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

Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Pericyclic Cascade Reactions Affording Thienyl- and Benzo[b]thienyl-Fused Architectures: A Synthetic and Density Functional Theory Analysis of Asynchronous Diels-Alder Reactions of Thioarylmaleimides

Herein, we report the synthesis and characterization of a series of thioarylmaleimides and their varied propensity toward highly selective domino Diels-Alder (D-A)/rearrangement, D-A/ene/elimination, and D-A/oxidation reactions to give three types of thienyl-fused architectures. Stereochemical assignment was achieved using a combination of nuclear magnetic resonance (NMR) studies, gauge independent atomic orbital (GIAO) NMR chemical shift calculations, and DP4+ analysis. Transition-state calculations support an asynchronous concerted mechanism and provide support for rationalizing the observed regio- and stereoselectivity.

Reactivity and Selectivity of the Diels-Alder Reaction of Anthracene in [Pd6L4]12+ Supramolecular Cages: A Computational Study

The field of supramolecular metal-organic cage catalysis has grown rapidly in recent years. However, theoretical studies regarding the reaction mechanism and reactivity and selectivity controlling factors for supramolecular catalysis are still underdeveloped. Herein, we demonstrate a detailed density functional theory study on the mechanism, catalytic efficiency, and regioselectivity of the Diels-Alder reaction in bulk solution and within two [Pd₆L₄]¹²⁺ supramolecular cages. Our calculations are consistent with experiments. The origins of the catalytic efficiency of the bowl-shaped cage 1 have been elucidated to be the host-guest stabilization of the transition states and the favorable entropy effect. The reasons for the switch of the regioselectivity from 9,10-addition to 1,4-addition within the octahedral cage 2 were attributed to the confinement effect and the noncovalent interactions. This work would shed light on the understanding of [Pd₆L₄]¹²⁺ metallocage-catalyzed reactions and provide a detailed mechanistic profile otherwise difficult to obtain from experiments. The findings of this study could also aid to the improvement and development of more efficient and selective supramolecular catalysis.

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.

Enantioselective palladium-catalyzed C(sp2)-C(sp2) σ bond activation of cyclopropenones by merging desymmetrization and (3 + 2) spiroannulation with cyclic 1,3-diketones

Catalytic asymmetric variants for functional group transformations based on carbon–carbon bond activation still remain elusive. Herein we present an unprecedented palladium-catalyzed (3 + 2) spiro-annulation merging C(sp²)–C(sp²) σ bond activation and click desymmetrization to form synthetically versatile and value-added oxaspiro products. The operationally straightforward and enantioselective palladium-catalyzed atom-economic annulation process exploits a TADDOL-derived bulky P-ligand bearing a large cavity to control enantioselective spiro-annulation that converts cyclopropenones and cyclic 1,3-diketones into chiral oxaspiro cyclopentenone–lactone scaffolds with good diastereo- and enantio-selectivity. The click-like reaction is a successful methodology with a facile construction of two vicinal carbon quaternary stereocenters and can be used to deliver additional stereocenters during late-state functionalization for the synthesis of highly functionalized or more complex molecules.

An unprecedented palladium-catalyzed (3 + 2) spiro-annulation merging C–C bond activation and desymmetrization was developed for the enantioselective construction of synthetically versatile and value-added oxaspiro products with up to 95% ee.

Catalytic Asymmetric Aza-Diels-Alder Reaction of Ketimines and Unactivated Dienes

The enantioselective aza-Diels-Alder reaction is efficient for constructing chiral tetrahydropyridines, but the catalytic asymmetric aza-Diels-Alder reaction of ketimines with unactivated dienes is still a challenging topic. Herein, guided by computational screening, a highly enantioselective aza-Diels-Alder reaction of 2-aryl-3H-indol-3-ones with unactivated dienes was realized by using a B(C₆ F₅ )₃ /chiral phosphoric acid catalyst system under mild conditions. The reaction has a broad scope with respect to both aza-Diels-Alder reaction partners and hence offers rapid access to an array of tetrahydropyridine derivatives with pretty outcomes (up to 99 % yield, >20:1 dr and 98:2 er). The reaction is very efficient: lowering catalyst loadings for the model reaction to 0.1 mol %, enantioselectivity is still maintained. The synthetic utility was confirmed by transformations of the products. DFT calculations provide convincing evidence for the interpretation of stereoselection.

