Mode-Specific SN2 Reaction Dynamics

Accurate ab initio based potential energy surface and kinetics of the Cl + NH3 → HCl + NH2 reaction

The gas-phase reaction Cl + NH3 → HCl + NH2 is a prototypical hydrogen abstraction reaction, whose minimum energy path involves several intermediate complexes. In this work, a full-dimensional, spin-orbit corrected potential energy surface (SOC PES) is constructed for the ground electronic state of the Cl + NH3 reaction. About 52 000 energy points are sampled and calculated at the UCCSD(T)-F12a/aug-cc-pVTZ level, in which the data points located in the entrance channel are spin-orbit corrected. The spin-orbit corrections are predicted by a fitted three-dimensional energy surface from about 7520 energy points in the entrance channel at the level of CASSCF (15e, 11o)/aug-cc-pVTZ. The fundamental-invariant neural network method is utilized to fit the SOC PES, resulting in a total root mean square error of 0.12 kcal mol-1. The calculated thermal rate constants of the Cl + NH3 → HCl + NH2 reaction on the SOC PES with the soft-zero-point energy constraint agree reasonably well with the available experimental values.

First-principles mode-specific reaction dynamics

Controlling the outcome of chemical reactions by exciting specific vibrational and/or rotational modes of the reactants is one of the major goals of modern reaction dynamics studies. In the present Perspective, we focus on first-principles vibrational and rotational mode-specific dynamics computations on reactions of neutral and anionic systems beyond six atoms such as X + C2H6 [X = F, Cl, OH], HX + C2H5 [X = Br, I], OH- + CH3I, and F- + CH3CH2Cl. The dynamics simulations utilize high-level ab initio analytical potential energy surfaces and the quasi-classical trajectory method. Besides initial state specificity and the validity of the Polanyi rules, mode-specific vibrational-state assignment for polyatomic product species using normal-mode analysis and Gaussian binning is also discussed and compared with experiment.

Vibrational mode-specificity in the dynamics of the OH- + CH3I multi-channel reaction

We report a comprehensive characterization of the vibrational mode-specific dynamics of the OH- + CH3I reaction. Quasi-classical trajectory simulations are performed at four different collision energies on our previously-developed full-dimensional high-level ab initio potential energy surface in order to examine the impact of four different normal-mode excitations in the reactants. Considering the 11 possible pathways of OH- + CH3I, pronounced mode-specificity is observed in reactivity: In general, the excitations of the OH- stretching and CH stretching exert the greatest influence on the channels. For the SN2 and proton-abstraction products, the reactant initial attack angle and the product scattering angle distributions do not show major mode-specific features, except for SN2 at higher collision energies, where forward scattering is promoted by the CI stretching and CH stretching excitations. The post-reaction energy flow is also examined for SN2 and proton abstraction, and it is unveiled that the excess vibrational excitation energies rather transfer into the product vibrational energy because the translational and rotational energy distributions of the products do not represent significant mode-specificity. Moreover, in the course of proton abstraction, the surplus vibrational energy in the OH- reactant mostly remains in the H2O product owing to the prevailing dominance of the direct stripping mechanism.

Alternating Stereospecificity upon Central-Atom Change: Dynamics of the F- +PH2 Cl SN 2 Reaction Compared to its C- and N-Centered Analogues

Central-atom effects on bimolecular nucleophilic substitution (SN 2) reactions are well-known in chemistry, however, the atomic-level SN 2 dynamics at phosphorous (P) centers has never been studied. We investigate the dynamics of the F- +PH2 Cl reaction with the quasi-classical trajectory method on a novel full-dimensional analytical potential energy surface fitted on high-level ab initio data. Our computations reveal intermediate dynamics compared to the F- +CH3 Cl and the F- +NH2 Cl SN 2 reactions: phosphorus as central atom leads to a more indirect SN 2 reaction with extensive complex-formation with respect to the carbon-centered one, however, the title reaction is more direct than its N-centered pair. Stereospecificity, characteristic at C-center, does not appear here either, due to the submerged front-side-attack retention path and the repeated entrance-channel inversional motion, whereas the multi-inversion mechanism discovered at nitrogen center is also undermined by the deep Walden-well. At low collision energies, 6 % of the PH2 F products form with retained configuration, mostly through complex-mediated mechanisms, while this ratio reaches 24 % at the highest energy due to the increasing dominance of the direct front-side mechanism and the smaller chance for hitting the deep Walden-inversion minimum. Our results suggest pronounced central-atom effects in SN 2 reactions, which can fundamentally change their (stereo)dynamics.

