Ion-Pair SN 2 Substitution: Activation Strain Analyses of Counter-Ion and Solvent Effects

Nucleophilic Reactions Using Alkali Metal Fluorides Activated by Crown Ethers and Derivatives

We review crown ether-facilitated nucleophilic reactions using metal salts, presenting the studies using kinetic measurements and quantum chemical methods. We focus on the mechanistic features, specifically on the contact ion-pair (CIP) mechanism of metal salts for nucleophilic processes promoted by crown ethers and derivatives. Experimental verification of the CIP form of the metal salt CsF complexed with [18-Crown-6] by H-NMR spectroscopy is described. The use of chiral crown ethers and derivatives for enantioselective nucleophilic processes is also discussed.

Diastereoselectivity on Intramolecular Alder-ene Reaction of 1,6-Dienes

A detailed computational study of the intramolecular Alder-ene reaction of different 1,6-dienes at M06-2X(PCM)/TZ2P level of theory has been performed. We want to understand the influence of enophile-geminal substitution pattern in the cis : trans selectivity of the cyclization process. Our analysis of the reaction coordinate by means of activation strain model of chemical reactivity (ASM-distortion interaction model) reveals that the cis-selectivity observed for unactivated reagents is related with high stabilizing orbital interaction and lower strain energy, consequence of an early transition structure. On the other hand, the presence of activating groups increases the asynchronicity of the transition structures and reduces the activation barrier due to more stabilizing orbital and electrostatic interactions, favoring trans-selectivity.

Rationalizing the Substituent Effects in Diels-Alder Reactions of Triazolinediones with Anthracene

In this work we tackle the problem of the substituent effects in the Diels-Alder cycloadditions between triazolinediones (TADs) and anthracene. Experiments showed that aryl TADs substituted with electron-withdrawing groups (EWG) are more reactive than those substituted with electron-donating (EDG) or alkyl groups. However, the molecular origin of this preference is not yet understood. By a combination of methods including the activation strain model (ASM), energy decomposition analysis (EDA), molecular orbital (MO) theory, and conceptual density functional theory (CDFT), we disclosed the substituent effects of TADs. First, ASM/EDA analysis revealed that the reactivity of alkyl and aryl-substituted TADs is controlled by interaction energies, ΔE_int, which are ultimately defined by orbital interactions between frontier molecular orbitals. Moreover, alkyl-TADs are also controlled by the extent of strain at the transition state. The MO analysis suggested that the rate acceleration for EWG-substituted TADs is due to a more favorable orbital interaction between the HOMO of anthracene and the LUMO of the TADs, which is corroborated by calculations of charge transfer at the transition states. From CDFT, the chemical potential of anthracene is higher than those of TADs, indicating a flow of electron density from anthracene to TADs, in agreement with the results from the electrophilicity index.

Computational insights into the inverse electron-demand Diels-Alder reaction of norbornenes with 1,2,4,5-tetrazines: norbornene substituents' effects on the reaction rate

The study of the reaction rates and mechanism of click chemistry reactions still remains an interesting challenge in organic chemistry. In this regard, the inverse electron demand Diels-Alder (IEDDA) reaction represents a promising metal-free alternative with enhanced reaction rates compared to other reactions of the click chemistry toolbox. Among the different types of dienophiles used in the IEDDA reactions, norbornenes have been widely used given their high stability and fast reaction rates. The inverse electron-demand Diels Alder reaction of 3,6-dipyridin-2-yl-1,2,4,5-tetrazine with a series of norbornene derivatives was studied with quantum mechanical calculations at the M06-2X/6-311+G(d,p) level of theory. The theoretical predictions were confirmed with the experimental data and analyzed with the use of the distortion/interaction model. The obtained results will help in obtaining a better understanding of the factors that affect the relative cycloaddition rates of norbornenes with tetrazines, which are crucial for selectively tuning their efficacy.

Theoretical study of a derivative of chlorophosphine with aliphatic and aromatic Grignard reagents: SN2@P or the novel SN2@Cl followed by SN2@C?

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett., 2017, 19, 5384–5387] were studied theoretically in order to explain the observed stereochemistry of the products.

Unbalanced-Ion-Pair-Catalyzed Nucleophilic Fluorination Using Potassium Fluoride

An unbalanced ion pair promoter (e.g., tetrabutylammonium sulfate), consisting of a bulky and charge-delocalized cation and a small and charge-localized anion, greatly accelerates nucleophilic fluorinations using easy handling KF. We also successfully converted an inexpensive and commercially available ion-exchange resin to the polymer-supported ion pair promoter (A26-SO₄^2-), which could be reused after filtration. Moreover, A26-SO₄^2- can be used in continuous flow conditions. In our conditions, water is well-tolerated.

