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.

Competing C and N as Reactive Centers for Microsolvated Ambident Nucleophiles CN-(H2O)n=0-3: A Theoretical Study of E2/SN2 Reactions with CH3CH2X (X = Cl, Br, I)

As an ambident nucleophile, CN- has both C and N atoms that can act as the reactive center to facilitate substitution reactions. We investigate in detail the potential energy profiles of CN-(H2O)0-3 with CH3CH2X (X = Cl, Br, I) to explore the influence of solvent molecules on competition between the different nucleophilic atoms C and N involving the SN2 and E2 pathways. The energy barrier sequence for the transition states follows C@inv-SN2 < N@inv-SN2 < C@anti-E2 < N@anti-E2. When two different atoms act as nucleophilic atoms, the SN2 reaction is always preferred over the E2 reaction, and this preference increases with microsolvation. For the ambident nucleophiles CN-(H2O)0-3, C as the reactive center always has stronger nucleophilicity and basicity than N acting as the reactive center. Regarding the leaving group, the height of the energy barrier is positively correlated with the acidity of the CH3CH2X substrate for the E2 pathway and with X-heterolysis for the SN2 pathway. Furthermore, we found that in the gas phase, the energy barrier for different leaving group systems decreases gradually in the order Cl > Br > I, while in the SMD solution, the energy barrier and product energy increase slightly in the system from X = Cl to Br; this change may be due to the significantly weakened transition-state interaction for the X = Br system. Our activation strain, quantitative molecular orbital, and charge analyses reveal the physical mechanisms underlying the various computed trends. In addition, we also demonstrate the two points recently proposed by Vermeeren, P. . Chem. Eur. J. 2020, 26, 15538-15548.

Benchmark ab initio characterization of the complex potential energy surfaces of the HOO- + CH3Y [Y = F, Cl, Br, I] reactions

The α-effect is a well-known phenomenon in organic chemistry, and is related to the enhanced reactivity of nucleophiles involving one or more lone-pair electrons adjacent to the nucleophilic center. The gas-phase bimolecular nucleophilic substitution (SN2) reactions of α-nucleophile HOO- with methyl halides have been thoroughly investigated experimentally and theoretically; however, these investigations have mainly focused on identifying and characterizing the α-effect of HOO-. Here, we perform the first comprehensive high-level ab initio mapping for the HOO- + CH3Y [Y = F, Cl, Br and I] reactions utilizing the modern explicitly-correlated CCSD(T)-F12b method with the aug-cc-pVnZ [n = 2-4] basis sets. The present ab initio characterization considers five distinct product channels of SN2: (CH3OOH + Y-), proton abstraction (CH2Y- + H2O2), peroxide ion substitution (CH3OO- + HY), SN2-induced elimination (CH2O + HY + HO-) and SN2-induced rearrangement (CH2(OH)O- + HY). Moreover, besides the traditional back-side attack Walden inversion, the pathways of front-side attack, double inversion and halogen-bond complex formation have also been explored for SN2. With regard to the Walden inversion of HOO- + CH3Cl, the previously unaddressed discrepancies concerning the geometry of the corresponding transition state are clarified. For the HOO- + CH3F reaction, the recently identified SN2-induced elimination is found to be more exothermic than the SN2 channel, submerged by ∼36 kcal mol-1. The accuracy of our high-level ab initio calculations performed in the present study is validated by the fact that our new benchmark 0 K reaction enthalpies show excellent agreement with the experimental data in nearly all cases.