Theoretical studies on the kinetics and dynamics of the BeH+ + H2O reaction: comparison with the experiment

The reaction of BeH+ with background gaseous H2O may play a role in qubit loss for quantum information processing with Be+ as trapped ions, and yet its reaction mechanism has not been well understood until now. In this work, a globally accurate, full-dimensional ground-state potential energy surface (PES) for the BeH+ + H2O reaction was constructed by fitting a total of 170 438 ab initio energy points at the level of RCCSD(T)-F12/aug-cc-pVTZ using the fundamental invariant-neural network method. The total root-mean-square error of the final PES was 0.178 kcal mol-1. For comparison, quasi-classical trajectory calculations were carried out on the PES at an experimental temperature of 150 K. The obtained thermal rate constant and product branching ratio of the BeD+ + H2O reaction agreed quite well with experimental results. In addition, the vibrational state distributions and energy disposals of the products were calculated and rationalized using the sudden vector projection model.

Exploring the versatile reactivity of the F- + SiH3Cl system on a full-dimensional coupled-cluster potential energy surface

We develop a full-dimensional analytical potential energy surface (PES) for the F- + SiH3Cl reaction using Robosurfer for automatically sampling the configuration space, the robust [CCSD-F12b + BCCD(T) - BCCD]/aug-cc-pVTZ composite level of theory for computing the energy points, and the permutationally invariant polynomial method for fitting. Evolution of the fitting error and the percentage of the unphysical trajectories are monitored as a function of the iteration steps/number of energy points and polynomial order. Quasi-classical trajectory simulations on the new PES reveal rich dynamics resulting in high-probability SN2 (SiH3F + Cl-) and proton-transfer (SiH2Cl- + HF) products as well as several lower-probability channels, such as SiH2F- + HCl, SiH2FCl + H-, SiH2 + FHCl-, SiHFCl- + H2, SiHF + H2 + Cl-, and SiH2 + HF + Cl-. The Walden-inversion and front-side-attack-retention SN2 pathways are found to be competitive, producing nearly racemic products at high collision energies. The detailed atomic-level mechanisms of the various reaction pathways and channels as well as the accuracy of the analytical PES are analyzed along representative trajectories.

Reaction mechanism conversion induced by the contest of nucleophile and leaving group

Direct dynamic simulations have been employed to investigate the OH^- + CH₃Cl reaction with the chosen B3LYP/aug-cc-pVDZ method. The calculated rate coefficient for the bimolecular nucleophilic substitution reaction (S_N2), 1.0 × 10^-9 cm³ mol^-1 s^-1 at 300 K, agrees well with the experimental result of (1.3-1.6) × 10^-9 cm³ mol^-1 s^-1. The simulations reveal that the majority of the S_N2 reactions are temporarily trapped in the hydrogen-bonded complex at E_coll = 0.89 kcal mol^-1. Importantly, the influences of the leaving group and nucleophile have been discussed by comparisons of X^- + CH₃Y (X = F, OH; Y = Cl, I) reactions. For the X = F^- reactions, the reaction probability of S_N2 increases along the increased leaving group ability Cl < I, suggesting that the thermodynamic factor plays a key role. The indirect mechanisms were found to be dominant for both reactions. In contrast, for X = OH^-, the fraction of S_N2 drops with the enhanced leaving group ability. In particular, a dramatic transition occurs for the dominant atomic reaction mechanisms, i.e., from complex-mediated indirect to direct, implying an interesting contest between the leaving group and the nucleophile and the importance of the dynamic factors, i.e., the dipole moment, steric hindrance, and electronegativity.

Vibrational mode-specific dynamics of the F- + CH3CH2Cl multi-channel reaction

We investigate the mode-specific dynamics of the ground-state, C-Cl stretching (v₁₀), CH₂ wagging (v₇), sym-CH₂ stretching (v₁), and sym-CH₃ stretching (v₃) excited F^- + CH₃CH₂Cl(v_k = 0, 1) [k = 10, 7, 1, 3] → Cl^- + CH₃CH₂F (S_N2), HF + CH₃CHCl^-, FH⋯Cl^- + C₂H₄, and Cl^- + HF + C₂H₄ (E2) reactions using a full-dimensional high-level analytical global potential energy surface and the quasi-classical trajectory method. Excitation of the C-Cl stretching, CH₂ stretching, and CH₂/CH₃ stretching modes enhances the S_N2, proton abstraction, and FH⋯Cl^- and E2 channels, respectively. Anti-E2 dominates over syn-E2 (kinetic anti-E2 preference) and the thermodynamically-favored S_N2 (wider reactive anti-E2 attack angle range). The direct (a) S_N2, (b) proton abstraction, (c) FH⋯Cl^- + C₂H₄, (d) syn-E2, and (e) anti-E2 channels proceed with (a) back-side/backward, (b) isotropic/forward, (c) side-on/forward, (d) front-side/forward, and (e) back-side/forward attack/scattering, respectively. The HF products are vibrationally cold, especially for proton abstraction, and their rotational excitation increases for proton abstraction, anti-E2, and syn-E2, in order. Product internal-energy and mode-specific vibrational distributions show that CH₃CH₂F is internally hot with significant C-F stretching and CH₂ wagging excitations, whereas C₂H₄ is colder. One-dimensional Gaussian binning technique is proved to solve the normal mode analysis failure caused by methyl internal rotation.