Origins of Endo Selectivity in Diels-Alder Reactions of Cyclic Allene Dienophiles

Strained cyclic allenes, first discovered in 1966 by Wittig and co-workers, have recently emerged as valuable synthetic building blocks. Previous experimental investigations, and computations reported here, demonstrate that the Diels-Alder reactions of furans and pyrroles with 1,2-cyclohexadiene and oxa- and azaheterocyclic analogs proceed with endo selectivity. This endo selectivity gives the adduct with the allylic saturated carbon of the cyclic allene endo to the diene carbons. The selectivity is very general and useful in synthetic applications. Our computational study establishes the origins of this endo selectivity. We analyze the helical frontier molecular orbitals of strained cyclic allenes and show how secondary orbital and electrostatic effects influence stereoselectivity. The LUMO of carbon-3 of the allene (C-3 is not involved in primary orbital interactions) interacts in a stabilizing fashion with the HOMO of the diene in such a way that the carbon of the cyclic allene attached to C-1 favors the endo position in the transition state. The furan LUMO, allene HOMO interaction reinforces this preference. These mechanistic studies are expected to prompt the further use of long-avoided strained cyclic allenes in chemical synthesis.

Total Synthesis of (-)-Strictosidine and Interception of Aryne Natural Product Derivatives "Strictosidyne" and "Strictosamidyne"

Monoterpene indole alkaloids are a large class of natural products derived from a single biosynthetic precursor, strictosidine. We describe a synthetic approach to strictosidine that relies on a key facially selective Diels-Alder reaction between a glucosyl-modified alkene and an enal to set the C15-C20-C21 stereotriad. DFT calculations were used to examine the origin of stereoselectivity in this key step, wherein two of 16 possible isomers are predominantly formed. These calculations suggest the presence of a glucosyl unit, also inherent in the strictosidine structure, guides diastereoselectivity, with the reactive conformation of the vinyl glycoside dienophile being controlled by an exo-anomeric effect. (-)-Strictosidine was subsequently accessed using late-stage synthetic manipulations and an enzymatic Pictet-Spengler reaction. Several new natural product analogs were also accessed, including precursors to two unusual aryne natural product derivatives termed "strictosidyne" and "strictosamidyne". These studies provide a strategy for accessing glycosylic natural products and a new platform to access monoterpene indole alkaloids and their derivatives.

Looking at the big picture in activation strain model/energy decomposition analysis: the case of the ortho-para regioselectivity rule in Diels-Alder reactions

The regioselectivity of the Diels-Alder reaction is predicted by the ortho-para rule which has been explained from FMO theory. Using DFT calculations, the activation-strain model and energy decomposition analysis we studied the reaction of methyl acrylate with four unsymmetrical dienes. We found that if the analysis is carried out considering the TS structures, the selectivity would not be explained by the interaction energy as expected considering the FMO arguments. However, a thorough analysis along the reaction path revealed that the interaction energy is responsible for the regioselectivity. A deeper analysis with the EDA model showed that the decisive term that accounts for the HOMO-LUMO interactions favors the ortho and para paths, as predicted by FMO arguments.