Backside versus Frontside SN2 Reactions of Alkyl Triflates and Alcohols

Nucleophilic substitution reactions are elementary reactions in organic chemistry that are used in many synthetic routes. By quantum chemical methods, we have investigated the intrinsic competition between the backside SN2 (SN2-b) and frontside SN2 (SN2-f) pathways using a set of simple alkyl triflates as the electrophile in combination with a systematic series of phenols and partially fluorinated ethanol nucleophiles. It is revealed how and why the well-established mechanistic preference for the SN2-b pathway slowly erodes and can even be overruled by the unusual SN2-f substitution mechanism going from strong to weak alcohol nucleophiles. Activation strain analyses disclose that the SN2-b pathway is favored for strong alcohol nucleophiles because of the well-known intrinsically more efficient approach to the electrophile resulting in a more stabilizing nucleophile-electrophile interaction. In contrast, the preference of weaker alcohol nucleophiles shifts to the SN2-f pathway, benefiting from a stabilizing hydrogen bond interaction between the incoming alcohol and the leaving group. This hydrogen bond interaction is strengthened by the increased acidity of the weaker alcohol nucleophiles, thereby steering the mechanistic preference toward the frontside SN2 pathway.

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.

Computational Insights into SN 2 and Proton Transfer Reactions of CH3 O- with NH2 Y and CH3 Y

Bimolecular nucleophilic substitution (SN 2) reactions have been extensively studied in both theory and experiment. While research on C-centered SN 2 reactions (SN 2@C) has been ongoing, SN 2 reactions at neutral nitrogen (SN 2@N) have received increased attention in recent years. To recommend methods for dynamics simulations, the comparison for the properties of the geometries, vibrational frequencies, and energies is done between MP2 and six DFT functional calculations and experimental data as well as the high-level CCSD(T) method for CH3 O- +NH2 Cl/CH3 Cl reactions. The relative energy diagrams at the M06 method for CH3 O- with CH3 Y/NH2 Y reactions (Y=F, Cl, Br, I) in the gas and solution phase are explored to investigate the effects of the leaving groups, different reaction centers, and solvents. We mainly focus on the computational of inv-SN 2 and proton transfer (PT) pathways. The PT channel in the gas phase is more competitive than the SN 2 channel for N-center reactions, while the opposite is observed for C-centered reactions. Solvation completely inhibits the PT channel, making SN 2 the dominant pathway. Our study provides new insight into the SN 2 reaction mechanisms and rich the novel reaction model in gas-phase organic chemistry.

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.

Competition between Elimination and Substitution for Ambident Nucleophiles CN- and Iodoethane Reactions in Gaseous and Aqueous Medium

Nucleophilic substitution (SN2) and elimination (E2) reactions between ambident nucleophiles have long been considered as typical reactions in organic chemistry, and exploring the competition between the two reactions is of great importance in chemical synthesis. As a nucleophile, CN- can use its C and N atoms as the reactive centers to undergo E2 and SN2 reactions, but related research is currently limited. This study uses the CCSD(T)/pp/t//MP2/ECP/d electronic structure method to perform detailed investigations on the potential energy profiles for SN2 and E2 reactions between CN- and CH3CH2I in gaseous and aqueous media. The potential energy profiles reveal that the energy barriers for SN2 and E2 reactions with the C atom as the reactive center are consistently lower than those with the N atom, indicating that the C atom has a stronger nucleophilic ability and stronger basicity. Furthermore, the potential energy profiles in both gas and aqueous environments show that the barriers of SN2 reactions are lower than those for E2 reactions with both C and N as the attacking atom. By using the frontier molecular orbital and activation strain models to explain the interesting phenomenon, the transition from the gas phase to solution was investigated, specifically in the gas-microsolvation-water transition. The results show that water molecules reduce the nucleophilicity and basicity of CN-, while strain energy (ΔEstrain) causes a greater increase in the energy barrier for E2 reactions. This study provides new insights and perspectives on the understanding of CN- as a nucleophile in SN2 reactions and serves as theoretical guidance for organic synthesis.