Chemical reactivity from an activation strain perspective

Chemical reactions are ubiquitous in the universe, they are at the core of life, and they are essential for industrial processes. The drive for a deep understanding of how something occurs, in this case, the mechanism of a chemical reaction and the factors controlling its reactivity, is intrinsically valuable and an innate quality of humans. The level of insight and degree of understanding afforded by computational chemistry cannot be understated. The activation strain model is one of the most powerful tools in our arsenal to obtain unparalleled insight into reactivity. The relative energy of interacting reactants is evaluated along a reaction energy profile and related to the rigidity of the reactants' molecular structure and the strength of the stabilizing interactions between the deformed reactants: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). Owing to the connectedness between the activation strain model and Kohn-Sham molecular orbital theory, one is able to obtain a causal relationship between both the sterics and electronics of the reactants and their mutual reactivity. Only when this is accomplished one can eclipse the phenomenological explanations that are commonplace in the literature and textbooks and begin to rationally tune and optimize chemical transformations. We showcase how the activation strain model is the ideal tool to elucidate fundamental organic reactions, the activation of small molecules by metallylenes, and the cycloaddition reactivity of cyclic diene- and dipolarophiles.

Inter- and Intra-Molecular Organocatalysis of SN2 Fluorination by Crown Ether: Kinetics and Quantum Chemical Analysis

We present the intra- and inter-molecular organocatalysis of S_N2 fluorination using CsF by crown ether to estimate the efficacy of the promoter and to elucidate the reaction mechanism. The yields of intramolecular S_N2 fluorination of the veratrole substrates are measured to be very small (<1% in 12 h) in the absence of crown ether promoters, whereas the S_N2 fluorination of the substrate possessing a crown ether unit proceeds to near completion (~99%) in 12 h. We also studied the efficacy of intermolecular rate acceleration by an independent promoter 18-crown-6 for comparison. We find that the fluorinating yield of a veratrole substrate (leaving group = −OMs) in the presence of 18-crown-6 follows the almost identical kinetic course as that of intramolecular S_N2 fluorination, indicating the mechanistic similarity of intra- and inter-molecular organocatalysis of the crown ether for S_N2 fluorination. The calculated relative Gibbs free energies of activation for these reactions, in which the crown ether units act as Lewis base promoters for S_N2 fluorination, are in excellent agreement with the experimentally measured yields of fluorination. The role of the metal salt CsF is briefly discussed in terms of whether it reacts as a contact ion pair or as a “free” nucleophile F⁻.

Transition-State Expansion: A Quantitative Model for Counterion Effects in Ionic Reactions

Ionic reactions are the most common reactions used in chemical synthesis. In relatively low dielectric constant solvents (e.g., dichloromethane, toluene), ions usually exist as ion pairs. Despite the importance of counterions, a quantitative description of how the paired 'counterion' affects the reaction kinetic is still elusive. We introduce a general and quantitative model, namely transition-state expansion (TSE), that describes how the size of a counterion affects the transition-state structure and the kinetics of an ionic reaction. This model could rationalize the counterion effects in nucleophilic substitutions and gold-catalyzed enyne cycloisomerizations.

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A quantitative model for counterion effects was introduced

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'Transition State Expansion' was used to describes how the size of a counterion affects the kinetics

Ambident Nucleophilic Substitution: Understanding Non-HSAB Behavior through Activation Strain and Conceptual DFT Analyses

The ability to understand and predict ambident reactivity is key to the rational design of organic syntheses. An approach to understand trends in ambident reactivity is the hard and soft acids and bases (HSAB) principle. The recent controversy over the general validity of this principle prompted us to investigate the competing gas-phase SN 2 reaction channels of archetypal ambident nucleophiles CN- , OCN- , and SCN- with CH3 Cl (SN 2@C) and SiH3 Cl (SN 2@Si), using DFT calculations. Our combined analyses highlight the inability of the HSAB principle to correctly predict the reactivity trends of these simple, model reactions. Instead, we have successfully traced reactivity trends to the canonical orbital-interaction mechanism and the resulting nucleophile-substrate interaction energy. The HOMO-LUMO orbital interactions set the trend in both SN 2@C and SN 2@Si reactions. We provide simple rules for predicting the ambident reactivity of nucleophiles based on our Kohn-Sham molecular orbital analysis.

Understanding chemical reactivity using the activation strain model

Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN 2 Reaction of NH 2 - and CH3 Cl

We have computationally studied the bimolecular nucleophilic substitution (S_N 2) reactions of M_n NH₂ ^(n-1) + CH₃ Cl (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_N 2-b) versus frontside attack (S_N 2-f). The results were compared to the corresponding ion-pair S_N 2 reactions involving F^- and OH^- nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in S_N 2 reactivity along the nucleophiles F^- , OH^- , and NH 2 - , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.