Parameter free evaluation of SN2 reaction rates for halide substitution in halomethane

We estimate the kinetic constants of a series of archetypal S_N2 reactions, i.e., the nucleophilic substitutions of halides in halomethane. A parameter free, multiscale approach recently developed [Campeggio et al., Phys. Chem. Chem. Phys., 2020, 22, 3455] is employed. The protocol relies on quantum mechanical calculations for the description of the energy profile along the intrinsic reaction coordinate, which is then mapped onto a reaction coordinate conveniently built for the reactive process. A Kramers-Klein equation is used to describe the stochastic time evolution of the reaction coordinate and its velocity; friction is parameterized using a hydrodynamic model and Kramers theory is used to derive the rate constant of the reaction. The method is here applied to six S_N2 reactions in water at 295.15 K, which differ in the nucleophile and the leaving group. The computed reaction rates are in good agreement with the experimental data and correlate well with the trends observed for the activation energies.

Toward a Comprehensive Understanding of Mode-Specific Dynamics of Polyatomic Reactions: A Full-Dimensional Quantum Dynamics Study of the H + NH3 Reaction

Mode specificity not only sheds light on reaction dynamics but also opens the door for chemical reaction control. This work reports a state-of-the-art full-dimensional quantum dynamics study on the prototypical hydrogen abstraction reaction of hydrogen with ammonia, which serves as a benchmark for advancing our fundamental understanding of polyatomic reaction dynamics. By taking advantage of the (3 + 1) Radau-Jacobi coordinates, the bond-specific probabilities are resolved with the reactant NH₃ initiated from either a non-degenerate or degenerate stretching vibrational state. The observed different atom-specific abstraction probabilities from individual states of the degenerate pair are rationalized in the local mode representation according to the different vibrational energy deposited in each N-H bond. It is verified that the three H atoms in NH₃ have the same abstraction probability as that from the degenerate pair and the linear combination of the degenerate pair gives the same reaction probability. In addition, the symmetric and asymmetric stretching modes of the reactant NH₃ have comparable efficacies on driving the reaction.

Reaction mechanism of an intracluster SN2 reaction induced by electron capture

Bimolecular nucleophilic substitution (S_N2) reactions have been widely investigated from both experimental and theoretical points of view because they represent one of the simplest organic reactions. Most studies on S_N2 reactions have been focused on bimolecular collision. In contrast, information on intracluster S_N2 reactions is limited. In this study, an intracluster S_N2 reaction of NF₃-CH₃Cl triggered by electron attachment was investigated using a direct ab initio molecular dynamics (AIMD) method. In the structure of NF₃-CH₃Cl, the N-F bond in NF₃ is oriented collinearly toward the carbon atom of CH₃Cl. After electron capture by NF₃-CH₃Cl, the F^- ion that is generated from the (NF₃)^- moiety collides with the carbon atom of CH₃Cl. The intracluster S_N2 reaction occurs as follows: (NF₃-CH₃Cl)^- (electron capture state) → NF₂-(F^-)-CH₃Cl (pre-reaction complex) → transition state (TS) → NF₂-CH₃F-Cl^- (post-reaction complex) → NF₂ + CH₃F + Cl^- (product state). The reaction energy is efficiently transferred to the translational mode of Cl^-, and the Cl^- ion with a high translational energy is then removed from the system. This energy is significantly larger than that of Cl^- formed in the bimolecular S_N2 reaction (F^- + CH₃Cl). The reaction mechanism is discussed based on the theoretical results.

Kinetic and dynamic studies of the NH2+ + H2 reaction on a high-level ab initio potential energy surface

The dynamics and kinetics of the NH2+ + H2 reaction are investigated on a newly developed ab initio potential energy surface using the quasi-classical trajectory method.

Effect of microsolvation on the mode specificity of the OH˙(H2O) + HCl reaction

The present study investigates the mode specificity in the microsolvated OH˙(H₂O) + HCl reaction using on-the-fly direct dynamics simulation. To the best of our knowledge, this is the first study which aims to gain insights into the effect of microsolvation on the mode selectivity. Our investigation reveals that, similar to the gas phase OH˙ + HCl reaction, the microsolvated reaction is also predominantly affected by the vibrational excitation of the HCl mode, whereas the OH vibrational mode behaves as a spectator. Interestingly, in contrast to the behavior of the bare reaction, the integral cross section at the ground state of the microsolvated reaction decreases with an increase in translational energy. However, for the vibrational excited states, the reactivity of the microsolvated reaction is found to be higher than that of the bare reaction within the selected range of translational energies.

