Ion‐Pair SN2 Reaction of OH− and CH3Cl: Activation Strain Analyses of Counterion and Solvent Effects

We have theoretically studied the non‐identity S_N2 reactions of M_nOH^(n?1)+CH₃Cl (M⁺=Li⁺, Na⁺, K⁺, and MgCl⁺; n=0, 1) in the gas phase and in THF solution at the OLYP/6‐31++G(d,p) level using polarizable continuum model (PCM) implicit solvation. We want to explore and understand the effect of the metal counterion M⁺ and solvation on the reaction profile and the stereoselectivity of these processes. To this end, we have explored the potential energy surfaces of the backside (S_N2‐b) and frontside (S_N2‐f) pathways. To explain the computed trends, we have carried out analyses with an extended activation strain model (ASM) of chemical reactivity that includes the treatment of solvation effects.     

Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via SN2 Reactions

The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the “electrophilic trap” that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C₆H₁₀Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C−Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMO_Nu–LUMO_Substrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.     

Double Group Transfer Reactions: Role of Activation Strain and Aromaticity in Reaction Barriers

Double group transfer (DGT) reactions, such as the bimolecular automerization of ethane plus ethene, are known to have high reaction barriers despite the fact that their cyclic transition states have a pronounced in‐plane aromatic character, as indicated by NMR spectroscopic parameters. To arrive at a way of understanding this somewhat paradoxical and incompletely understood phenomenon of high‐energy aromatic transition states, we have explored six archetypal DGT reactions using density functional theory (DFT) at the OLYP/TZ2P level. The main trends in reactivity are rationalized using the activation strain model of chemical reactivity. In this model, the shape of the reaction profile ΔE(ζ) and the height of the overall reaction barrier ΔE^≠=ΔE(ζ=ζ^TS) is interpreted in terms of the strain energy ΔE_strain(ζ) associated with deforming the reactants along the reaction coordinate ζ plus the interaction energy ΔE_int(ζ) between these deformed reactants: ΔE(ζ)=ΔE_strain(ζ)+ΔE_int(ζ). We also use an alternative fragmentation and a valence bond model for analyzing the character of the transition states.     

Nucleophilic Substitution at Phosphorus Centers (SN2@P)

We have studied the characteristics of archetypal model systems for bimolecular nucleophilic substitution at phosphorus (S_N2@P) and, for comparison, at carbon (S_N2@C) and silicon (S_N2@Si) centers. In our studies, we applied the generalized gradient approximation (GGA) of density functional theory (DFT) at the OLYP/TZ2P level. Our model systems cover nucleophilic substitution at carbon in X^?+CH₃Y (S_N2@C), at silicon in X^?+SiH₃Y (S_N2@Si), at tricoordinate phosphorus in X^?+PH₂Y (S_N2@P3), and at tetracoordinate phosphorus in X^?+POH₂Y (S_N2@P4). The main feature of going from S_N2@C to S_N2@P is the loss of the characteristic double‐well potential energy surface (PES) involving a transition state [X? CH₃? Y]^? and the occurrence of a single‐well PES with a stable transition complex, namely, [X? PH₂? Y]^? or [X? POH₂? Y]^?. The differences between S_N2@P3 and S_N2@P4 are relatively small. We explored both the symmetric and asymmetric (i.e. X, Y=Cl, OH) S_N2 reactions in our model systems, the competition between backside and frontside pathways, and the dependence of the reactions on the conformation of the reactants. Furthermore, we studied the effect, on the symmetric and asymmetric S_N2@P3 and S_N2@P4 reactions, of replacing hydrogen substituents at the phosphorus centers by chlorine and fluorine in the model systems X^?+PR₂Y and X^?+POR₂Y, with R=Cl, F. An interesting phenomenon is the occurrence of a triple‐well PES not only in the symmetric, but also in the asymmetric S_N2@P4 reactions of X^?+POCl₂? Y.     

Type‐I Dyotropic Reactions: Understanding Trends in Barriers

To understand the factors that control the activation barrier of type‐I 1,2‐dyotropic reactions (X‐EH₂‐CH₂‐X*→X*‐EH₂‐CH₂‐X, with E=C and Si, X=H, CH₃, SiH₃, F to I) and trends therein as a function of the migrating groups X, we have explored ten archetypal model reactions of this class using relativistic density functional theory (DFT) at ZORA‐OLYP/TZ2P. The main trends in reactivity are rationalized using the activation strain model of chemical reactivity, which had to be extended from bimolecular to unimolecular reactions. Thus, the above type‐I dyotropic reactions can be conceived as a relative rotation of the CH₂CH₂ and [X???X] fragments in X‐CH₂‐CH₂‐X. The picture that emerges from these analyses is that reduced C? X bonding in the transition state is the origin of the reaction barrier. Also the trends in reactivity on variation of X can be understood in terms of how sensitive the C? X interaction is towards adopting the transition‐state geometry. A valence bond analysis complements the analyses and confirms the picture emerging from the activation strain model.     

