Computationally designed and experimentally confirmed diastereoselective rhodium-catalyzed Pauson-Khand reaction at room temperature

Combined molecular dynamics and coordinate driving method for automatically searching complicated reaction pathways

The combined molecular dynamics and coordinate driving (MD/CD) method is updated and generalized in this work to broaden its applications in automatically searching reaction pathways for complicated reactions. In this updated version, MD simulations are performed with the GFN's family of methods to systematically sample conformers for almost any systems with atomic numbers Z ≤ 86. The improved CD procedure is greatly accelerated by applying a pre-screening stage at the semiempirical GFN2-xTB level. An automatic module based on the Marcus theory and its improved version (the Wolynes theory) is designed to include single electron transfer (SET) processes into reaction pathways. The capabilities of this method are demonstrated by exploring the most possible reaction pathways of three experimentally reported reactions: the organophosphine-catalyzed trans phosphinoboration, the Fe(II) complex-mediated C(sp2)-H borylation reaction, and the SET-triggered deaminative radical cross-coupling reaction. Comprehensive reaction networks are obtained for all three reactions with reasonable computational costs. Detailed mechanisms for these reactions can account for the reported experimental facts.

Machine Learning and Quantum Calculation for Predicting Yield in Cu-Catalyzed P-H Reactions

The paper discussed the use of machine learning (ML) and quantum chemistry calculations to predict the transition state and yield of copper-catalyzed P-H insertion reactions. By analyzing a dataset of 120 experimental data points, the transition state was determined using density functional theory (DFT). ML algorithms were then applied to analyze 16 descriptors derived from the quantum chemical transition state to predict the product yield. Among the algorithms studied, the Support Vector Machine (SVM) achieved the highest prediction accuracy of 97%, with over 80% correlation in Leave-One-Out Cross-Validation (LOOCV). Sensitivity analysis was performed on each descriptor, and a comprehensive investigation of the reaction mechanism was conducted to better understand the transition state characteristics. Finally, the ML model was used to predict reaction plans for experimental design, demonstrating strong predictive performance in subsequent experimental validation.

Mechanism and Stereochemistry of Rhodium-Catalyzed [5 + 2 + 1] Cycloaddition of Ene-Vinylcyclopropanes and Carbon Monoxide Revealed by Visual Kinetic Analysis and Quantum Chemical Calculations

Previously, we developed a rhodium-catalyzed [5 + 2 + 1] cycloaddition of ene-vinylcyclopropanes (ene-VCPs) and carbon monoxide to synthesize eight-membered carbocycles. The efficiency of this reaction can be appreciated from its application in the synthesis of several natural products. Herein we report the results of a 15-year investigation into the mechanism of the [5 + 2 + 1] cycloaddition by applying visual kinetic analysis and high-level quantum chemical calculations at the DLPNO-CCSD(T)//BMK level. According to the kinetic measurements, the resting state of the catalyst possesses a dimeric structure (with two rhodium centers) whereas the active catalytic species is monomeric (with one rhodium center). The catalytic cycle consists of cyclopropane cleavage (the turnover-limiting step), alkene insertion, CO insertion, reductive elimination, and catalyst transfer steps. Other reaction pathways have also been considered but then have been ruled out. The steric origin of the diastereoselectivity (cis versus trans) was revealed by comparing the alkene insertion transition states. In addition, how the double-bond configuration of the VCPs (Z versus E) affects the substrate reactivity and the origins of chemoselectivity ([5 + 2 + 1] versus [5 + 2]) were also investigated. The present study will provide assistance in understanding other carbonylative annulations catalyzed by transition metals.

Asymmetric Total Synthesis of (-)-Spirochensilide A, Part 1: Diastereoselective Synthesis of the ABCD Ring and Stereoselective Total Synthesis of 13(R)-Demethyl Spirochensilide A

A concise and diastereoselective construction of the ABCD ring system of spirochensilide A is described. The key steps of this synthesis are a semipinacol rearrangement reaction to stereoselectively construct the AB ring system bearing two vicinal quaternary chiral centers and a Co-mediated Pauson-Khand reaction to form the spiro-based bicyclic CD ring system. This chemistry leads to the stereoselective synthesis of 13(R)-demethyl spirochensilide A, paving the way for the first asymmetric total synthesis of (-)-spirochensilide A.