Atomistic dynamics of elimination and nucleophilic substitution disentangled for the F- + CH3CH2Cl reaction

Chemical reaction dynamics are studied to monitor and understand the concerted motion of several atoms while they rearrange from reactants to products. When the number of atoms involved increases, the number of pathways, transition states and product channels also increases and rapidly presents a challenge to experiment and theory. Here we disentangle the dynamics of the competition between bimolecular nucleophilic substitution (S_N2) and base-induced elimination (E2) in the polyatomic reaction F^- + CH₃CH₂Cl. We find quantitative agreement for the energy- and angle-differential reactive scattering cross-sections between ion-imaging experiments and quasi-classical trajectory simulations on a 21-dimensional potential energy hypersurface. The anti-E2 pathway is most important, but the S_N2 pathway becomes more relevant as the collision energy is increased. In both cases the reaction is dominated by direct dynamics. Our study presents atomic-level dynamics of a major benchmark reaction in physical organic chemistry, thereby pushing the number of atoms for detailed reaction dynamics studies to a size that allows applications in many areas of complex chemical networks and environments.

Detailed quasiclassical dynamics of the F- + CH3Br reaction on an ab initio analytical potential energy surface

Dynamics and mechanisms of the F^- + CH₃Br(v = 0) → Br^- + CH₃F (S_N2 via Walden inversion, front-side attack, and double inversion), F^- + inverted-CH₃Br (induced inversion), HF + CH₂Br^- (proton abstraction), and FH⋯Br^- + ¹CH₂ reactions are investigated using a high-level global ab initio potential energy surface, the quasiclassical trajectory method, as well as non-standard configuration- and mode-specific analysis techniques. A vector-projection method is used to identify inversion and retention trajectories; then, a transition-state-attack-angle-based approach unambiguously separates the front-side attack and the double-inversion retention pathways. The Walden-inversion S_N2 channel becomes direct rebound dominated with increasing collision energy as indicated by backward scattering, initial back-side attack preference, and the redshifting of product internal energy peaks in accord with CF stretching populations. In the minor retention and induced-inversion pathways, almost the entire available energy transfers into product rotation-vibration, and retention mainly proceeds with indirect, slow double inversion following induced inversion with about 50% probability. Proton abstraction is dominated by direct stripping (evidenced by forward scattering) with CH₃-side initial attack preference, providing mainly vibrationally ground state products with significant zero-point energy violation.

Kinetic and Dynamic Studies of the F(2P) + ND3 → DF + ND2 Reaction

The fast F reaction with NH₃ poses a big challenge to experimental studies because of secondary chemical and collisional reactions. The quasi-classical trajectory method is utilized to investigate the mode specificity, product energy disposal, and temperature dependence of the thermal rate coefficient of F + ND₃ → DF + ND₂ on a recently developed potential energy surface. The effect of isotopic substitution is explored by comparing the F + ND₃ reaction with the F + NH₃ reaction. The computed results permit a better understanding of the F + ammonia reaction. The DF vibrational state has a Λ-type distribution, in accordance with the experimental measurement by the fast flow reactor technique. The product ND₂ is dominantly populated in the ground state, and a considerable amount of ND₂ is produced in the fundamental states of the bending mode. The similar vibrational state distributions of HF and NH₂ in the F + NH₃ reaction indicate a weak isotopic substitution effect on the product energy disposal. Exciting the umbrella mode of ND₃ suppresses the reaction at low energies below 5 kcal mol^-1, in sharp contrast to the observation in the F + NH₃ reaction. These dynamical behaviors can be partially explained by the sudden vector projection model. In addition, the thermal rate coefficient of F + ND₃ shows no temperature dependence in the range between 150 and 2000 K. There exists an inverse kinetic isotope effect at temperatures from 150 to 1500 K.

Study on the kinetics and dynamics of the H2 + NH2- reaction on a high-level ab initio potential energy surface

Gas-phase ion-molecule reactions play major roles in many fields of chemistry and physics. The reaction of an amino radical anion with a hydrogen molecule is one of the simplest proton transfer reactions involving anions. A globally accurate full-dimensional potential energy surface (PES) for the NH₂^- + H₂ reaction is developed by the fundamental invariant-neural network method, resulting in a root mean square error of 0.116 kcal mol^-1. Quasi-classical trajectory calculations are then carried out on the newly developed PES to give integral cross sections, differential cross sections and thermal rate coefficients. This reaction has two reaction channels, proton transfer and hydrogen exchange. The reactivity of the proton transfer channel is about one or two orders of magnitude stronger than that of the hydrogen exchange channel in the energy range studied. Vibrational excitation of H₂ promotes the proton transfer reaction, while fundamental excitation of each vibrational mode of NH₂^- has a negligible effect. In addition, the theoretical rate coefficients of the proton transfer reaction on the PES show inverse temperature dependence from 150 to 750 K, in accordance with the available experimental results.

