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

Computational Studies of Nucleophilic Substitution at Nitrogen Center: Reactions of NH2Cl with HO-, CH3O- and C2H5O. Chemphyschem 2024:e202400365. [PMID: 38923666 DOI: 10.1002/cphc.202400365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The atomic-level mechanisms of the nucleophilic substitution reactions at the nitrogen center (SN2@N) were investigated for the reactions of chloramine (NH2Cl) with the alkoxide ions (RO-, where R=H, CH3, and C2H5) using DFT and MP2 methods. The computed potential energy profiles for the SN2@N pathways involving the back-side attack of the nucleophiles show the typical double-well potential with submerged barriers similar to the SN2 reactions at the carbon center (SN2@C). However, the pre-reaction and post-reaction complexes are, respectively, the N-H⋅⋅⋅O and N-H⋅⋅⋅Cl hydrogen-bonded intermediates, which are different from those generally seen in SN2@C reactions. The SN2@N pathways involving front-side attack of the nucleophiles have high-energy barriers. The potential energy surfaces (PESs) along the proton-transfer pathways were flat. In addition to the proton-transfer and SN2 pathways, we also observed a new path for the methoxide and ethoxide nucleophiles where a hydride-transfer from the nucleophile to chloramine resulted in the products Cl-+R'CHO+NH3, (R'=H, CH3), and was the most exoergic. A comparison of the energetics obtained used different DFT and MP2 methods with that of the benchmark coupled-cluster methods reveals that CAM-B3LYP best describes the PESs.

Mechanistic Insights into the Proton Transfer and Substitution Dynamics of N-Atom Center Reactions: A Study of CH3O- with NH2Cl

Bimolecular substitution reactions involving N as the central atom have continuously improved our understanding of substitution dynamics. This work used chemical dynamics simulations to investigate the dynamics of NH2Cl with N as the central atom and the multiatomic nucleophile CH3O- and compared these results with the F- + NH2Cl reaction. The most noteworthy difference is in the competition between proton transfer (PT) and the SN2 pathways. Our results demonstrate that, for the CH3O- + NH2Cl system, the PT pathway is considerably more favorable than the SN2 pathway. In contrast, no PT pathway was observed for the F- + NH2Cl system at room temperature. This can be attributed to the exothermic reaction of the PT pathway for the CH3O- + NH2Cl reaction and is coupled with a more stable transition state compared to the substitution pathway. Furthermore, the bulky nature of the CH3O- group impedes its participation in SN2 reactions, which enhances both the thermodynamic and the dynamic advantages of the PT reaction. Interestingly, the atomic mechanism reveals that the PT pathway is primarily governed by indirect mechanisms, similar to the SN2 pathway, with trajectories commonly trapped in the entrance channel being a prominent feature. These trajectories are often accompanied by prolonged and frequent proton exchange or proton abstraction processes. This current work provides insights into the dynamics of N-centered PT reactions, which are useful in gaining a comprehensive understanding of the dynamics behavior of similar reactions.

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.

Direct dynamics in a proton transfer reaction of isomer product competition. Insight into the suppressed formation of the isoformyl cation

Proton transfer between HOCO⁺ and CO produces the formyl cation HCO⁺ and isoformyl cation HOC⁺ isomers initiating multiple astrochemical reaction networks. Here, the direct chemical dynamics simulations are performed to uncover the underlying atomistic dynamics of the above reaction. The simulations reproduce the measured product energy and scattering angle distributions and reveal that the reaction proceeds predominantly through a direct stripping mechanism which results in the prominent forward scattering observed in experiments. The reaction dynamics show propensity for the HCO⁺ product even at a collision energy larger than the threshold for HOC⁺ formation. This is a consequence of the larger opacity and impact parameter range for HCO⁺. In accordance with the revealed direct mechanistic feature, the reaction can be controlled by orienting the reactants into a reactive H-C orientation that also favors HCO⁺ formation. Considering the lack of equilibrated reactant complexes and the on the fly migration of the proton, the CO₂-catalyzed isomerization is assumed to have insignificant impact on the isomer ratios. This work provides insights of dynamical effects besides energetics into the interesting finding of strongly suppressed formation of the metastable isoformyl cation for related proton transfer reactions in the measurements.