Effects of Methyl Substitution and Leaving Group on E2/SN2 Competition for Reactions of F- with RY (R = CH3, C2H5, iC3H7, tC4H9; Y = Cl, I)

The competition between base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) is of significant importance in organic chemistry and is influenced by many factors. The electronic structure calculations for the gas-phase reactions of F- + RY (R = CH3, C2H5, iC3H7, tC4H9, and Y = Cl, I) are executed at the MP2 level with aug-cc-pVDZ or ECP/d basis set to investigate the α-methyl substitution effect. The variation in barrier height, reaction enthalpy, and competition of SN2/E2 as a function of methyl-substitution and leaving group ability has been emphasized. And the nature of these rules has been explored. As the degree of methyl substitution on α-carbon increases, the E2 channel becomes more competitive and dominant with R varying from C2H5, iC3H7, to tC4H9. Energy decomposition analysis offers new insights into the competition between E2 and SN2 processes, which suggests that the drop in interaction energy with an increasing degree of substitution cannot compensate for the rapid growth of preparation energy, leading to a rapid increase in the SN2 energy barrier. By altering the leaving group from Cl to I, the barriers of both SN2 and E2 monotonically decrease, and, with the increased number of substituents, they reduce more dramatically, which is attributed to the looser transition state structures with the stronger leaving group ability. Interestingly, ∆E0‡ exhibits a positive linear correlation with reaction enthalpy (∆H) and halogen electronegativity. With the added number of substituents, the differences in ∆E0‡ and ∆H between Y = Cl and I likewise exhibit good linearity.

Nucleophilic substitution reactions of microsolvated hydroperoxide anion HOO-(NH3)n with methyl chloride and comparison between ammonia and water as the solvent

Similar to microhydrated hydroperoxide anion HOO^-(H₂O)_n, the HOO^-(NH₃)_n=1-3 anion can induce alternative nucleophiles by proton transfer (PT) from the solvent molecule NH₃. The PT-induced species NH₂^-(H₂O₂)(NH₃)_n-1 is higher in energy than HOO^-(NH₃)_n, obeying the proton affinity (PA) prediction that HOO^- has a higher PA than NH₂^-. The potential energy profile of HOO^-(NH₃)_n reacting with CH₃Cl shows that the transition states of the traditional HOO^--S_N2 pathway are ∼10 kcal mol^-1 lower in energy than those of the PT-induced NH₂^--S_N2 pathway, indicating the latter path is unlikely to compete. The differential solvation energy for reactants and transition states with incremental solvation increases the barrier height of both HOO^--/NH₂^--S_N2 pathways and makes the transition structures more product-like. For HOO^-(sol)_n + CH₃Cl → CH₃OOH + Cl^-(sol)_n reactions, the barrier heights for sol = H₂O are higher than those for sol = NH₃, because H₂O is more polar than NH₃, and the electrostatic interaction is strengthened, hence H₂O molecules stabilize the microsolvated nucleophiles more. In addition, because the H₂O molecule is a better proton donor than the NH₃ molecule, the PT-induced HO^-S_N2 pathway is more likely to compete with the HOO^-S_N2 pathway. The HOMO level of nucleophiles, which negatively correlates with the S_N2 barrier heights, is found to be a good descriptor to predict the S_N2 barrier height of a microsolvated system with the same attacking nucleophile. This work adds to our understanding of the differential solvent effect on the prototype ion-molecule S_N2 reactions.

Spectroscopic Study of the Br- +CH3 I→I- +CH3 Br SN 2 Reaction

Mass spectrometry and anion photoelectron spectroscopy have been used to study the gas-phaseS N 2 ${{{\rm S}}_{{\rm N}}2}$ reaction involvingB r - ${{{\rm B}{\rm r}}^{-}}$ andC H 3 I ${{{\rm C}{\rm H}}_{3}{\rm I}}$ . The anion photoelectron spectra associated with the reaction intermediates of thisS N 2 ${{{\rm S}}_{{\rm N}}2}$ reaction are presented. High-level CCSD(T) calculations have been utilised to investigate the reaction intermediates that may form as a result of theS N 2 ${{{\rm S}}_{{\rm N}}2}$ reaction along various different reaction pathways, including back-side attack and front-side attack. In addition, simulated vertical detachment energies of each reaction intermediate have been calculated to rationalise the photoelectron spectra.

