Distortion-Controlled Reactivity and Molecular Dynamics of Dehydro-Diels–Alder Reactions

Substituent effects on the selectivity of ambimodal [6+4]/[4+2] cycloaddition

In this work, we report a density functional theory (DFT) study and a dynamical trajectory study of substituent effects on the ambimodal [6+4]/[4+2] cycloaddition proposed for 1,3,5,10,12-cycloheptadecapentaene, referred to as cycloheptadecapentaene. The proposed cycloaddition proceeds through an ambimodal transition state, which results in both a [6+4] adduct a [4+2] adduct directly. The [6+4] adduct can be readily converted to the [4+2] adduct via a Cope rearrangement. We study the selectivity of the reaction with regard to the position of substituents, steric effects of substituents, and electronic effects of substituents. In the dynamical trajectory study, we find that nitro-substituted reactants lead to a new product from the ambimodal transition state via the hetero Diels-Alder reaction, and this new product can then be converted to a [4+2] adduct by a hetero [3, 3]-sigmatropic rearrangement. These results may provide insights for designing more bridged heterocyclic compounds.

Discovery of new tetrazines for bioorthogonal reactions with strained alkenes via computational chemistry

Tetrazines are widely employed reagents in bioorthogonal chemistry, as they react readily with strained alkenes in inverse electron demand Diels-Alder reactions, allowing for selective labeling of biomacromolecules. For optimal performance, tetrazine reagents have to react readily with strained alkenes, while remaining inert against nucleophiles like thiols. Balancing these conditions is a challenge, as reactivity towards strained alkenes and nucleophiles is governed by the same factor - the energy of unoccupied orbitals of tetrazine. Herein, we utilize computational chemistry to screen a set of tetrazine derivatives, aiming to identify structural elements responsible for a better ratio of reactivity with strained alkenes vs. stability against nucleophiles. This advantageous trait is present in sulfone- and sulfoxide-substituted tetrazines. In the end, the distortion/interaction model helped us to identify that the reason behind this enhanced reactivity profile is a secondary orbital interaction between the strained alkene and sulfone-/sulfoxide-substituted tetrazine. This insight can be used to design new tetrazines for bioorthogonal chemistry with improved reactivity/stability profiles.

C-H Insertion in Dirhodium Tetracarboxylate-Catalyzed Reactions despite Dynamical Tendencies toward Fragmentation: Implications for Reaction Efficiency and Catalyst Design

Rh-catalyzed C-H insertion reactions to form β-lactones suffer from post-transition state bifurcations, with the same transition states leading to ketones and ketenes via fragmentation in addition to β-lactones. In such a circumstance, traditional transition state theory cannot predict product selectivity, so we employed ab initio molecular dynamics simulations to do so and provide a framework for rationalizing the origins of said selectivity. Weak interactions between the catalyst and substrate were studied using energy decomposition and noncovalent interaction analyses, which unmasked an important role of the 2-bromophenyl substituent that has been used in multiple β-lactone-forming C-H insertion reactions. Small and large catalysts were shown to behave differently, with the latter providing a means of overcoming dynamically preferred fragmentation by lowering the barrier for the recombination of the product fragments in the grip of the large catalyst active site cavity.

Accessing a regiospecific isomer and a metastable polymorph through crystal engineering and solid-state reaction

We describe a solid-state Diels–Alder reaction where crystal engineering was used to design a reaction site yielding one regioisomer. Reaction was followed with SCXRD, compared to solution synthesis and rationalised using computational modelling.

Mechanistic and Kinetic Factors of ortho-Benzyne Formation in Hexadehydro-Diels-Alder (HDDA) Reactions

With the rapid development of the hexadehydro-Diels-Alder reaction (HDDA) from its first discovery in 1997, the question of whether a concerted or stepwise mechanism better describes the thermally activated formation of ortho-benzyne from a diyne and a diynophile has been debated. Mechanistic and kinetic investigations were able to show that this is not a black or white situation, as minor changes can tip the balance. For that reason, especially, linked yne-diynes were studied to examine steric, electronic, and radical-stabilizing effects of their terminal substituents on the reaction mechanism and kinetics. Furthermore, the influence of the nature of the linker on the HDDA reaction was explored. The more recently discovered photochemical HDDA reaction also gives ortho-arynes, which display the same reactivity as the thermally generated ones, but their formation might not proceed by the same mechanism. This minireview summarizes the current state of mechanistic understanding of the HDDA reaction.

