Bond Memory in Dynamically Determined Stereoselectivity

Uncatalyzed Carbometallation Involving Group 13 Elements: Carboboration and Carboalumination of Alkenes and Alkynes

Carbometallation of alkenes and alkynes are powerful carbon-carbon bond-forming reactions. The use of compounds containing bonds between carbon and group 13 elements, particularly boron and aluminum, are particularly attractive because of the versatility of subsequent transformations. Uncatalyzed carboboration and carboalumination represent less common classes of reactions. This Short Review discusses uncatalyzed carboboration and carboalumination reactions of alkenes and alkynes, including the reaction design and mechanism.

Sodium mediated deprotonative borylation of arenes using sterically demanding B(CH2SiMe3)3: unlocking polybasic behaviour and competing lateral borane sodiation

The deprotonative metalation of organic molecules has become a convenient route to prepare functionalised aromatic substrates. Amongst the different metallating reagents available, sodium bases have recently emerged as a more sustainable and powerful alternative to their lithium analogues. Here we report the study of the sterically demanding electrophilic trap B(CH₂SiMe₃)₃ for the deprotonative borylation of arenes using NaTMP (TMP = 2,2,6,6-tetramethylpiperidide) in combination with tridentate Lewis donor PMDETA (PMDETA = N,N,N',N'',N''-pentamethyldiethylenetriamine). Using anisole and benzene as model substrates, unexpected polybasic behaviour has been uncovered, which enables the formal borylation of two equivalents of the relevant arene. The combination of X-ray crystallographic and NMR monitoring studies with DFT calculations has revealed that while the first B-C bond forming process takes place via a sodiation/borylation sequence to furnish [(PMDETA)NaB(Ar)(CH₂SiMe₃)₃] species, the second borylation step is facilitated by the formation of a borata-alkene intermediate, without the need of an external base. For non-activated benzene, it has also been found that under stoichimetric conditions the lateral sodiation of B(CH₂SiMe₃)₃ becomes a competitive reaction pathway furnishing a novel borata-alkene complex. Showing a clear alkali-metal effect, the use of the sodium base is key to access this reactivity, while the metalation/borylation of the amine donor PMDETA is observed instead when LiTMP is used.

Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials

Direct trajectory calculations have become increasingly popular in recent computational chemistry investigations. However, the exorbitant computational cost of ab initio trajectory calculations usually limits its application in mechanistic explorations. Recently, machine learning-based potential energy surface (ML-PES) provides a powerful strategy to circumvent the heavy computational cost and meanwhile maintain the required accuracy. Despite the appealing potential, constructing a robust ML-PES is still challenging since the training set of the PES should cover a broad enough configuration space. In this work, we demonstrate that when the concerned properties could be collected by the localized sampling of the configuration space, quasiclassical trajectory (QCT) calculations can be invoked to efficiently obtain locally accurate ML-PESs. We prove our concept with two model reactions: methyl migration of i-pentane cation and dimerization of cyclopentadiene. We found that the locally accurate ML-PESs are sufficiently robust for reproducing the static and dynamic features of the reactions, including the time-resolved free energy and entropy changes, and time gaps.

Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities

Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.

Enzymatic Control over Reactive Intermediates Enables Direct Oxidation of Alkenes to Carbonyls by a P450 Iron-Oxo Species

The aerobic oxidation of alkenes to carbonyls is an important and challenging transformation in synthesis. Recently, a new P450-based enzyme (aMOx) has been evolved in the laboratory to directly oxidize styrenes to their corresponding aldehydes with high activity and selectivity. The enzyme utilizes a heme-based, high-valent iron-oxo species as a catalytic oxidant that normally epoxidizes alkenes, similar to other catalysts. How the evolved aMOx enzyme suppresses the commonly preferred epoxidation and catalyzes direct carbonyl formation is currently not well understood. Here, we combine computational modelling together with mechanistic experiments to study the reaction mechanism and unravel the molecular basis behind the selectivity achieved by aMOx. Our results describe that although both pathways are energetically accessible diverging from a common covalent radical intermediate, intrinsic dynamic effects determine the strong preference for epoxidation. We discovered that aMOx overrides these intrinsic preferences by controlling the accessible conformations of the covalent radical intermediate. This disfavors epoxidation and facilitates the formation of a carbocation intermediate that generates the aldehyde product through a fast 1,2-hydride migration. Electrostatic preorganization of the enzyme active site also contributes to the stabilization of the carbocation intermediate. Computations predicted that the hydride migration is stereoselective due to the enzymatic conformational control over the intermediate species. These predictions were corroborated by experiments using deuterated styrene substrates, which proved that the hydride migration is cis- and enantioselective. Our results demonstrate that directed evolution tailored a highly specific active site that imposes strong steric control over key fleeting biocatalytic intermediates, which is essential for accessing the carbonyl forming pathway and preventing competing epoxidation.

Computational discoveries of reaction mechanisms: recent highlights and emerging challenges

This review examines some of the notable advances and trends that have shaped the field of computational elucidation of organic reaction mechanisms over the last 10-15 years. It highlights the types of mechanistic problems that have recently become possible to study and summarizes the methodological developments that have permitted these new advances. Case studies are taken from three representative areas of organic chemistry-asymmetric catalysis, glycosylation reactions, and single electron transfer reactions-which illustrate themes common to the broader field. These include the trend towards modelling systems that are increasingly complex (both structurally and mechanistically), the growing appreciation of the mechanistic roles of non-covalent interactions, and the increasing ability to explore dynamical features of reaction mechanisms. Some interesting new challenges that have emerged in the field are identified.

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.

Deoxygenative α-alkylation and α-arylation of 1,2-dicarbonyls

Construction of C-C bonds at the α-carbon is a challenging but synthetically indispensable approach to α-branched carbonyl motifs that are widely represented among drugs, natural products, and synthetic intermediates. Here, we describe a simple approach to generation of boron enolates in the absence of strong bases that allows for introduction of both α-alkyl and α-aryl groups in a reaction of readily accessible 1,2-dicarbonyls and organoboranes. Obviation of unselective, strongly basic and nucleophilic reagents permits carrying out the reaction in the presence of electrophiles that intercept the intermediate boron enolates, resulting in two new α-C-C bonds in a tricomponent process.