Frontside versus Backside SN2 Substitution at Group 14 Atoms: Origin of Reaction Barriers and Reasons for Their Absence

We have theoretically studied the gas‐phase nucleophilic substitution at group‐14 atoms (S_N2@A) in the model reactions of Cl^?+AH₃Cl (A=C, Si, Ge, Sn, and Pb) using relativistic density functional theory (DFT) at ZORA‐OLYP/TZ2P. Firstly, we wish to explore and understand how the reaction coordinate ζ, and potential energy surfaces (PES) along ζ, vary as the center of nucleophilic attack changes from carbon to the heavier group‐14 atoms. Secondly, a comparison between the more common backside reaction (S_N2‐b) and the frontside pathway (S_N2‐f) is performed. The S_N2‐b reaction is found to have a central barrier for A=C, but none for the other group‐14 atoms, A=Si–Pb. Relativistic effects destabilize reactant complexes and transition species by up to 10 kcal mol^?1 (for S_N2‐f@Pb), but they do not change relative heights of barriers. We also address the nature of the transformation in the frontside S_N2‐f reactions in terms of turnstile rotation versus Berry‐pseudorotation mechanism.     

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN2 Reaction of and CH3Cl

We have computationally studied the bimolecular nucleophilic substitution (S_N2) reactions of M_nNH₂⁽ⁿ⁻¹⁾ + CH₃Cl (M⁺ = Li⁺, Na⁺, K⁺, and MgCl⁺; n = 0, 1) in the gas phase and in tetrahydrofuran solution at OLYP/6-31++G(d,p) using polarizable continuum model implicit solvation. We wish to explore and understand the effect of the metal counterion M⁺ and of solvation on the reaction profile and the stereochemical preference, that is, backside (S_N2-b) versus frontside attack (S_N2-f). The results were compared to the corresponding ion-pair S_N2 reactions involving F⁻ and OH⁻ nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in S_N2 reactivity along the nucleophiles F⁻, OH⁻, and , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.     

Competition between Nucleophilic Substitution of Halogen (SNAr) versus Substitution of Hydrogen (SNArH)—A Mass Spectrometry and Computational Study

The mechanism of intramolecular gas‐phase reactions of N‐(2‐X‐5‐nitrophenyl)‐N‐methylacetamide carbanions (X=H, F, Cl) has been studied using negative ion electrospray mass spectrometry ((?)ESI‐MS) technique and modelled computationally. It was proven that all three anions form cyclic σ^H adducts, which undergo elimination of water. In the case of X=F, formation of the σ^F adduct, leading to S_NAr reaction, was a competing process. This is the first proof that also in the gas phase formation of σ^H adduct proceeds faster than σ^X adduct and only when X=F, rates of these two processes are comparable. The experimental results are in full agreement with quantum chemical calculations.     

Understanding the 1,3-Dipolar Cycloadditions of Allenes

We have quantum chemically studied the reactivity, site-, and regioselectivity of the 1,3-dipolar cycloaddition between methyl azide and various allenes, including the archetypal allene propadiene, heteroallenes, and cyclic allenes, by using density functional theory (DFT). The 1,3-dipolar cycloaddition reactivity of linear (hetero)allenes decreases as the number of heteroatoms in the allene increases, and formation of the 1,5-adduct is, in all cases, favored over the 1,4-adduct. Both effects find their origin in the strength of the primary orbital interactions. The cycloaddition reactivity of cyclic allenes was also investigated, and the increased predistortion of allenes, that results upon cyclization, leads to systematically lower activation barriers not due to the expected variations in the strain energy, but instead from the differences in the interaction energy. The geometric predistortion of cyclic allenes enhances the reactivity compared to linear allenes through a unique mechanism that involves a smaller HOMO–LUMO gap, which manifests as more stabilizing orbital interactions.     