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.

Atomic-Level Mechanism, Solvent Effect, and Potential of the Mean Force of the F- + CH3CH2Cl SN2 Reaction in Aqueous Solution

We investigate the bimolecular nucleophilic substitution (S_N2) reaction of F^- with CH₃CH₂Cl in aqueous solution using combined multilevel quantum mechanism (ML-QM) theories with molecular mechanics (MM). The synchronized, atomic-level structural and charge evolutions are analyzed along the reaction path. The potential mean force along the reaction path in water is calculated at high-accuracy CCSD(T)/aug-cc-pVTZ/MM level of theory with a free energy barrier of 16.8 kcal/mol and a free energy of reaction of -9.7 kcal/mol. The water solvent hinders the reactivity by raising its reaction barrier by 15.1 kcal/mol, of which 13.6 kcal/mol comes from solvent energy contribution and 1.5 kcal/mol comes from the polarization effect. This indicates that the water solvent plays an essential role on this reaction in aqueous solution. We also predict the potential mean force profile based on the gas-phase reaction path and the solvation free energies of the stationary points; the comparison between our calculated result at CCSD(T)/MM level shows an excellent agreement with the predicted one with the free energy barrier at 16.2 kcal/mol and the free energy of reaction at -8.3 kcal/mol.

Dynamical Effects of SN2 Reactivity Suppression by Microsolvation: Dynamics Simulations of the F-(H2O) + CH3I Reaction on a 21-Dimensional Potential Energy Surface

A comparison of atomistic dynamics between microsolvated and unsolvated reactions can expose the precise role of solvent molecules and thus provide deep insight into how solvation influences chemical reactions. Here we developed the first full-dimensional analytical potential energy surface of the F-(H2O) + CH3I reaction, which facilitates the efficient dynamics simulations on a quantitatively accurate level. The computed SN2 reactivity suppression ratio of the monosolvated F-(H2O) + CH3I reaction relative to the unsolvated F- + CH3I reaction as a function of collision energy first increases and then decreases steadily, forming an inverted-V shape, due to the combined dynamical effects of interaction time, steric hindrance, and collision-induced dehydration. Moreover, further analysis reveals that the steric effect of the F-(H2O) + CH3I reaction resulting from the single water molecule is manifested mainly in dragging the F- anion away from the central C atom, rather than shielding F- from C. Our study shows there is great potential in rigorously studying the role of the solvent in more complicated reactions.

Unconventional SN2 retention pathways induced by complex formation: High-level dynamics investigation of the NH2 - + CH3I polyatomic reaction

Investigations on the dynamics of chemical reactions have been a hot topic for experimental and theoretical studies over the last few decades. Here, we carry out the first high-level dynamical characterization for the polyatom-polyatom reaction between NH₂ ^- and CH₃I. A global analytical potential energy surface is developed to describe the possible pathways with the quasi-classical trajectory method at several collision energies. In addition to S_N2 and proton abstraction, a significant iodine abstraction is identified, leading to the CH₃ + [NH₂⋯I]^- products. For S_N2, our computations reveal an indirect character as well, promoting the formation of [CH₃⋯NH₂] complexes. Two novel dominant S_N2 retention pathways are uncovered induced by the rotation of the CH₃ fragment in these latter [CH₃⋯NH₂] complexes. Moreover, these uncommon routes turn out to be the most dominant retention paths for the NH₂ ^- + CH₃I S_N2 reaction.