Quantum-mechanical transition-state model combined with machine learning provides catalyst design features for selective Cr olefin oligomerization

The use of data science tools to provide the emergence of non-trivial chemical features for catalyst design is an important goal in catalysis science. Additionally, there is currently no general strategy for computational homogeneous, molecular catalyst design. Here, we report the unique combination of an experimentally verified DFT-transition-state model with a random forest machine learning model in a campaign to design new molecular Cr phosphine imine (Cr(P,N)) catalysts for selective ethylene oligomerization, specifically to increase 1-octene selectivity. This involved the calculation of 1-hexene : 1-octene transition-state selectivity for 105 (P,N) ligands and the harvesting of 14 descriptors, which were then used to build a random forest regression model. This model showed the emergence of several key design features, such as Cr-N distance, Cr-α distance, and Cr distance out of pocket, which were then used to rapidly design a new generation of Cr(P,N) catalyst ligands that are predicted to give >95% selectivity for 1-octene.

Rhodium-catalyzed [(3+2)+1] carbocyclizations of alkynylidenecyclopropanes with carbon monoxide: construction of polysubstituted bicyclohexa-2,5-dienones

A rhodium-catalyzed carbocyclization reaction of alkynylidenecyclopropanes with carbon monoxide to prepare bicyclohexa-2,5-dienones is described. This protocol offers convenient access to doubly conjugated cyclic enones and is tolerant of functionalized alkynes and cyclopropanes. Furthermore, a photochemical rearrangement of a bicyclohexa-2,5-dienone facilitates the construction of a highly functionalized bicyclopentenone containing two contiguous stereogenic centres, which represents a versatile intermediate for target directed synthesis.

Computationally Guided Catalyst Design in the Type I Dynamic Kinetic Asymmetric Pauson-Khand Reaction of Allenyl Acetates

The Rh(I)-catalyzed allenic Pauson-Khand reaction (APKR) is an efficient, redox-neutral method of synthesizing α-acyloxy cyclopentenones. An enantioselective APKR could provide access to chiral, nonracemic α-acyloxy and α-hydroxy cyclopentenones and their corresponding redox derivatives, such as thapsigargin, a cytotoxic natural product with potent antitumor activity. Rapid scrambling of axial chirality of allenyl acetates in the presence of Rh(I) catalysts enables the conversion of racemic allene to enantiopure cyclopentenone product in a dynamic kinetic asymmetric transformation (DyKAT). A combined experimental and computational approach was taken to develop an effective catalytic system to achieve the asymmetric transformation. The optimization of the denticity, and steric and electronic properties of the ancillary ligand (initially (S)-MonoPhos, 58:42 er), afforded a hemilabile bidentate (S)-MonoPhos-alkene-Rh(I) catalyst that provided α-acyloxy cyclopentenone product in up to 14:86 er. Enantioselectivity of the Rh(I)-(S)-MonoPhos-alkene catalyst was rationalized using ligand-substrate steric interactions and distortion energies in the computed transition states. This asymmetric APKR of allenyl acetates is a rare example of a Type I DyKAT reaction of an allene, the first example of DyKAT in a cyclocarbonylation reaction, and the first catalyst-controlled enantioselective APKR.

Recent Advances in the Pauson-Khand Reaction

The Pauson-Khand [2+2+1] cycloaddition of alkynes, alkenes, and carbon monoxide has been a vibrant area of research for more than 40 years. This review highlights recent achievements in the Pauson-Khand reaction, particularly in catalytic and asymmetric variants. Discussion of regioselectivity and advances in substrate scope is also presented.

Mechanism of Rh-Catalyzed Oxidative Cyclizations: Closed versus Open Shell Pathways

