Nucleophilic substitution with two reactive centers: The CN(-) + CH3I case

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.

Reaction dynamics of the methoxy anion CH3O- with methyl iodide CH3I

Studying larger nucleophiles in bimolecular nucleophilic substitution (SN2) reactions bridges the gap from simple model systems to those relevant to organic chemistry. Therefore, we investigated the reaction dynamics between the methoxy anion (CH3O-) and iodomethane (CH3I) in our crossed-beam setup combined with velocity map imaging at the four collision energies 0.4, 0.7, 1.2, and 1.6 eV. We find the two ionic products I- and CH2I-, which can be attributed to the SN2 and proton transfer channels, respectively. The proton transfer channel progresses in a previously observed fashion from indirect to direct scattering with increasing collision energy. Interestingly, the SN2 channel exhibits direct dynamics already at low collision energies. Both the direct stripping, leading to forward scattering, and the direct rebound mechanism, leading to backward scattering into high angles, are observed.

Shapeshifting Nucleophile Singly Hydrated Hydroperoxide Anion Leads to the Occurrence of the Thermodynamically Unfavored SN2 Product

Single water molecules alone may introduce unusual features into the kinetics and dynamics of chemical reactions. The singly hydrated hydroperoxide anion, HOO-(H2O), was found to be a shapeshifting nucleophile, which can be transformed to HO- solvated by hydrogen peroxide HO-(HOOH). Herein, we performed direct dynamics simulations of its reaction with methyl iodide to investigate the effect of individual water molecules. In addition to the normal SN2 product CH3OOH, the thermodynamically unfavored proton transfer-induced HO--SN2 path (produces CH3OH) was also observed, contributing ∼4%. The simulated branching ratio of the HO--SN2 path exceeded the statistical estimation (0.6%) based on the free energy barrier difference. The occurrence of the HO--SN2 path was attributed to the shallow entrance channel well before a submerged saddle point, thus providing a region for extensive proton exchange and ultimately leading to the formation of CH3OH. In comparison, changing the leaving group from Cl to I increased the overall reaction rate as well as the proportion of the HO--SN2 path because the CH3I system has a smaller internal barrier. This work elucidates the importance of the dynamic effect introduced by a single solvent molecule to alter the product channel and kinetics of typical ion-molecule SN2 reactions.

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.

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.

Imaging Frontside and Backside Attack in Radical Ion-Molecule Reactive Scattering

We report on the reactive scattering of methyl iodide, CH₃I, with atomic oxygen anions O^-. This radical ion-molecule reaction can produce different ionic products depending on the angle of attack of the nucleophile O^- on the target molecule. We present results on the backside and frontside attack of O^- on CH₃I, which can lead to I^- and IO^- products, respectively. We combine crossed-beam velocity map imaging with quantum chemical calculations to unravel the chemical reaction dynamics. Energy-dependent scattering experiments in the range of 0.3-2.0 eV relative collision energy revealed that three different reaction pathways can lead to I^- products, making it the predominant observed product. Backside attack occurs via a hydrogen-bonded complex with observed indirect, forward, and sideways scattered iodide products. Halide abstraction via frontside attack produces IO^-, which mainly shows isotropic and backward scattered products at low energies. IO^- is observed to dissociate further to I^- + O at a certain energy threshold and favors more direct dynamics at higher collision energies.

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.

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).

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.

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.

Rethinking the X− + CH3Y [X = OH, SH, CN, NH2, PH2; Y = F, Cl, Br, I] SN2 reactions

Explicitly-correlated ab initio computations reveal novel inversion and retention pathways for several S_N2 reactions with different nucleophiles and leaving groups.

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.

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.

Imaging the dynamics of ion–molecule reactions

A range of ion–molecule reactions have been studied in the last years using the crossed-beam ion imaging technique, from charge transfer and proton transfer to nucleophilic substitution and elimination.