Dual Activation of Aromatic Diels-Alder Reactions

The unusually fast Diels-Alder reactions of [5]cyclophanes were analyzed by DFT at the BLYP-D3(BJ)/TZ2P level of theory. The computations were guided by an integrated activation-strain and Kohn-Sham molecular orbital analysis. It is revealed why both [5]metacyclophane and [5]paracyclophane exhibit a significant rate enhancement compared to their planar benzene analogue. The activation strain analyses revealed that the enhanced reactivity originates from 1) predistortion of the aromatic core resulting in a reduced activation strain of the aromatic diene, and/or 2) enhanced interaction with the dienophile through a distortion-controlled lowering of the HOMO-LUMO gap within the diene. Both of these physical mechanisms and thus the rate of Diels-Alder cycloaddition can be tuned through different modes of geometrical distortion (meta versus para bridging) and by heteroatom substitution in the aromatic ring. Judicious choice of the bridge and heteroatom in the aromatic core enables effective tuning of the aromatic Diels-Alder reactivity to achieve activation barriers as low as 2 kcal mol-1 , which is an impressive 35 kcal mol-1 lower than that of benzene.

Cyclopropeniminium Ions Exhibit Unique Reactivity Profiles with Bioorthogonal Phosphines

We report a new ligation of cyclopropeniminium ions with bioorthogonal phosphines. Cyclopropeniminium scaffolds are sufficiently stable in biological media and, unlike related isomers, react with functionalized phosphines via formal 1,2-addition to a π-system. The ligation can be performed in aqueous solution and is compatible with existing bioorthogonal transformations. Such mutually compatible reactions are useful for multicomponent labeling.

Role of Water in the Reaction Mechanism and endo/exo Selectivity of 1,3-Dipolar Cycloadditions Elucidated by Quantum Chemistry and Machine Learning

Asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are among the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the role of water molecules in the reactivity and endo/exo selectivity remains unclear. To explore how water accelerates the reactions and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide (1) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules was used. It is demonstrated that not only the nature of both the dipolarophile and the 1,3-dipole, but also the solvent medium, can perturb or even alter the reaction mechanism. An extreme case was found for the reaction of 1,3-dipole 1 with methyl vinyl ketone, in which the reaction mechanism changes from a concerted to a stepwise mode on going from MeCN to H₂ O as solvent, with formation of a zwitterionic intermediate that is a very shallow minimum on the energy surface. Thus, high stereocontrol can still be expected despite the stepwise nature of the mechanism. The results indicate that water can induce global polarization along the reaction coordinate and highlight the role of microsolvation effects and bulk-phase effects in reproducing the experimentally observed aqueous acceleration and enhanced endo/exo selectivity.

Insights into N-Heterocyclic Carbene-Catalyzed Oxidative α-C(sp3)-H Activation of Aliphatic Aldehydes and Cascade [2 + 2] Cycloaddition with Ketimines

Predicting the chemoselectivity of [2 + 2] cyclizations is an important challenge in organic chemistry. Herein, we provided a valuable case for this issue. Density functional theory calculations were performed to systematically study the possible mechanisms and origin of selectivities for the N-heterocyclic carbene (NHC)-catalyzed oxidative α-C(sp³)-H activation of aliphatic aldehydes and the cascade [2 + 2] cycloaddition with ketimines. The [2 + 2] cycloaddition of azolium enolate intermediates to the C═N bond, rather than the C═O bond of ketimine, is revealed to be determined by chemo- and stereoselectivity. By comparing the energy gap between the frontier molecular orbitals (FMOs) of the two reacting parts involved in the [2 + 2] cycloaddition transition states, we propose a new strategy to determine the origin of the reaction chemoselectivity. Moreover, the local nucleophilic index can efficiently predict the active site of ketimines. Further analyses illustrate that NHC can increase the nucleophilicity of aldehydes and the acidity of the α-C(sp³)-H bond, and 3,3',5,5'-tetra- tert-butyl diphenoquinone (DQ) acts as an oxidant and promotes α-C(sp³)-H bond deprotonation. This work is useful not only for understanding the NHC-catalyzed oxidative [2 + 2] annulation but also for developing new applications of the FMO theory in organocatalytic cyclizations.

exo/endo Selectivity Control in Diels-Alder Reactions of Geminal Bis(silyl) Dienes: Theoretical and Experimental Studies