A conceptual theory for analyzing and understanding oxidative addition reactions that form the cornerstone of many transition metal mediated catalytic cycles that activate C-C and C-H bonds, for example, was developed. The cleavage of the σ- or π-bond in the organic substrate can be envisioned to follow a closed or an open shell formalism, which is matched by a corresponding electronic structure at the metal center of the catalyst. Whereas the assignment of one or the other mechanistic scenario appears formal and equivalent at first sight, they should be recognized as different classes of reactions, because they lead to different reaction optimization and control strategies. The closed-shell mechanism involves heterolytic bond cleavages, which give rise to highly localized charges to form at the transition state. In the open-shell pathway, bonds are broken homolytically avoiding localized charges to accumulate on molecular fragments at the transition states. As a result, functional groups with inductive effects may exert a substantial influence on the energies of the intermediate and transition states, whereas no such effect is expected if the mechanism proceeds through the open-shell mechanism. If these functional groups are placed in a way that opens an electronic communication pathway to the molecular sites where charges accumulate, for example, using hyperconjugation, electron donating groups may stabilize a positive charge at that site. An instructive example is discussed, where this stereoelectronic effect allowed for rendering the oxidative addition diastereoselective. No such control is possible, however, when the open-shell reaction pathway is followed, because the inductive effects of functional groups have little to no effect on the stabilities of radical-like substrate states that are encountered when the bonds are broken in a homolytic fashion. Whether the closed-shell or open-shell mechanism for oxidative addition is followed is determined by the ordering of the d-orbital dominated frontier orbitals. If the highest occupied molecular orbital (HOMO) is oriented in space in such a way that will give the organic substrate easy access to the valence electron pair, the closed-shell mechanism can be followed. If the shape and orientation of the HOMO is not appropriate, however, an alternative pathway involving singlet excited states of the metal that will invoke the matching radicaloid cleavage of the organic substrate will dominate the oxidative addition. This novel paradigm for formally analyzing and understanding oxidative additions provides a new way of systematically understanding and planning catalytic reactions, as demonstrated by the in silico design of room-temperature Pauson-Khand reactions.

Catalytic Control in Cyclizations: From Computational Mechanistic Understanding to Selectivity Prediction

This Account describes the use of quantum-chemical calculations to elucidate mechanisms and develop catalysts to accomplish highly selective cyclization reactions. Chemistry is awash with cyclic molecules, and the creation of rings is central to organic synthesis. Cyclization reactions, the formation of rings by the reaction of two ends of a linear precursor, have been instrumental in the development of predictive models for chemical reactivity, from Baldwin's classification and rules for ring closure to the Woodward and Hoffmann rules based on the conservation of orbital symmetry and beyond. Ring formation provides a productive and fertile testing ground for the exploration of catalytic mechanisms and chemo-, regio-, diastereo-, and enantioselectivity using computational and experimental approaches. This Account is organized around case studies from our laboratory and illustrates the ways in which computations provide a deeper understanding of the mechanisms of catalysis in 5-endo cyclizations and how computational predictions can lead to the development of new catalysts for enhanced stereoselectivities in asymmetric cycloisomerizations. We have explored the extent to which several cation-directed 5-endo ring-closing reactions may be considered as electrocyclic and demonstrated that reaction pathways and magnetic parameters of transition structures computed using quantum chemistry are inconsistent with this notion, instead favoring a polar mechanism. A rare example of selectivity in favor of 5-endo-trig ring closure is shown to result from subtle substrate effects that bias the reactant conformation out-of-plane, limiting the involvement of cyclic conjugation. The mode of action of a chiral ammonium counterion was deduced via conformational sampling of the transition state assembly and involves coordination to the substrate via a series of nonclassical hydrogen bonds. We describe how computational mechanistic understanding has led directly to the discovery of new catalyst structures for enantioselective cycloisomerizations. Calculations have revealed that stepwise C-C bond formation and proton transfer dictate the exclusive endo diastereoselectivity of the intramolecular Michael addition to form 2-azabicyclo[3.3.1]nonane skeletons catalyzed by primary amines. These insights have led to development of a highly enantioselective catalyst with higher atom economy than previous generations. This Account also explores transition-metal-catalyzed cycloisomerizations, where our theoretical investigations have uncovered an unexpected reaction pathway in the [5 + 2] cycloisomerization of ynamides. This has led to the design of new phosphoramidite ligands to enable double-stereodifferentiating cycloisomerizations in both matched and mismatched catalyst-substrate settings. Computational understanding of the factors responsible for the regio-, enantio-, and diasterocontrol is shown to generate tangible predictions leading to an acceleration of catalyst development for selective cyclizations.