Alkali Metal Cation Affinities of Neutral Maingroup-Element Hydrides across the Periodic Table

We have carried out an extensive quantum chemical exploration of gas-phase alkali metal cation affinities (AMCAs) of archetypal neutral bases across the periodic system using relativistic density functional theory. One objective of this work is to provide an intrinsically consistent set of values of the 298 K AMCAs of all neutral maingroup-element hydrides XH_n of groups 15–18 along the periods 1–6. Our main purpose is to understand these trends in terms of the underlying bonding mechanism using Kohn–Sham molecular orbital theory together with a canonical energy decomposition analysis (EDA). We compare the trends in XH_n AMCAs with the trends in XH_n proton affinities (PAs). We also examine the differences between the trends in AMCAs of the neutral XH_n bases with those in the corresponding anionic XH_n–1^– bases. Furthermore, we analyze how the cation affinity of our neutral Lewis bases changes along the group-1 cations H⁺, Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺.

Effect of an α-Methyl Substituent on the Dienophile on Diels-Alder endo:exo Selectivity

A detailed computational study of the Diels‐Alder reaction of cyclopentadiene with acrylonitrile, methylacrylate and their α‐methylated counterparts methacrylonitrile and methyl methacrylate at the M06‐2X(PCM)/TZVP level of theory has been performed. We want to understand the excellent exo‐selectivities observed experimentally due the presence of this substituent. To this end, analysis of the reaction coordinate by means of activation strain model of chemical reactivity (ASM‐distortion interaction model) including solvation effects and NBO second order perturbation energy have been carried out.

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

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

Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent

The reaction potential energy surface (PES), and thus the mechanism of bimolecular nucleophilic substitution (SN 2), depends profoundly on the nature of the nucleophile and leaving group, but also on the central, electrophilic atom, its substituents, as well as on the medium in which the reaction takes place. Here, we provide an overview of recent studies and demonstrate how changes in any one of the aforementioned factors affect the SN 2 mechanism. One of the most striking effects is the transition from a double-well to a single-well PES when the central atom is changed from a second-period (e. g. carbon) to a higher-period element (e.g, silicon, germanium). Variations in nucleophilicity, leaving group ability, and bulky substituents around a second-row element central atom can then be exploited to change the single-well PES back into a double-well. Reversely, these variations can also be used to produce a single-well PES for second-period elements, for example, a stable pentavalent carbon species.

Nucleophilic Substitution in Solution: Activation Strain Analysis of Weak and Strong Solvent Effects

We have quantum chemically studied the effect of various polar and apolar solvents on the shape of the potential energy surface (PES) of a diverse collection of archetypal nucleophilic substitution reactions at carbon, silicon, phosphorus, and arsenic by using density functional theory at the OLYP/TZ2P level. In the gas phase, all our model SN 2 reactions have single-well PESs, except for the nucleophilic substitution reaction at carbon (SN 2@C), which has a double-well energy profile. The presence of the solvent can have a significant effect on the shape of the PES and, thus, on the nature of the SN 2 process. Solvation energies, charges on the nucleophile or leaving group, and structural features are compared for the various SN 2 reactions in a spectrum of solvents. We demonstrate how solvation can change the shape of the PES, depending not only on the polarity of the solvent, but also on how the charge is distributed over the interacting molecular moieties during different stages of the reaction. In the case of a nucleophilic substitution at three-coordinate phosphorus, the reaction can be made to proceed through a single-well [no transition state (TS)], bimodal barrier (two TSs), and then through a unimodal transition state (one TS) simply by increasing the polarity of the solvent.

How Mg2+ ions lower the SN2@P barrier in enzymatic triphosphate hydrolysis

Our quantum chemical activation strain analyses demonstrate how Mg2+ lowers the barrier of the enzymatic triphosphate hydrolysis through two distinct mechanisms: (a) weakening of the leaving-group bond, thereby decreasing activation strain; and (b) transition state (TS) stabilization through enhanced electrophilicity of the triphosphate PPP substrate, thereby strengthening the interaction with the nucleophile.

Ion-Pair SN 2 Reaction of OH- and CH3 Cl: Activation Strain Analyses of Counterion and Solvent Effects

We have theoretically studied the non-identity S_N 2 reactions of M_n OH^(n-1) +CH₃ Cl (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_N 2-b) and frontside (S_N 2-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.

Origins of the Endo and Exo Selectivities in Cyclopropenone, Iminocyclopropene, and Triafulvene Diels-Alder Cycloadditions

The endo and exo stereoselectivities of Diels-Alder reactions of cyclopropenone, iminocyclopropene, and substituted triafulvenes with butadiene were rationalized using density functional theory calculations. When cyclopropenone is the dienophile, there is a 1.8 kcal/mol preference for the exo cycloaddition with butadiene, while the reaction of 3-difluoromethylene triafulvene with butadiene favors the endo cycloaddition by 2.8 kcal/mol. The influence of charge transfer and secondary orbital interactions on the stereoselectivity of Diels-Alder reactions involving triafulvenes and heteroanalogs is discussed. The predicted stereoselectivity correlates with both the charge and highest occupied molecular orbital (HOMO) coefficient at the C3 carbon of the triafulvene motif.

Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.