The factors controlling the reactivity and exo/ endo selectivity of Diels-Alder reactions of geminal bis(silyl) dienes catalyzed by AlEt₂Cl are studied at the B3LYP-D3(BJ)(SMD,CH₂Cl₂)/6-31++G**//B3LYP-D3(BJ)(SMD,CH₂Cl₂)/6-31+G* theoretical level. The reaction proceeds via a two-stage one-step mechanism, and the AlEt₂Cl as a Lewis acid catalyst enhances the electrophilicity of the carbonyl compound by coordination, consequently accelerating a cycloaddition reaction with a low energy barrier. A geminal bis(silyl) group of the diene and an α-substituent in α,β-unsaturated carbonyl compounds adjust the interaction energy (Δ E_int) as well as the deformation energy (Δ E_strain) of the diene and dienophile, affecting the barrier height and the diastereochemical outcome accordingly. The steric repulsion between the geminal bis(silyl) group and Al(III) catalyst increases the Pauli repulsion energy (Δ E_Pauli) and strain energy of dienophile fragment (Δ E_{strain(dienophile-LA)}) in the endo pathway, ensuring the exo selectivity. The introduction of a halogen atom (Cl or Br) or methyl group at the α-position of α,β-unsaturated carbonyl compounds increases the deformation energy of the diene fragment. Meanwhile, the noncovalent interactions (that is, dispersion and electrostatic interaction) stabilize the endo transition state, leading to predominant endo products. The theoretical predictions of the exo/ endo selectivity for Diels-Alder reactions of the substituted α,β-unsaturated carbonyl compound with Cl or Br atoms by the DFT method are also well confirmed by experiment.

Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies

The reactivities of 2‐butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3‐dipolar cycloaddition reaction with methyl azide were evaluated through DFT calculations at the M06‐2X/6‐311++G(d)//M06‐2X/6‐31+G(d) level of theory. Computed activation free energies for the cycloadditions of cycloalkynes are 16.5–22.0 kcal mol⁻¹ lower in energy than that of the acyclic 2‐butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction–activation strain analysis has been revealed that the degree of geometrical predistortion of the cycloalkyne ground‐state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO–LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.

Theoretical Study of Ruthenium(0)-Catalyzed Transfer Hydrogenative Cycloaddition of Cyclohexadiene and Norbornadiene with 1,2-Diols to Form Bridged Carbocycles

The recent success of Krische et al. ( Angew. Chem., Int. Ed. 2017 , 56 , 14667 -14671 ) in achieving a ruthenium(0)-catalyzed transfer hydrogenative cycloaddition of 1,2-diols with cyclohexadiene and norbornadiene in excellent yield with exo- and diastereoselectivity represents an exciting development in the synthesis of bridged carbocycles. In the present work, the possible catalytic mechanisms and origin of the exo- and diastereoselectivity for cyclohexadiene and norbornadiene were studied in detail by density functional theory calculations. The theoretical results indicate that the exoselective pathway for the cyclohexadiene substrate proceeds by a novel two-step successive C-C coupling, while the endoselective pathway undergoes the C-C coupling reaction in a conventional concerted manner. The origin of the preferential chemoselectivity of dione-cyclohexadiene C-C coupling over aromatization to benzene was investigated. Aromatization to benzene is unfavorable because of the large distortion energy of the three-membered ring in the transition state of hydrogen migration. From distortion/interaction analysis, for norbornadiene, the distortion energy plays the main role in determining the exoselectivity.

Secondary Orbital Interactions Enhance the Reactivity of Alkynes in Diels-Alder Cycloadditions

We have investigated the inverse electron-demand Diels–Alder reactions of trans-cyclooctene (TCO) and endo-bicyclo[6.1.0]nonyne (BCN) with a 1,2,4,5-tetrazine, a cyclopentadienone, and an ortho-benzoquinone. Tetrazines react significantly faster with TCO compared to BCN because the highest occupied molecular orbital (HOMO) of TCO is significantly higher in energy than the HOMO of BCN and there is less distortion of the tetrazine. Despite the different HOMO energies, TCO and BCN have similar reactivities toward cyclopentadienones, while BCN is significantly more reactive than TCO in the cycloaddition with ortho-benzoquinone. We find that the higher reactivity of BCN compared to TCO with ortho-benzoquinone is due to secondary orbital interactions of the BCN HOMO-1 with the diene LUMO.