Facilitated inversion complicates the stereodynamics of an SN2 reaction at nitrogen center

Bimolecular nucleophilic substitution (S_N2) reactions at carbon center are well known to proceed with the stereospecific Walden-inversion mechanism. Reaction dynamics simulations on a newly developed high-level ab initio analytical potential energy surface for the F⁻ + NH₂Cl nitrogen-centered S_N2 and proton-transfer reactions reveal a hydrogen-bond-formation-induced multiple-inversion mechanism undermining the stereospecificity of the N-centered S_N2 channel. Unlike the analogous F⁻ + CH₃Cl S_N2 reaction, F⁻ + NH₂Cl → Cl⁻ + NH₂F is indirect, producing a significant amount of NH₂F with retention, as well as inverted NH₂Cl during the timescale within the unperturbed NH₂Cl molecule gets inverted with only low probability, showing the important role of facilitated inversions via an FH…NHCl⁻-like transition state. Proton transfer leading to HF + NHCl⁻ is more direct and becomes the dominant product channel at higher collision energies.

Multiple-inversion, the analogue of the double-inversion pathway recently revealed for S_N2@C, is the key mechanism in S_N2 at N center undermining stereospecificity.

Theoretical Study of the Dynamics of the HBr+ + CO2 → HOCO+ + Br Reaction

The dynamics of the HBr⁺ + CO₂ → HOCO⁺ + Br reaction was recently investigated with guided ion beam experiments under various excitations (collision energy of the reactants, rotational and spin-orbital states of HBr⁺, etc.), and their impacts were probed through the change of the cross section of the reaction. The potential energy profile of this reaction has also been accurately characterized by high-level ab initio methods such as CCSD(T)/CBS, and the UMP2/cc-pVDZ/lanl08d has been identified as an ideal method to study its dynamics. This manuscript reports the first ab initio molecular dynamics simulations of this reaction at two different collision energies, 8.1 kcal/mol and 19.6 kcal/mol. The cross sections measured from the simulations agree very well with the experiments measured with HBr⁺ in the ²∏_1/2 state. The simulations reveal three distinct mechanisms at both collision energies: direct rebound (DR), direct stripping (DS), and indirect (Ind) mechanisms. DS and Ind make up 97% of the total reaction. The dynamics of this reaction is also compared with nucleophilic substitution (S_N2) reactions of X^- + CH₃Y → CH₃X + Y^- type. In summary, this research has revealed interesting dynamics of the HBr⁺ + CO₂ → HOCO⁺ + Br reaction at different collision energies and has laid a solid foundation for using this reaction to probe the impact of rotational excitation of ion-molecule reactions in general.

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.

Multilevel Quantum Mechanics and Molecular Mechanics Study of the Double-Inversion Mechanism at Nitrogen: F- + NH2Cl in Aqueous Solution

We employ a multilevel quantum mechanics and molecular mechanics method to investigate the double-inversion mechanism of the nucleophilic substitution reaction at the N center: the F^- + NH₂Cl reaction in aqueous solution. We find that the structures of the stationary points along the reaction path are quite different from the ones in the gas phase owing to the hydrogen-bond interactions between the solute and the surrounding water molecules. The atomic-level evolutions of the structures and charge transfer along the reaction path show that this double-inversion mechanism consists of an upside-down proton inversion process and a Walden-inversion process. The computed potential of mean force at the coupled-cluster singles and doubles with perturbative triples (CCSD(T))/molecular mechanics (MM) level of theory has the two-inversion barrier heights, and reaction free energy at 11.7, 29.6, and 12.6 kcal/mol, agreeing well with the predicted ones at 12.6, 32.5, and 12.2 kcal/mol obtained on the basis of the gas-phase reaction path and the solvation free energies of the stationary points.

