role in countless chemical transformations, but they come in many physical variants which are hard to distinguish experimentally. While present theoretical approaches to treat these events are mostly based on physical rate coefficient models of various complexity, it is now argued that it is both feasible and fruitful to directly analyze the electronic N‐electron wavefunctions of these processes along their intrinsic reaction coordinate (IRC). In particular, for model systems of lipoxygenase and the high‐valent oxoiron(IV) intermediate TauD‐J it is shown that by invoking the intrinsic bond orbital (IBO) representation of the wavefunction, the common boundary cases of hydrogen atom transfer (HAT) and concerted PCET (cPCET) can be directly and unambiguously distinguished in a straightforward manner.

CPCET versus HAT: A Direct Theoretical Method for Distinguishing X-H Bond-Activation Mechanisms.

Proton‐coupled electron transfer (PCET) events play a key role in countless chemical transformations, but they come in many physical variants which are hard to distinguish experimentally. While present theoretical approaches to treat these events are mostly based on physical rate coefficient models of various complexity, it is now argued that it is both feasible and fruitful to directly analyze the electronic N‐electron wavefunctions of these processes along their intrinsic reaction coordinate (IRC). In particular, for model systems of lipoxygenase and the high‐valent oxoiron(IV) intermediate TauD‐J it is shown that by invoking the intrinsic bond orbital (IBO) representation of the wavefunction, the common boundary cases of hydrogen atom transfer (HAT) and concerted PCET (cPCET) can be directly and unambiguously distinguished in a straightforward manner.

A molecular electron density theory study of the asymmetric hetero-Diels-Alder cycloaddition reaction between ferrocenyl-substituted thiabutadiene and methyl propiolate

The present work includes a molecular electron density theory (MEDT) study on the regioselectivity and molecular mechanism of 6-ferrocenyl-substituted 4H-thiopyran (cycloadduct 6) synthesis over the course of an asymmetric hetero-Diels-Alder (HDA) cycloaddition reaction between ferrocenyl-substituted thiabutadiene (FTBD 4) and methyl propiolate (MP 5) at 298 K in the presence of chloroform. In agreement with the experimental findings, the obtained results obviously indicate that the reaction takes place in an entirely S1-C5 regioselective fashion to yield cycloadduct 6 as an almost equimolar enantiomeric mixture. The electron localization function (ELF) analysis of the most relevant points P1 through P5 located over the intrinsic reaction coordinate (IRC) profile of the energetically most preferred TS1-1s characterizes a non-concerted two-stage one-step molecular mechanism in which formation of the advanced S1-C5 single bond and delayed C4-C6 one at cycloadduct 6 takes place through S1- to -C5 and C4- to -C6 coupling of these pseudoradical centers.

Visualization of the Intrinsic Reaction Coordinate and Global Reaction Route Map by Classical Multidimensional Scaling.

A classical multidimensional scaling (CMDS) method is employed to visualize an intrinsic reaction coordinate (IRC) and a global reaction route map consisting of the equilibrium minima and transition state structures connected by the IRC network. As demonstrations, the method was applied to the IRCs of the intramolecular proton transfer in malonaldehyde and the SN2 reaction of OH- + CH3F → CH3OH + F-, which are both well described by two principal coordinates. Next, the method was applied to the global reaction route map of the Au5 cluster; the resulting map shows appropriate positions of five minima and 14 transition states in a reduced 2- or 3-dimensional coordinate space successfully.

Using reduced density matrix techniques to capture static and dynamic correlation in the energy landscape for the decomposition of the CH2CH2ONO radical and support a non-IRC pathway.

The unexpected abundance of HNO in the photodecomposition of the radical 2-nitrosooxy ethyl (CH2CH2ONO) is investigated through calculations of the potential energy surface by the anti-Hermitian contracted Schrödinger equation (ACSE) method, which directly generates the 2-electron reduced density matrix. The ACSE, which is able to balance single-reference (dynamic) and multi-reference (static) correlation effects, reveals some subtle correlation effects along the intrinsic reaction coordinate (IRC) en route to NO + oxirane, an IRC which offers a potential bifurcation to the HNO + vinoxy product channel. These effects were not fully captured by either single-reference techniques, such as coupled cluster, or multi-reference techniques, such as second-order multi-reference perturbation theory. These correlation effects reveal small to moderate energy changes in key transition states, which have implications for the reaction mechanism as related to the production of HNO.

Reactivity of pyrazole derivatives with halomethanes: A DFT theoretical study

The N-alkylation reaction of pyrazole derivatives with halomethanes was studied using density functional theory (DFT). The hybrid method B3LYP was employed, along with an ECP basis set such as LANL2DZ for halogen atoms (X = Cl, Br, I) and the 6-311 + G(d,p) basis set for all other atoms. In order to predict the specific site at which the pyrazole derivatives interact with halomethanes, local reactivity descriptors such as the Fukui functions were calculated. Detailed analysis of transition-state energies showed that alkylation occurred at the nitrogen atom N2 in the pyrazole derivatives, in agreement with the chemical reactivity results. The reaction mechanisms were elucidated by performing intrinsic reaction coordinate (IRC) calculations that considered the effects of the solvent and the species of halogen in the halomethane.