Tuning the reactivity of alkoxyl radicals from 1,5-hydrogen atom transfer to 1,2-silyl transfer

Controlling the reactivity of reactive intermediates is essential to achieve selective transformations. Due to the facile 1,5-hydrogen atom transfer (HAT), alkoxyl radicals have been proven to be important synthetic intermediates for the δ-functionalization of alcohols. Herein, we disclose a strategy to inhibit 1,5-HAT by introducing a silyl group into the α-position of alkoxyl radicals. The efficient radical 1,2-silyl transfer (SiT) allows us to make various α-functionalized products from alcohol substrates. Compared with the direct generation of α-carbon radicals from oxidation of α-C-H bond of alcohols, the 1,2-SiT strategy distinguishes itself by the generation of alkoxyl radicals, the tolerance of many functional groups, such as intramolecular hydroxyl groups and C-H bonds next to oxygen atoms, and the use of silyl alcohols as limiting reagents.

Hexadehydro-Diels-Alder Reaction: Benzyne Generation via Cycloisomerization of Tethered Triynes

The hexadehydro-Diels-Alder (HDDA) reaction is the thermal cyclization of an alkyne and a 1,3-diyne to generate a benzyne intermediate. This is then rapidly trapped, in situ, by a variety of species to yield highly functionalized benzenoid products. In contrast to nearly all other methods of aryne generation, no other reagents are required to produce an HDDA benzyne. The versatile and customizable nature of the process has attracted much attention due not only to its synthetic potential but also because of the fundamental mechanistic insights the studies often afford. The authors have attempted to provide here a comprehensive compilation of publications appearing by mid-2020 that describe experimental results of HDDA reactions.

Ab Initio Molecular Dynamics Simulations of the SN1/SN2 Mechanistic Continuum in Glycosylation Reactions

We report a computational approach to evaluate the reaction mechanisms of glycosylation using ab initio molecular dynamics (AIMD) simulations in explicit solvent. The reaction pathways are simulated via free energy calculations based on metadynamics and trajectory simulations using Born-Oppenheimer molecular dynamics. We applied this approach to investigate the mechanisms of the glycosylation of glucosyl α-trichloroacetimidate with three acceptors (EtOH, i-PrOH, and t-BuOH) in three solvents (ACN, DCM, and MTBE). The reactants and the solvents are treated explicitly using density functional theory. We show that the profile of the free energy surface, the synchronicity of the transition state structure, and the time gap between leaving group dissociation and nucleophile association can be used as three complementary indicators to describe the glycosylation mechanism within the SN1/SN2 continuum for a given reaction. This approach provides a reliable means to rationalize and predict reaction mechanisms and to estimate lifetimes of oxocarbenium intermediates and their dependence on the glycosyl donor, acceptor, and solvent environment.

Enantioselective synthesis of chiral tetrasubstituted allenes: harnessing electrostatic and noncovalent interactions in a bifunctional activation model for N-triflylphosphoramide catalysis

DFT calculation reveals that the oxygen activation model is preferred than the nitrogen activation model due to the preferred chiral electrostatic environment.

Dynamical Trajectory Study of the Transannular [6+4] and Ambimodal Cycloaddition in the Biosynthesis of Heronamides

We report the dynamical trajectory study of the transannular [6+4] and ambimodal cycloaddition proposed in the biosynthesis of heronamide natural products. The originally proposed bifurcation of the potential energy surface is found to strongly favor the formation of the [6+4] product, both in the gas phase and in an explicit water environment, as evidenced by our trajectory simulations. The detailed information on how the bonds are formed and how water influences the bonding dynamics was analyzed at the femtosecond time scale.