Catalytic borylation of methane

Despite steady progress in catalytic methods for the borylation of hydrocarbons, methane has not yet been subject to this transformation. Here we report the iridium-catalyzed borylation of methane using bis(pinacolborane) in cyclohexane solvent. Initially, trace amounts of borylated products were detected with phenanthroline-coordinated Ir complexes. A combination of experimental high-pressure and high-throughput screening, and computational mechanism discovery techniques helped to rationalize the foundation of the catalysis and identify improved phosphine-coordinated catalytic complexes. Optimized conditions of 150°C and 3500-kilopascal pressure led to yields as high as ~52%, turnover numbers of 100, and improved chemoselectivity for monoborylated versus diborylated methane.

The origin of the ligand-controlled regioselectivity in Rh-catalyzed [(2 + 2) + 2] carbocyclizations: steric vs. stereoelectronic effects

Density functional theory calculations demonstrate that the reversal of regiochemical outcome of the addition for substituted methyl propiolates in the rhodium-catalyzed [(2 + 2) + 2] carbocyclization with PPh₃ and (S)-xyl-binap as ligands is both electronically and sterically controlled.

Density functional theory calculations demonstrate that the reversal of regiochemical outcome of the addition for substituted methyl propiolates in the rhodium-catalyzed [(2 + 2) + 2] carbocyclization with PPh₃ and (S)-xyl-binap as ligands is both electronically and sterically controlled. For example, the ester functionality polarizes the alkyne π* orbital to favor overlap of the methyl-substituted terminus of the alkyne with the p_π-orbital of the alkenyl fragment of the rhodacycle during alkyne insertion with PPh₃ as the ligand. In contrast, the sterically demanding xyl-binap ligand cannot accommodate the analogous alkyne orientation, thereby forcing insertion to occur at the sterically preferred ester terminus, overriding the electronically preferred orientation for alkyne insertion.

Mechanisms and stereoselectivities of the Rh(i)-catalyzed carbenoid carbon insertion reaction of benzocyclobutenol with diazoester

Mechanisms and stereoselectivities of a Rh(i)-catalyzed carbenoid carbon insertion reaction of benzocyclobutenol with diazoester have been investigated using the DFT method.

Reactivity and chemoselectivity of allenes in Rh(I)-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes: allene-mediated rhodacycle formation can poison Rh(I)-catalyzed cycloadditions

Allenes are important 2π building blocks in organic synthesis and engage as 2-carbon components in many metal-catalyzed reactions. Wender and co-workers discovered that methyl substituents on the terminal allene double bond counterintuitively change the reactivities of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes (VCPs). More sterically encumbered allenes afford higher cycloadduct yields, and such effects are also observed in other Rh(I)-catalyzed intermolecular cycloadditions. Through density functional theory calculations (B3LYP and M06) and experiment, we explored this enigmatic reactivity and selectivity of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with VCPs. The apparent low reactivity of terminally unsubstituted allenes is associated with a competing allene dimerization that irreversibly sequesters rhodium. With terminally substituted allenes, steric repulsion between the terminal substituents significantly increases the barrier of allene dimerization while the barrier of the (5 + 2) cycloaddition is not affected, and thus the cycloaddition prevails. Computation has also revealed the origin of chemoselectivity in (5 + 2) cycloadditions with allene-ynes. Although simple allene and acetylene have similar reaction barriers, intermolecular (5 + 2) cycloadditions of allene-ynes occur exclusively at the terminal allene double bond. The terminal double bond is more reactive due to the enhanced d-π* backdonation. At the same time, insertion of the internal double bond of an allene-yne has a higher barrier as it would break π conjugation. Substituted alkynes are more difficult to insert compared with acetylene, because of the steric repulsion from the additional substituents. This leads to the greater reactivity of the allene double bond relative to the alkynyl group in allene-ynes.

Rh(I)-catalyzed Pauson-Khand-type cycloaddition reaction of ene-vinylidenecyclopropanes with carbon monoxide (CO)

An intramolecular Pauson-Khand type cycloaddition reaction of ene-vinylidenecyclopropanes with carbon monoxide has been established by using [Rh(COD)Cl](2) as the catalyst. The reaction was found to be highly efficient in solvents of 1,2-dichloroethane and 1,1,2,2-tetrachloroethane to give excellent yields of 90-99%. The reaction provides easy access to a series of fused 6,5-ring structures containing spiro-cyclopropane units that are useful for drug design and development. A mechanism of this cycloaddition process has been proposed accounting for structures of resulting products that were unambiguously assigned by X-ray diffractional analysis.