Fifty years of nucleophilic substitution in the gas phase

Bimolecular nucleophilic substitution ( S N 2 ) reactions have become a model system for the investigation of structure-reactivity relationships, stereochemistry, solvent influences, and detailed atomistic dynamics. In this review, the progress during five decades of experimental and theoretical research on gas phase S N 2 reactions is discussed. Many advancements of the employed methods have led to a tremendous increase in our understanding of the properties and the dynamics of these reactions. For reactions involving six atoms a quantitative agreement of the differential reactive scattering cross sections has already been achieved, in the future it is expected that even larger polyatomic reactions systems become tractable. Furthermore, studies with higher precision, improved reactant control, and a more accurate theoretical treatment of quantum effects are envisioned.

Advances and New Challenges to Bimolecular Reaction Dynamics Theory

Dynamics of bimolecular reactions in the gas phase are of foundational importance in combustion, atmospheric chemistry, interstellar chemistry, and plasma chemistry. These collision-induced chemical transformations are a sensitive probe of the underlying potential energy surface(s). Despite tremendous progress in past decades, our understanding is still not complete. In this Perspective, we survey the recent advances in theoretical characterization of bimolecular reaction dynamics, stimulated by new experimental observations, and identify key new challenges.

Influence of Vibrational Excitation on the Reaction of F- with CH3I: Spectator Mode Behavior, Enhancement, and Suppression

Detailed insight into chemical reaction dynamics can be obtained by probing the effect of mode-specific vibrational excitation. Suppression or enhancement of reactivity is possible as is already known from the Polanyi rules. In the reaction F- + CH3I, we found vibrational enhancement, suppression, and spectator mode dynamics in the four different reaction channels. For this system we have probed the influence of symmetric CH-stretching vibration over a collision energy range of 0.7-2.3 eV. Proton transfer is significantly enhanced, while for the nucleophilic substitution channel the spectator mode dynamics at lower collision energies unexpectedly move toward enhancement at higher collision energies. In contrast, for two halide abstraction channels, forming FI- and FHI-, we found an overall suppression, which stems mainly from a suppression of the FHI- product. We compare these results to quasiclassical trajectory calculations and with the sudden vector projection model.

Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium

We present an approach to incorporate the effect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a specifically tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational efficacy and mode selectivity of vibrationally stimulated reactions can then be quantified in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We first validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the effect of vibrational excitation on a symmetric S_N2 reaction and radical addition on CO₂.

On the development of a gold-standard potential energy surface for the OH− + CH3I reaction

We develop the first accurate full-dimensional ab initio PES for the OH⁻ + CH₃I S_N2 and proton-transfer reactions treating the failure of CCSD(T) at certain geometries.

Benchmark ab initio and dynamical characterization of the stationary points of reactive atom + alkane and SN2 potential energy surfaces

We review composite ab initio and dynamical methods and their applications to characterize stationary points of atom/ion + molecule reactions.

Nucleophilic substitution vs elimination reaction of bisulfide ions with substituted methanes: exploration of chiral selectivity by stereodirectional first-principles dynamics and transition state theory

Control of molecular orientation is emerging as crucial for the characterization of the stereodynamics of kinetics processes beyond structural stereochemistry. The special role played in chiral discrimination phenomena has been particularly emphasized by Aquilanti and collaborators after their extensive probes of experimental control of molecular alignment and orientation. In this work, the manifestation of the Aquilanti mechanism has been demonstrated for the first time in first-principles molecular dynamics simulations: stationary points characterized on potential energy surfaces have been calculated for the study of chemical reactions occurring between the bisulfide anion HS^- and oriented prototypical chiral molecules CHFXY (where X = CH₃ or CN and Y = Cl or I). The important reaction channels are those corresponding to bimolecular nucleophilic substitution (S_N2) and to bimolecular elimination (E2): their relative role has been assessed and alternative pathways due to the mirror forms of the oriented chiral molecule are revealed by the different reactivity of the two enantiomers of CHFCNI in S_N2 reaction.

Theoretical study of the F(2P) + NH3→ HF + NH2 reaction on an accurate potential energy surface: dynamics and kinetics

The highly exothermic hydrogen abstraction reaction of the F atom with NH₃ is investigated using the quasi-classical trajectory method on a newly developed potential energy surface (PES) for the ground electronic state. The full-dimensional PES is constructed by fitting 41 282 ab initio energy points at the level of UCCSD(T)-F12/aug-cc-pVTZ. The flexible fundamental invariant-neural network method is applied in the fitting, resulting in a total root mean square error of 0.13 kcal mol^-1. On one hand, the calculated differential cross sections agree reasonably well with the experimental results and indicate that the reaction is dominated by the direct abstraction and stripping mechanisms while a considerable amount of reaction takes place by the indirect "yo-yo" mechanism. The product energy partition also reproduces well the experimental result, which can be understood according to the geometry change along the minimum energy path. On the other hand, the obtained vibrational state distribution of the product HF follows P_νHF=2≈P_νHF=1 > P_νHF=0 > P_νHF=3, less consistent with the scattered experimental results. In addition, the calculated thermal rate coefficients have practically no temperature dependence within the statistical errors.