SN2 Reactions with an Ambident Nucleophile: A Benchmark Ab Initio Study of the CN- + CH3Y [Y = F, Cl, Br, and I] Systems

We characterize the Walden-inversion, front-side attack, and double-inversion S_N2 pathways leading to Y^– + CH₃CN/CH₃NC and the product channels of proton abstraction (HCN/HNC + CH₂Y^–), hydride-ion substitution (H^– + YH₂CCN/YH₂CNC), halogen abstraction (YCN^–/YNC^– + CH₃ and YCN/YNC + CH₃^–), and YHCN^–/YHNC^– complex formation (YHCN^–/YHNC^– + ¹CH₂) of the CN^– + CH₃Y [Y = F, Cl, Br, and I] reactions. Benchmark structures and frequencies are computed at the CCSD(T)-F12b/aug-cc-pVTZ level of theory, and a composite approach is employed to obtain relative energies with sub-chemical accuracy considering (a) basis-set effects up to aug-cc-pVQZ, (b) post-CCSD(T) correlation up to CCSDT(Q), (c) core correlation, (d) relativistic effects, and (e) zero-point energy corrections. C–C bond formation is both thermodynamically and kinetically more preferred than N–C bond formation, though the kinetic preference is less significant. Walden inversion proceeds via low or submerged barriers (12.1/17.9(F), 0.0/4.3(Cl), −3.9/0.1(Br), and −5.8/–1.8(I) kcal/mol for C–C/N–C bond formation), front-side attack and double inversion have high barriers (30–64 kcal/mol), the latter is the lower-energy retention pathway, and the non-S_N2 electronic ground-state product channels are endothermic (ΔH₀ = 31–92 kcal/mol).

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.

High-Level Systematic Ab Initio Comparison of Carbon- and Silicon-Centered SN2 Reactions

We characterize the stationary points along the Walden inversion, front-side attack, and double-inversion pathways of the X^– + CH₃Y and X^– + SiH₃Y [X, Y = F, Cl, Br, I] S_N2 reactions using chemically accurate CCSD(T)-F12b/aug-cc-pVnZ [n = D, T, Q] levels of theory. At the carbon center, Walden inversion dominates and proceeds via prereaction (X^–···H₃CY) and postreaction (XCH₃···Y^–) ion-dipole wells separated by a usually submerged transition state (X–H₃C–Y)⁻, front-side attack occurs over high barriers, double inversion is the lowest-energy retention pathway for X = F, and hydrogen- (F^–···HCH₂Y) and halogen-bonded (X^–···YCH₃) complexes exist in the entrance channel. At the silicon center, Walden inversion proceeds through a single minimum (X–SiH₃–Y)⁻, the front-side attack is competitive via a usually submerged transition state separating pre- and postreaction minima having X–Si–Y angles close to 90°, double inversion occurs over positive, often high barriers, and hydrogen- and halogen-bonded complexes are not found. In addition to the S_N2 channels (Y^– + CH₃X/SiH₃X), we report reaction enthalpies for proton abstraction (HX + CH₂Y^–/SiH₂Y^–), hydride substitution (H^– + CH₂XY/SiH₂XY), XH···Y^– complex formation (XH···Y^– + ¹CH₂/¹SiH₂), and halogen abstraction (XY + CH₃^–/SiH₃^– and XY^– + CH₃/SiH₃).

Uncovering an oxide ion substitution for the OH- + CH3F reaction

Theoretical investigations on chemical reactions allow us to understand the dynamics of the possible pathways and identify new unexpected routes. Here, we develop a global analytical potential energy surface (PES) for the OH⁻ + CH₃F reaction in order to perform high-level dynamics simulations. Besides bimolecular nucleophilic substitution (S_N2) and proton abstraction, our quasi-classical trajectory computations reveal a novel oxide ion substitution leading to the HF + CH₃O⁻ products. This exothermic reaction pathway occurs via the CH₃OH⋯F⁻ deep potential well of the S_N2 product channel as a result of a proton abstraction from the hydroxyl group by the fluoride ion. The present detailed dynamics study of the OH⁻ + CH₃F reaction focusing on the surprising oxide ion substitution demonstrates how incomplete our knowledge is of fundamental chemical reactions.