Newly proposed proton-abstraction roundabout with backside attack mechanism for the SN2 reaction at the nitrogen center in F- + NH2Cl

Recent studies have improved our understanding of the mechanism and dynamics of the bimolecular nucleophilic substitution (S_N2) reaction at the carbon center. Nonetheless, the S_N2 reaction at the nitrogen center has received scarce attention and is less understood. Herein, we propose a new reaction mechanism for the S_N2 reaction at the nitrogen center in the F^- + NH₂Cl reaction using ab initio molecular dynamics calculations. The newly proposed mechanism involves the rotation of NHCl with one proton of NH₂Cl abstracted by the nucleophile, followed by the classical backside-attack process. The double-inversion mechanism revealed recently for the S_N2 reaction at the carbon center is also observed for the title reaction at the nitrogen center. In contrast to the F^- + CH₃Cl reaction with a proton abstraction-induced first inversion transition state, the F^- + NH₂Cl reaction is a hydrogen bond-induced inversion. This newly proposed reaction mechanism opens a reaction channel to avoid the proton abstraction mechanism at low collision energy. The double-inversion mechanism of the title reaction with a negative first-inversion transition relative to the energy of the reactants is expected to have larger contribution to the reaction rate than the F^- + CH₃Cl reaction with a positive first-inversion transition state.

Theoretical Investigation of the Gas-Phase SN2 Reactions of Anionic and Neutral Nucleophiles with Chloramines

The S_N2 reactions at nitrogen center (S_N2@N) play a significant role in organic synthesis, carcinogenesis, and the formation of some environmentally toxic compounds. However, the S_N2@N reactions specifically for neutral compounds as nucleophiles are less known. In this work, reactions of dimethylamine (DMA) and F^- with NH₂Cl were investigated as model reactions to validate an accurate functional from 24 DFT functionals by comparing with the CCSD(T) reference data. M06-2X functional was found to perform best and applied to systematically explore the trends in reactivity for halides (F^- and Cl^-) and simple amines toward the substrates NH₂Cl and NHCl₂ (S_N2@N) as well as CH₃Cl and CH₂Cl₂ (S_N2@C). The computational results show that the backside inversion channel dominates most the S_N2@N reactions except for the case of F^- + NHCl₂, which reacts preferentially via proton transfer. The overall activation free energies (Δ G^‡) of the inversion channel for the S_N2 reactions of F^- and Cl^- with chloramines are negative, whereas those for amines as nucleophiles are around 30-44 kcal/mol. The S_N2@N reactions for all the nucleophiles investigated here are faster than the corresponding S_N2@C. Moreover, amines react faster when they have a higher extent of methyl substitution. Additionally, the energy gap between the HOMO of nucleophile and LUMO of substrate generally correlates well with Δ G^‡ of the corresponding S_N2 reactions, which is consistent with previous results.

Benchmark ab Initio Characterization of the Complex Potential Energy Surfaces of the X- + NH2Y [X, Y = F, Cl, Br, I] Reactions

We report a comprehensive high-level explicitly correlated ab initio study on the X^- + NH₂Y [X,Y = F, Cl, Br, I] reactions characterizing the stationary points of the S_N2 (Y^- + NH₂X) and proton-transfer (HX + NHY^-) pathways as well as the reaction enthalpies of various endothermic additional product channels such as H^- + NHXY, XY^- + NH₂, XY + NH₂^-, and XHY^- + NH. Benchmark structures and harmonic vibrational frequencies are obtained at the CCSD(T)-F12b/aug-cc-pVTZ(-PP) level of theory, followed by CCSD(T)-F12b/aug-cc-pVnZ(-PP) [n = Q and 5] and core correlation energy computations. In the entrance and exit channels we find two equivalent hydrogen-bonded C₁ minima, X^-···HH'NY and X^-···H'HNY connected by a C_s first-order saddle point, X^-···H₂NY, as well as a halogen-bonded front-side complex, X^-···YNH₂. S_N2 reactions can proceed via back-side attack Walden inversion and front-side attack retention pathways characterized by first-order saddle points, submerged [X-NH₂-Y]^- and high-energy [H₂NXY]^-, respectively. Product-like stationary points below the HX + NHY^- asymptotes are involved in the proton-transfer processes.