Mode-specific quantum dynamics and kinetics of the hydrogen abstraction reaction OH + H2O → H2O + OH

The synergistic effect between the reactant stretching and bending modes on promoting the reaction.

Mode-Specific Quasiclassical Dynamics of the F- + CH3I SN2 and Proton-Transfer Reactions

Mode-specific quasiclassical trajectory computations are performed for the F^- + CH₃I( v _k = 0, 1) S_N2 and proton-transfer reactions at nine different collision energies in the range of 1.0-35.3 kcal/mol using a full-dimensional high-level ab initio analytical potential energy surface with ground-state and excited CI stretching ( v₃), CH₃ rocking ( v₆), CH₃ umbrella ( v₂), CH₃ deformation ( v₅), CH symmetric stretching ( v₁), and CH asymmetric stretching ( v₄) initial vibrational modes. Millions of trajectories provide statistically definitive mode-specific cross sections, opacity functions, scattering angle distributions, and product internal energy distributions. The excitation functions reveal slight vibrational S_N2 inversion inhibition/enhancement at low/high collision energies ( E_coll), whereas large decaying-with- E_coll vibrational enhancement effects for the S_N2 retention (double inversion) and proton-transfer channels. The most efficient vibrational enhancement is found by exciting the CI stretching (high E_coll) for S_N2 inversion and the CH stretching modes (low E_coll) for double inversion and proton transfer. Mode-specific effects do not show up in the scattering angle distributions and do blue-shift the hot/cold S_N2/proton-transfer product internal energies.

Low temperature reaction dynamics for CH3OH + OH collisions on a new full dimensional potential energy surface

Is the rise of the rate constant measured in laval expansion experiments of OH with organic molecules at low temperatures due to the reaction between the reactants or due to the formation of complexes with the buffer gas? This question has importance for understanding the evolution of prebiotic molecules observed in different astrophysical objects. Among these molecules methanol is one of the most widely observed, and its reaction with OH has been studied by several groups showing a fast increase in the rate constant under 100 K. Transition state theory doesn't reproduce this behavior and here dynamical calculations are performed on a new full dimensional potential energy surface developed for this purpose. The calculated classical reactive cross sections show an increase at low collision energies due to a complex forming mechanism. However, the calculated rate constant at temperatures below 100 K remains lower than the observed one. Quantum effects are likely responsible for the measured behavior at low temperatures.

Activation of Reactions in the Complex Region Using Microwave Irradiation

Many mode-specific behaviors in the gas phase and at the gas-surface interface have been reported in the past decades. Infrared activation of a reagent vibrational mode is often used to study these reactions. In this work, an inexpensive and easily applied scheme using microwave irradiation is proposed for activating complex-forming reactions by transferring populations between closely spaced resonances. The important combustion reaction of H + O₂ ↔ O + OH is used as a model system to demonstrate the feasibility of the proposed approach. The existence of a nonzero transition dipole moment matrix element between two highly excited resonance states separated by a small energy gap in the model system may allow one to use microwave irradiation to intervene and control the model reaction. The high energy resonance states of the model reaction can also release their energy by photon emission, which is in agreement with the experimentally observed chemiluminescence process.

New Method To Extract Final-State Information of Polyatomic Reactions Based on Normal Mode Analysis

State-to-state reaction dynamics provides a comprehensive insight into reaction mechanisms of chemical reactions at the atomic level. A new scheme to extract final-state information based on normal mode analysis is proposed in this work. Different from the traditional scheme extracting the coordinates and momenta from the last step of each trajectory, they are taken in the new scheme from a specific step of each reactive trajectory within the last vibrational period of the product molecule by demanding the corresponding geometry of the step to have the minimum potential energy. Test calculations on the collisions between the atom H and the molecules H₂O, H₂S, and NH₃ show that the new scheme works much better than the traditional one. In addition, the new scheme is applied to calculate the vibrational state distribution of the product NH₂ in the reaction H + NH₃ → H₂ + NH₂.

Understanding mode-specific dynamics in the local mode representation

Mode specificity is a main characteristic of transition state control of reaction dynamics. The normal mode representation has been widely employed to describe the mode specificity in elementary chemical reactions. However, spectroscopists have demonstrated that the local mode representation has advantages in analyzing the overtone and combination band spectra. In this work, the mode-specific reaction dynamics between the hydrogen atom and the molecules H2S and H2O is studied using a full-dimensional quantum scattering model in the (2 + 1) Radau-Jacobi coordinates. The mode specificities in the reactions that violates our physical intuition in the normal mode representation are well rationalized in the local mode representation. The energy flow between different XH bonds resulting from the intramolecular interaction and/or intermolecular interaction is unveiled, together with its impacts on dynamics of the abstraction and exchange reactions.