Reaction dynamics simulations on a high-level ab initio analytical potential energy surface reveal a novel oxide ion substitution channel for the OH⁻ + CH₃F reaction.

Theoretical investigation of the SN2 mechanism of X- [X = SH, PH2] + CH3Y [Y = F, Cl, Br, I] reactions in water

We investigated the S_N2 Walden-inversion mechanism of X^- (X = SH, PH₂) + CH₃Y (Y = F, Cl, Br, I) reactions in water using multi-level quantum mechanics (ML-QM) and molecular mechanics (MM) methods. The potentials of the mean force were mapped using not only the density functional theory (DFT)/MM method but also a high-level, accurate CCSD(T)/MM method using the aug-cc-pVTZ basis set. In particular, for the PH₂^- + CH₃I reaction, although the backside attack Walden-inversion mechanics were not observed in the gas phase, we found that this mechanism takes place in water. The atomic-level dynamics of the concerted S_N2 mechanism and the stationary points along the reaction paths were characterized. For these reactions in water, their Walden-inversion barriers are higher than their corresponding ones in the gas phase, indicating that the aqueous solution hinders their reactivity. For the reactions with the same nucleophile X^- in water, the reaction barrier heights with different leaving groups are in the order of F > Cl > Br > I. For the same leaving group Y with different nucleophiles SH^- and PH₂^-, the reaction barrier with SH^- is greater than that of PH₂^- due to the former having higher electronegativity than the latter.

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.

The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction

This communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.

A benchmark ab initio study of the complex potential energy surfaces of the OH- + CH3CH2Y [Y = F, Cl, Br, I] reactions

We provide the first benchmark characterization of the OH^- + CH₃CH₂Y [Y = F, Cl, Br, I] reactions utilizing the high-level explicitly-correlated CCSD(T)-F12b method with the aug-cc-pVnZ [n = 2(D), 3(T), 4(Q)] basis sets. We explore and analyze the stationary points of the elimination (E2) and substitution (S_N2) reactions, including anti-E2, syn-E2, back-side attack, front-side attack, and double inversion. In all cases, S_N2 is thermodynamically more preferred than E2. In the entrance channel of S_N2 a significant front-side complex formation is revealed, and in the product channel the global minimum of the title reactions is obtained at the hydrogen-bonded CH₃CH₂OHY^- complex. Similar to the OH^- + CH₃Y reactions, double inversion can proceed via a notably lower-energy pathway than front-side attack, moreover, for Y = I double inversion becomes barrier-less. For the transition state of the anti-E2, a prominent ZPE effect emerges, giving an opportunity for a kinetically more favored pathway than back-side attack. In addition to S_N2 and E2, other possible product channels are considered, and in most cases, the benchmark reaction enthalpies are in excellent agreement with the experimental data.

First-Principles Reaction Dynamics beyond Six-Atom Systems

Moving beyond the six-atomic benchmark systems, we discuss the new age and future of first-principles reaction dynamics, which investigates complex, multichannel chemical reactions. We describe the methodology starting from the benchmark ab initio characterization of the stationary points, followed by full-dimensional potential energy surface (PES) developments and reaction dynamics computations. We highlight our composite ab initio approach providing benchmark stationary-point properties with subchemical accuracy, the Robosurfer program system enabling automatic PES development, and applications for the Cl + C2H6, F + C2H6, and OH- + CH3I post-six-atom reactions focusing on ab initio issues and their solutions as well as showing the excellent agreement between theory and experiment.

Investigating the role of halogen-bonded complexes in microsolvated Y−(H2O)n + CH3I SN2 reactions

A halogen-bonded complex pathway is computed for Y⁻(H₂O)_n + CH₃I (Y = HO, F, Cl, Br, and I) ion–molecule nucleophilic substitution reactions and is compared with back-side and front-side attack pathways.