Understanding the Reactivity of Supported Late Transition Metals on a Bare Anatase (101) Surface: A Periodic Conceptual DFT Investigation

The rapidly growing interest for new heterogeneous catalytic systems providing high atomic efficiency along with high stability and reactivity triggered an impressive progress in the field of single-atom catalysis. Nevertheless, unravelling the factors governing the interaction strength between the support and the adsorbed metal atoms remains a major challenge. Based on periodic density functional theory (DFT) calculations, this paper provides insight into the adsorption of single late transition metals on a defect-free anatase surface. The obtained adsorption energies fluctuate, with the exception of Pd, between −3.11 and −3.80 eV and are indicative of a strong interaction. Depending on the considered transition metal, we could attribute the strength of this interaction with the support to i) an electron transfer towards anatase (Ru, Rh, Ni), ii) s-d orbital hybridisation effects (Pt), or iii) a synergistic effect between both factors (Fe, Co, Os, Ir). The driving forces behind the adsorption were also found to be strongly related to Klechkowsky's rule for orbital filling. In contrast, the deviating behaviour of Pd is most likely associated with the lower dissociation enthalpy of the Pd−O bond. Additionally, the reactivity of these systems was evaluated using the Fermi weighted density of states approach. The resulting softness values can be clearly related to the electron configuration of the catalytic systems as well as with the net charge on the transition metal. Finally, these indices were used to construct a model that predicts the adsorption strength of CO on these anatase-supported d-metal atoms. The values obtained from this regression model show, within a 95 % probability interval, a correlation of 84 % with the explicitly calculated CO adsorption energies.     

Alder-ene reaction: aromaticity and activation-strain analysis

We have computationally explored the trend in reactivity of the Alder-ene reactions between propene and a series of seven enophiles using density functional theory at M06-2X/def2-TZVPP. The reaction barrier decreases along the enophiles in the order H₂CCH₂ > HCCH > H₂CNH > H₂CCH(COOCH₃) > H₂CO > H₂CPH > H₂CS. Thus, barriers drop in particular, if third-period atoms become involved in the double bond of the enophile. Activation-strain analyses show that this trend in reactivity correlates with the activation strain associated with deforming reactants from their equilibrium structure to the geometry they adopt in the transition state. We discuss the origin of this trend and its relationship with the extent of synchronicity between H transfer from ene to enophile and the formation of the new C C bond. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

A Unified Framework for Understanding Nucleophilicity and Protophilicity in the SN2/E2 Competition

The concepts of nucleophilicity and protophilicity are fundamental and ubiquitous in chemistry. A case in point is bimolecular nucleophilic substitution (S_N2) and base-induced elimination (E2). A Lewis base acting as a strong nucleophile is needed for S_N2 reactions, whereas a Lewis base acting as a strong protophile (i.e., base) is required for E2 reactions. A complicating factor is, however, the fact that a good nucleophile is often a strong protophile. Nevertheless, a sound, physical model that explains, in a transparent manner, when an electron-rich Lewis base acts as a protophile or a nucleophile, which is not just phenomenological, is currently lacking in the literature. To address this fundamental question, the potential energy surfaces of the S_N2 and E2 reactions of X⁻+C₂H₅Y model systems with X, Y = F, Cl, Br, I, and At, are explored by using relativistic density functional theory at ZORA-OLYP/TZ2P. These explorations have yielded a consistent overview of reactivity trends over a wide range in reactivity and pathways. Activation strain analyses of these reactions reveal the factors that determine the shape of the potential energy surfaces and hence govern the propensity of the Lewis base to act as a nucleophile or protophile. The concepts of “characteristic distortivity” and “transition state acidity” of a reaction are introduced, which have the potential to enable chemists to better understand and design reactions for synthesis.     

Ion‐Pair SN2 Substitution: Activation Strain Analyses of Counter‐Ion and Solvent Effects

The ion‐pair S_N2 reactions of model systems M_nF^n?1+CH₃Cl (M⁺=Li⁺, Na⁺, K⁺, and MgCl⁺; n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6‐31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M⁺ modifies ion‐pair S_N2 reactivity relative to the parent reaction F^?+CH₃Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion‐pair S_N2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor‐made substitution reactions.     

Switch From Pauli‐Lowering to LUMO‐Lowering Catalysis in Brønsted Acid‐Catalyzed Aza‐Diels‐Alder Reactions

Brønsted acid‐catalyzed inverse‐electron demand (IED) aza‐Diels‐Alder reactions between 2‐aza‐dienes and ethylene were studied using quantum chemical calculations. The computed activation energy systematically decreases as the basic sites of the diene progressively become protonated. Our activation strain and Kohn‐Sham molecular orbital analyses traced the origin of this enhanced reactivity to i) “Pauli‐lowering catalysis” for mono‐protonated 2‐aza‐dienes due to the induction of an asynchronous, but still concerted, reaction pathway that reduces the Pauli repulsion between the reactants; and ii) “LUMO‐lowering catalysis” for multi‐protonated 2‐aza‐dienes due to their highly stabilized LUMO(s) and more concerted synchronous reaction path that facilitates more efficient orbital overlaps in IED interactions. In all, we illustrate how the novel concept of “Pauli‐lowering catalysis” can be overruled by the traditional concept of “LUMO‐lowering catalysis” when the degree of LUMO stabilization is extreme as in the case of multi‐protonated 2‐aza‐dienes.     