Solvent Effect on the Potential Energy Surfaces of the F- + CH3CH2Br Reaction

Although substantial work has been undertaken on reaction pathways involved in base-promoted elimination reactions and bimolecular nucleophilic substitution reaction of F^- on CH₃CH₂X (X = Cl, Br, I), the effect of solvents with varying dielectric constants on the stereochemistry of each of the reaction species involved across the reaction profile have not yet been clearly understood. The present investigation reports the effect of solvents on the potential energy surfaces (PES) and structures of the species appearing in the reaction pathway of F^- with bromoethane. The PESs in the gas phase have been computed at MP2 level and CCSD(T) level. The performance of several hybrid density functional, such as B3LYP, M06, M06L, BHandH, X3LYP, M05, M05-2X, and M06-2X have also been investigated toward describing the elimination and nucleophilic substitution reactions. With respect to MAE values and to make the computation cost-effective, we have explored the implicit continuum solvent model, CPCM in solvents like cyclohexane, methanol, acetonitrile, dimethyl sulfoxide and water. The reactant complexes proceed through the subsequent steps to produce fluoroethane as the substitution product and ethylene as one of the elimination products. For elimination reaction both syn and anti elimination have been explored. The calculated relatives energies values, which are negative in the gas phase, are found to be positive in polar solvents since the point charge in the separated reactants are more stabilized than the dispersed charge in the transient complex, which has also been analyzed through NBO analysis.

Stretching vibration is a spectator in nucleophilic substitution

How chemical reactions are influenced by reactant vibrational excitation is a long-standing question at the core of chemical reaction dynamics. In reactions of polyatomic molecules, where the Polanyi rules are not directly applicable, certain vibrational modes can act as spectators. In nucleophilic substitution reactions, CH stretching vibrations have been considered to be such spectators. While this picture has been challenged by some theoretical studies, experimental insight has been lacking. We show that the nucleophilic substitution reaction of F^- with CH₃I is minimally influenced by an excitation of the symmetric CH stretching vibration. This contrasts with the strong vibrational enhancement of the proton transfer reaction measured in parallel. The spectator behavior of the stretching mode is supported by both quasi-classical trajectory simulations and the Sudden Vector Projection model.

Active vs. spectator modes in nonadiabatic photodissociation dynamics of the hydroxymethyl radical via the 22A(3s) Rydberg state

The choice of the active degrees of freedom (DOFs) is a pivotal issue in a reduced-dimensional model of quantum dynamics when a full-dimensional one is not feasible. Here, several five-dimensional (5D) models are used to investigate the nonadiabatic photodissociation dynamics of the hydroxymethyl (CH₂OH) radical, which possesses nine internal DOFs, in its lowest absorption band. A normal-mode based scheme is used to identify the active and spectator modes, and its predictions are confirmed by 5D quantum dynamical calculations. Our results underscore the important role of the CO stretching mode in the photodissociation dynamics of CH₂OH, originating from the photo-induced promotion of an electron from the half-occupied π*_CO antibonding orbital to a carbon Rydberg orbital.

Full dimensional potential energy surface and low temperature dynamics of the H2CO + OH → HCO + H2O reaction

A new method is proposed to analytically represent the potential energy surface of reactions involving polyatomic molecules capable of accurately describing long-range interactions and saddle points, needed to describe low-temperature collisions. It is based on two terms, a reactive force field term and a many-body term. The reactive force field term accurately describes the fragments, long-range interactions among them and the saddle points for reactions. The many-body term increases the desired accuracy everywhere else. This method has been applied to the OH + H2CO → H2O + HCO reaction, giving a barrier of 27.4 meV. The simulated classical rate constants with this potential are in good agreement with recent experimental results [Ocaña et al., Astrophys. J., 2017, submitted], showing an important increase at temperatures below 100 K. The reaction mechanism is analyzed in detail here, and explains the observed behavior at low energy by the formation of long-lived collision complexes, with roaming trajectories, with a capture observed for very long impact parameters, >100 a.u., determined by the long-range dipole-dipole interaction.