The importance of the composite mechanisms with two transition states in the F- + NH2I SN2 reaction

The dynamics of the bimolecular nucleophilic substitution (S_N2) reactions at nitrogen are less understood than those of their corresponding reactions at carbon. In this paper, we report an ab initio molecular dynamics approach to investigate the reaction mechanisms of the F^- + NH₂I S_N2 reaction at nitrogen. We found not only the one-transition-state mechanisms, but also the composite mechanisms with two and three transition states. For the two-transition-state mechanisms, the double inversion mechanism and the proton-abstraction roundabout followed by the backside-attack reaction mechanism have been reported before; but we discovered that there is also a new, front-side attack followed by the backside-attack Walden-inversion mechanism. Furthermore, a composite mechanism with three transition states also shows up in the reactive trajectories. Our results show that, as the collision energy increases, the S_N2 reactivity decreases, and the proton-abstraction reactivity increases. The two-transition-state mechanisms, especially the double-inversion mechanism, make the largest contribution to the S_N2 reactivity, followed then by the one-transition-state mechanisms, with the three-transition-state mechanism contributing the least. The potential energy profiles of the reaction mechanisms are characterized at the CCSD(T)/aug-cc-pVTZ(PP) level of theory. The analysis on stationary points shows that the proton-abstraction inversion transition state is ∼12.4 kcal mol^-1 lower than the Walden-inversion transition state in contrast to the corresponding reaction at carbon F^- + CH₃I, in which the former is ∼26.1 kcal mol^-1 higher than the latter. This might explain why the composite mechanism of the double inversion mechanism contributes the most to the S_N2 reactivity in the F^- + NH₂I reaction.

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.

Imaging Reaction Dynamics of F-(H2O) and Cl-(H2O) with CH3I

The dynamics of microhydrated nucleophilic substitution reactions have been studied using crossed beam velocity map imaging experiments and quasiclassical trajectory simulations at different collision energies between 0.3 and 2.6 eV. For F^–(H₂O) reacting with CH₃I, a small fraction of hydrated product ions I^–(H₂O) is observed at low collision energies. This product, as well as the dominant I^–, is formed predominantly through indirect reaction mechanisms. In contrast, a much smaller indirect fraction is determined for the unsolvated reaction. At the largest studied collision energies, the solvated reaction is found to also occur via a direct rebound mechanism. The measured product angular distributions exhibit an overall good agreement with the simulated angular distributions. Besides nucleophilic substitution, also ligand exchange reactions forming F^–(CH₃I) and, at high collision energies, proton transfer reactions are detected. The differential scattering images reveal that the Cl^–(H₂O) + CH₃I reaction also proceeds predominantly via indirect reaction mechanisms.

Self-assembly of pendant functional groups grafted PEDOT as paracetamol detection material

In this paper, pendant functional group grafted EDOTs, such as EDOTCH₂NH₂, EDOTCH₂OH and EDOTCH₂SH, were selected as monomers for the preparation of their respective polymers via a common chemical oxidative polymerization method in the absence of CTAB by varying the [monomer]/[oxidant] ratios. The self-assembly mechanism of the polymers was systematically studied by discussing the hydrogen bonding effect, acidity and electron-donating ability, as well as the chain initiation and chain growth of the chemically oxidated polymerized monomers. These functional group grafted PEDOTs were applied to the electrochemical determination of paracetamol (PAR) to further investigate the effect of the pendant functional groups (-SH, -OH, -NH₂) on the electrochemical sensing behaviour of the polymers. The results indicated that the hydrogen bonding effect of the pendant functional groups was vital to the self-assembly of the polymer chains, and the PEDOTs with -OH and -SH groups had a tendency to self-assemble into a spherical structure, while the PEDOT with an -NH₂ group exhibited a fibrous structure. The electrochemical response of PEDOTs with functional groups was better than that that of PEDOT alone, and the highest electrochemical response was observed in PEDOT with an -SH group ([monomer]/[oxidant] = 1 : 8).

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.