Switch From Pauli-Lowering to LUMO-Lowering Catalysis in Brønsted Acid-Catalyzed Aza-Diels-Alder Reactions

Brønsted acid-catalyzed inverse-electron demand (IED) aza-Diels-Alder reactions between 2-aza-dienes and ethylene were studied using quantum chemical calculations. The computed activation energy systematically decreases as the basic sites of the diene progressively become protonated. Our activation strain and Kohn-Sham molecular orbital analyses traced the origin of this enhanced reactivity to i) “Pauli-lowering catalysis” for mono-protonated 2-aza-dienes due to the induction of an asynchronous, but still concerted, reaction pathway that reduces the Pauli repulsion between the reactants; and ii) “LUMO-lowering catalysis” for multi-protonated 2-aza-dienes due to their highly stabilized LUMO(s) and more concerted synchronous reaction path that facilitates more efficient orbital overlaps in IED interactions. In all, we illustrate how the novel concept of “Pauli-lowering catalysis” can be overruled by the traditional concept of “LUMO-lowering catalysis” when the degree of LUMO stabilization is extreme as in the case of multi-protonated 2-aza-dienes.     

Macrocycles All Aflutter: Substitution at an Allylic Center Reveals the Conformational Dynamics of [13]‐Macrodilactones

The shapes adopted by large‐ring macrocyclic compounds play a role in their reactivity and their ability to be bound by biomolecules. We investigated the synthesis, conformational analysis, and properties of a specific family of [13]‐macrodilactones as models of natural‐product macrocycles. The features of our macrodilactones enabled us to study the relationship between stereogenic centers and planar chirality through the modular synthesis of new members of this family of macrocycles. Here we report on insights gained from a new [13]‐macrodilactone that is substituted at a position adjacent to the alkene in the molecule. Analysis of the compound, in comparison to an α‐substituted regioisomer, by using X‐ray crystallography, NMR coupling constants, and reaction‐product characterization in concert with computational chemistry, revealed that the alkene unit is dynamic. That is, the data support a model in which the alkene in our [13]‐macrodilactones oscillates between two conformations. A difference in reactivity of one conformation compared to the other leads to manifestation of this dynamic behavior. The results underscore the local conformational dynamics observed in some natural‐product macrocycles, which could have implications for biomolecule binding.     

Computational Study of the Mechanism and Selectivity of Palladium‐Catalyzed Propargylic Substitution with Phosphorus Nucleophiles

The mechanism and sources of selectivity in the palladium‐catalyzed propargylic substitution reaction that involves phosphorus nucleophiles, and which yields predominantly allenylphosphonates and related compounds, have been studied computationally by means of density functional theory. Full free‐energy profiles are computed for both H‐phosphonate and H‐phosphonothioate substrates. The calculations show that the special behavior of H‐phosphonates among other heteroatom nucleophiles is indeed reflected in higher energy barriers for the attack on the central carbon atom of the allenyl/propargyl ligand relative to the ligand‐exchange pathway, which leads to the experimentally observed products. It is argued that, to explain the preference of allenyl‐ versus propargyl‐phosphonate/phosphonothioate formation in reactions that involve H‐phosphonates and H‐phosphonothioates, analysis of the complete free‐energy surfaces is necessary, because the product ratio is determined by different transition states in the respective branches of the catalytic cycle. In addition, these transition states change in going from a H‐phosphonate to a H‐phosphonothioate nucleophile.     

Lewis Acid-Catalyzed Diels-Alder Reactions: Reactivity Trends across the Periodic Table

The catalytic effect of various weakly interacting Lewis acids (LAs) across the periodic table, based on hydrogen (Group 1), pnictogen (Group 15), chalcogen (Group 16), and halogen (Group 17) bonds, on the Diels-Alder cycloaddition reaction between 1,3-butadiene and methyl acrylate was studied quantum chemically by using relativistic density functional theory. Weakly interacting LAs accelerate the Diels-Alder reaction by lowering the reaction barrier up to 3 kcal mol⁻¹ compared to the uncatalyzed reaction. The reaction barriers systematically increase from halogen<hydrogen<chalcogen<pnictogen-bonded LAs, i. e., the latter have the least catalytic effect. Our detailed activation strain and Kohn-Sham molecular orbital analyses reveal that these LAs lower the Diels-Alder reaction barrier by increasing the asynchronicity of the reaction to relieve the otherwise destabilizing Pauli repulsion between the closed-shell filled π-orbitals of diene and dienophile. Notably, the reactivity can be further enhanced on going from a Period 3 to a Period 5 LA, as these species amplify the asynchronicity of the Diels-Alder reaction due to a stronger binding to the dienophile. These findings again demonstrate the generality of the Pauli repulsion-lowering catalysis concept.