Indirect dynamics in SN2@N: insight into the influence of central atoms

Central atoms have a significant influence on the reaction kinetics and dynamics of nucleophilic substitution (S_N2). Herein, atomistic dynamics of a prototype S_N2@N reaction F^- + NH₂Cl is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for a S_N2@C congener F^- + CH₃Cl. Indirect scattering is found to prevail, which proceeds predominantly through a hydrogen-bonded F^--HNHCl complex in the reactant entrance channel. This unexpected finding of a pronounced contribution of indirect reaction dynamics, even at a high collision energy, is in strong contrast to a general evolution from indirect to direct dynamics with enhanced energy that characterizes S_N2@C. This result suggests that the relative importance of different atomic-level mechanisms may depend essentially on the interaction potential of reactive encounters and the coupling between inter- and intramolecular modes of the pre-reaction complex. For F^- + NH₂Cl the proton transfer pathway is less competitive than S_N2. A remarkable finding is that the more favorable energetics for NH₂Cl proton transfer, as compared to that for CH₃Cl, does not manifest itself in the reaction dynamics. The present work sheds light on the underlying reaction dynamics of S_N2@N, which remain largely unclear compared to well-studied S_N2@C.

Potential energy surface stationary points and dynamics of the F- + CH3I double inversion mechanism

Direct dynamics simulations were performed to study the S_N2 double inversion mechanism S_N2-DI, with retention of configuration, for the F^- + CH₃I reaction. Previous simulations identified a transition state (TS) structure, i.e. TS0, for the S_N2-DI mechanism, including a reaction path. However, intrinsic reaction coordinate (IRC) calculations from TS0 show it is a proton transfer (PT) TS connected to the F^-HCH₂I S_N2 pre-reaction complex and the FHCH₂I^- proton transfer post-reaction complex. Inclusion of TS0 in the S_N2-DI mechanism would thus involve non-IRC atomistic dynamics. Indeed, trajectories initiated at TS0, with random ensembles of energies as assumed by RRKM theory, preferentially form the S_N2-DI products and ∼70% follow the proposed S_N2-DI pathway from TS0 to the products. In addition, the Sudden Vector Projection (SVP) method was used to identify which CH₃I vibrational mode excitations promote access to TS0 and the S_N2-DI mechanism. Results of F^- + CH₃I simulations, with SVP specified mode excitations, are disappointing. With the CH₃ deformations of CH₃I excited, the S_N2 single inversion mechanism is the dominant pathway. If the CH stretch modes are also excited, proton transfer dominates the reaction. S_N2-DI occurs, but with a very small probability of ∼1%. The reasons behind these results are discussed.

Conservation of direct dynamics in sterically hindered SN2/E2 reactions

Nucleophilic substitution (S_N2) and base-induced elimination (E2), two indispensable reactions in organic synthesis, are commonly assumed to proceed under stereospecific conditions. Understanding the way in which the reactants pre-orient in these reactions, that is its stereodynamics, is essential in order to achieve a detailed atomistic picture and control over such processes. Using crossed beam velocity map imaging, we study the effect of steric hindrance in reactions of Cl^- and CN^- with increasingly methylated alkyl iodides by monitoring the product ion energy and scattering angle. For both attacking anions the rebound mechanism, indicative of a direct S_N2 pathway, is found to contribute to the reaction at high relative collision energies despite being increasingly hindered. An additional forward scattering mechanism, ascribed to a direct E2 reaction, also contributes at these energies. Inspection of the product energy distributions confirms the direct and fast character of both mechanisms as opposed to an indirect reaction mechanism which leads to statistical energy redistribution in the reaction complex. This work demonstrates that nonstatistical dynamics and energetics govern S_N2 and E2 pathways even in sterically hindered exchange reaction systems.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S_N2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S_N2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F^- + CH₃Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S_N2 mechanism, (b) frontside complex formation,

Deciphering Front-Side Complex Formation in SN2 Reactions via Dynamics Mapping

Due to their importance in organic chemistry, the atomistic understanding of bimolecular nucleophilic substitution (S_N2) reactions shows exponentially growing interest. In this publication, the effect of front-side complex (FSC) formation is uncovered via quasi-classical trajectory computations combined with a novel analysis method called trajectory orthogonal projection (TOP). For both F^- + CH₃Y [Y = Cl,I] reactions, the lifetime distributions of the F^-···YCH₃ front-side complex revealed weakly trapped nucleophiles (F^-). However, only the F^- + CH₃I reaction features strongly trapped nucleophiles in the front-side region of the prereaction well. Interestingly, both back-side and front-side attack show propensity to long-lived FSC formation. Spatial distributions of the nucleophile demonstrate more prominent FSC formation in case of the F^- + CH₃I reaction compared to F^- + CH₃Cl. The presence of front-side intermediates and the broad spatial distribution in the back-side region may explain the indirect nature of the F^- + CH₃I reaction.

Imaging dynamic fingerprints of competing E2 and SN2 reactions

The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X⁻ + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity. This characteristic fingerprint is also confirmed by direct dynamics simulations for ethyl as residue and attributed to the dynamics of elimination reactions. This work opens the door to a detailed atomistic understanding of transformation reactions in even larger systems.

The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.