Development of Magnesium Oxide-Silver Hybrid Nanocatalysts for Synergistic Carbon Dioxide Activation to Afford Esters and Heterocycles at Ambient Pressure

Multi-metallic hybrid nancatalysts consisting of a porous metal oxide host and metal satellite guests serve as a scaffold for multi-step transformations of divergent and energy-challenging substrates. Here we have developed a 3D porous MgO framework (Lewis basic host) with Ag⁰ nanoparticles (noble metal guest) for ambient pressure activation and insertion of CO₂ into unsaturated alkyne substrates. The hybrid MgO@Ag-x (x = 2, 5, 7, 8 at % Ag) catalysts are synthesized by impregnating Ag⁺ ions in porous MgO cubes followed by reduction using NaBH₄. Morphological (SEM, TEM, EDX mapping) and structural (PXRD, XPS) characterization reveal that the micron-sized hybrid cubes derive from self-assembly of ~100 nm (edge length) MgO cubes decorated with ~ 5 to 25 nm Ag⁰ NPs. Detailed XPS analysis illustrates Ag⁰ is present in two forms, <10 nm NPs and ~25 nm aggregates. The MgO@Ag-7 catalyst is effective for inserting CO₂ into aryl alkynes followed by S_N2 coupling with allylic chlorides to afford a wide range of ester and lactone heterocycles in excellent yields (61-93%) and with low E-factor (2.8). The proposed mechanism suggests a CO₂ capture and substrate assembly role for 3D porous MgO while Ag⁰ performs the key activation of alkyne and CO₂ insertion steps. The catalyst is recyclable (5x) with no significant loss of product yield. Overall, these results demonstrate viable approaches to hybrid catalyst development for challenging conversions such as CO₂ utilization in a green and sustainable manner.

Chiral Phosphoric Acid-Catalyzed Enantioselective Direct Arylation of Iminoquinones: A Case Study of the Model Selectivity

Chiral phosphoric acid (CPA)-catalyzed enantioselective arylation reactions have attracted immense attention recently. However, the preferential activation model in the stereodetermining step is controversial, and hence, the origin of enantioselectivity is still far from being understood. Two stereochemical models are provided on the basis of the asymmetric arylations of iminoquinones with naphthylamines (reaction 1) or naphthols (reaction 2) catalyzed by (R/S)-TRIP to explain the high enantioselectivity and the effect of CPAs scaffolds. Unexpectedly, our calculations reveal that substrate naphthylamines or naphthols prefer enantioselective aminal formation model II or 1,4-addition model I, respectively, which is the reverse of Tan's and Xu's model. The different noncovalent and steric interactions between catalysts and substrates are responsible for the observed model preference. Moreover, the enantioselectivity arises from distortion (reaction 1) and noncovalent interactions (reaction 2) that discriminate between the diastereomeric transition states. We further investigated the effect of SPINOL-based CPAs on the enantioselectivity and found that the more rigid skeleton and a smaller binding pocket lead to lower enantioselectivity as compared with that of BINOL-based CPA. The new insights into the reaction activation model rationalize the stereoselectivity outcome of direct asymmetric arylation reactions, and our general model can be extended to related transformations.

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

The ruthenium tetroxide-mediated oxidation of cyclopentane, tetrahydrofuran, tetrahydrothiophene and N-substituted pyrrolidines has been studied computationally by DFT and topological (analysis of the electron localization function, ELF) methods. In agreement with experimental observations and previous DFT calculations, the rate-limiting step of the reaction takes place through a highly asynchronous (3 + 2) concerted cycloaddition through a single transition structure (one kinetic step). The ELF analysis identifies the reaction as a typical one-step-two-stages process and corroborates the existence of a transient carbocation. In the case of pyrrolidines, the carbocation is completely stabilized as an energy minimum in the form of an iminium ion and the reaction takes place in two steps.

Mechanism and Regioselectivity of an Unsymmetrical Hexadehydro-Diels-Alder (HDDA) Reaction

Hoye reported intramolecular hexadehydro-Diels-Alder (HDDA) reactions to generate arynes that functionalize natural product phenols and amines. In their studies, Hoye found that unsymmetrical tetraynes selectively form a single aryne. We report density functional theory (DFT) calculations that reveal the factors controlling the regioselectivity.