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.

Molecular design principles towards exo-exclusive Diels–Alder reactions

The exo selective Diels–Alder reactions, reported as special cases, usually involve catalytic reaction conditions and specific cyclic structural motifs on the diene and/or the dienophile. Here we report a systematic computational investigation on the substituent effect for simple, linear dienes and dienophiles towards exo control in Diels–Alder reactions under thermal conditions. Through detailed characterization of reaction pathways for Diels–Alder cycloadditions between linear dienes and dienophiles with various substituents, we summarize a set of design principles aiming for an optimal and nearly-exclusive exo selectivity. These results shall lead to valuable guidelines and more versatile strategies in organic synthesis that are in accordance with the principles of green chemistry.

Exo-exclusive stereoselectivity for simple, terminal-substituted dienes and dienophiles may be achieved under thermal conditions through a delicate control of substituent identities.

Prediction on the origin of chemoselectivity in Lewis base-mediated competition cyclizations between allenoates and chalcones: a computational study

The HOMO_TSs and p-orbital contributions of the center atoms were used to predict the origin of chemoselectivity in this work.

Factors Controlling the Diels-Alder Reactivity of Hetero-1,3-Butadienes

We have quantum chemically explored the Diels-Alder reactivities of a systematic series of hetero-1,3-butadienes with ethylene by using density functional theory at the BP86/TZ2P level. Activation strain analyses provided physical insight into the factors controlling the relative cycloaddition reactivity of aza- and oxa-1,3-butadienes. We find that dienes with a terminal heteroatom, such as 2-propen-1-imine (NCCC) or acrolein (OCCC), are less reactive than the archetypal 1,3-butadiene (CCCC), primarily owing to weaker orbital interactions between the more electronegative heteroatoms with ethylene. Thus, the addition of a second heteroatom at the other terminal position (NCCN and OCCO) further reduces the reactivity. However, the introduction of a nitrogen atom in the backbone (CNCC) leads to enhanced reactivity, owing to less Pauli repulsion resulting from polarization of the diene HOMO in CNCC towards the nitrogen atom and away from the terminal carbon atom. The Diels-Alder reactions of ethenyl-diazene (NNCC) and 1,3-diaza-butadiene (NCNC), which contain heteroatoms at both the terminal and backbone positions, are much more reactive due to less activation strain compared to CCCC.

Hyperconjugative Aromaticity and Antiaromaticity Control the Reactivities and π-Facial Stereoselectivities of 5-Substituted Cyclopentadiene Diels-Alder Cycloadditions

The reactivities and π-facial stereoselectivities of Diels-Alder reactions of 5-substituted cyclopentadienes were studied using density functional theory. Burnell and co-workers previously showed that the π-facial selectivities result from the energies required to distort the reactants into the transition state geometries. We have discovered the origins of these distortions. C₅-X σ-donors predistort the cyclopentadiene into an envelope conformation that maximizes the stabilizing hyperconjugative interaction between the C₅-X σ-bond and the diene π-system. This envelope conformation geometrically resembles the anti transition state. To minimize the destabilizing effect of negative hyperconjugation, C₅-X σ-acceptors predistort in the opposite direction toward an envelope geometry that resembles the syn transition state. We now show how hyperconjugative effects of the C₅-X substituent influence the stereoselectivities and have developed a unified model rationalizing the stereoselectivities and reactivities of 5-substituted cyclopentadiene Diels-Alder reactions.

Fluorine substituent effect on the stereochemistry of catalyzed and non-catalyzed Diels–Alder reactions. The case of R-butenone with cyclopentadiene: a computational assessment of the mechanism

A semiquantitative prediction of stereoselectivity due to substitutions of dienophile is obtained.