The control effects of different scaffolds in chiral phosphoric acids: a case study of enantioselective asymmetric arylation

DFT calculations disclosed that the sign of enantioselectivity in chiral-phosphoric-acid catalyzed reactions can be tuned by BINOL- or SPINOL-derived backbones.

Nucleophilic substitution reactions of cyclic thiosulfinates are accelerated by hyperconjugative interactions

Cyclic thiosulfinates are a class of biocompatible molecules, currently expanding our in vivo toolkit.

Mechanistic investigation-inspired activation mode of DBU and the function of the α-diazo group in the reaction of the α-amino ketone compound and EDA: [DBU-H]+-DMF-H2O and α-diazo as strong N-terminal nucleophiles

DFT calculations disclosed a dramatic electronic turnover of the α-diazo group based on an unexpected DBU activation mode.

Mechanistic insight on water and substrate catalyzed the synthesis of 3-(1H-indol-3-yl)-2-(4-methoxybenzyl)isoindolin-1-one: Driving by noncovalent interactions

The mechanisms of the synthesis of 2-substituted-3-(1H-indol-3-yl)-isoindolin-1-one derivatives have been investigated theoretically under unassisted, self-assisted, and water-assisted conditions. Being different from previously proposed catalyst-free by Hu et al., our results show that the title mechanism can be altered and accelerated by solvent and substrate 2. Two types of mechanisms have been developed by DFT calculations differ in the reaction sequence of substrates 1 with 3 (M1) or 2 (M2) followed by 2 (M1) or 3 (M2), and water-assisted M1 is the most favored one. It was found that the nucleophilicity of substrate 3 is stronger than that of 2. Our calculations suggest that the water-assisted pathway in M1 is the most favorable case, which undergoes nucleophilic addition and H-shift, C-N bond formation and water elimination, and intramolecular cyclization and water elimination. The rate-determining step is the nucleophilic attack process. Moreover, we also explored the effect of nucleophilic attack of the nitrogen of (4-methoxyphenyl)methanamine on hydroxyl or carbonyl group carbon of phthalaldehydic acid on the activation energy. More importantly, we found that water molecules play a critical role in the whole reaction, not only act as solvent but also as an efficient catalyst, proton shuttle, and stabilizer to stabilize the structures of transition states and intermediates via π···H-O, O···H-N, O···H-C, and O···H-O interactions. The origin of the different reactivity of M1 and M2 is ascribed to the pivotal noncovalent interactions exist between catalyst (water and substrate 2) and reactants. © 2018 Wiley Periodicals, Inc.

Spin crossover dynamics studies on the thermally activated molecular oxygen binding mechanism on a model copper complex

The theoretical description of the primary dioxygen (O₂) binding and activation step in many copper or iron enzymes, suffers from the instrinsically electronic non-adiabaticity of the spin flip events of the triplet dioxygen molecule (³O₂), mediated by spin–orbit couplings.

A computational mechanistic study of substrate-controlled competitive O–H and C–H insertion reactions catalyzed by dirhodium(ii) carbenoids: insight into the origin of chemoselectivity

DFT calculations disclosed the chemoselectivity of rhodium carbenoid and water co-catalyzed O–H and C–H insertion reactions with three 1,3-diketone substrates.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.

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.

Synthesis of Illudinine from Dimedone

A total synthesis of the illudalane sesquiterpene illudinine was realized in eight steps and 14% overall yield from commercially available dimedone. The approach features tandem fragmentation/Knoevenagel-type condensation and microwave-assisted oxidative cycloisomerization to establish the isoquinoline core. Completion of the synthesis involves a recently reported cascade S_NAr/Lossen rearrangement on a densely functionalized aryl bromide and an optimized procedure for O-methylation of 8-hydroxyisoquinolines. The oxidative cycloisomerization proceeds by way of a novel inverse-demand intramolecular dehydro-Diels-Alder cycloaddition, which has a potentially broader appeal for preparing substituted isoquinolines.

Methodology and applications of the hexadehydro-Diels–Alder (HDDA) reaction

Hexadehydro-Diels–Alder (HDDA) reactions between alkynes and 1,3-diynes readily generate highly reactive and synthetically useful arynes.