Computational discoveries of reaction mechanisms: recent highlights and emerging challenges

Origins of Temperature-Dependent Anomeric Selectivity in Glycosylations with an L-Idose Thioglycoside

L-Idose thioglycosides are useful glycosyl donors for the construction of glycosaminoglycan oligosaccharides. When activated with NIS and catalytic TMSOTf in the presence of methanol, the stereoselectivity of O-glycosylation displays an intriguing dependence on the reaction temperature, with an increased preference for formation of the α-glycoside at higher temperatures. Using a combination of vt-NMR spectroscopy and DFT calculations, we show how a simple mechanistic model, based on competing reactions of the iodinated thioglycoside, can explain the main features of the temperature dependence. In this model, the increased selectivity at high temperature is attributed to differences among the entropy and energy terms of the competing reaction pathways. Neighbouring-group participation (giving an intermediate acyloxonium ion) plays an increasingly dominant role as temperature is raised. The general features of this kinetic regime may also apply more broadly to other glycosylations that likewise favour α-glycoside formation at high temperature.

Bispericyclic Ambimodal Dimerization of Pentafulvene: The Origin of Asynchronicity and Kinetic Selectivity of the Endo Transition State

The propensity of fulvenes to undergo dimerization has long been known, although the in-depth mechanism and electronic behavior during dimerization are still elusive. Herein, we made an attempt to gain insights into the reactivity of pentafulvene for Diels-Alder (DA) and [6 + 4]-cycloadditions via conventional and ambimodal routes. The result emphasizes that pentafulvene dimerization preferentially proceeds through a unique bifurcation mechanism where two DA pathways merge together to produce two degenerate [4 + 2]-cycloadducts from a single TS. Despite the [6 + 4]-cycloadduct being thermodynamically preferred, [4 + 2]-cycloaddition reactions are kinetically driven. Singlet biradicaloid is involved in through-space 6e- delocalization as a secondary orbital interaction that originates asynchronicity and stabilizes the bispericyclic transition state (TS). The transformation of various actively participating intrinsic bonding orbitals (IBOs) unambiguously forecasts the formation of multiple products from a single TS and rationalizes the mechanism of ambimodal reactions that are rather difficult to probe with other analyses. The changes in active IBOs clearly distinguish the conventional reactions from bifurcation reactions and can be employed to characterize and confirm the ambimodal mechanism. This report gains a crucial theoretical insight into the mechanism of bifurcation, the origin of asynchronicity, and electronic behavior in ambimodal TS, which will certainly be of enormous value for future studies.

Evaluation of Retro-Aldol vs Retro-Carbonyl-Ene Mechanistic Pathways in a Complexity-Generating C-C Bond Fragmentation

We report an experimental and computational investigation of the likely mechanism of a cascade reaction. The reaction involves an intramolecular Diels-Alder reaction, followed by a C-C bond cleavage, to afford a complex bridged bicyclic product. As multiple reaction pathways could be envisioned for the latter step, the mechanism of the C-C bond cleavage step was investigated. Two reasonable reaction pathways were evaluated. Both computations and experiments indicate that the C-C bond cleavage step proceeds by a retro-carbonyl-ene pathway rather than a retro-aldol pathway. This report underscores the synergy between computational and experimental studies and establishes the mechanism of an interesting complexity-generating transformation.

Mechanism of the Visible-Light-Promoted C(sp3)-H Oxidation via Uranyl Photocatalysis

Uranyl cation, as an emerging photocatalyst, has been successfully applied to synthetic chemistry in recent years and displayed remarkable catalytic ability under visible light. However, the molecular-level reaction mechanisms of uranyl photocatalysis are unclear. Here, we explore the mechanism of the stepwise benzylic C-H oxygenation of typical alkyl-substituted aromatics (i.e., toluene, ethylbenzene, and cumene) via uranyl photocatalysis using theoretical and experimental methods. Theoretical calculation results show that the most favorable reaction path for uranyl photocatalytic oxidation is as follows: first, hydrogen atom transfer (HAT) from the benzyl position to form a carbon radical ([R•]), then oxygen addition ([R•] + O2 → [ROO•]), then radical-radical combination ([ROO•] + [R•] → [ROOR] → 2[RO•]), and eventually [RO•] reduction to produce alcohols, of which 2° alcohol would further be oxidized to ketones and 1° would be stepwise-oxygenated to acids. The results of the designed verification experiments and the capture of reactive intermediates were consistent with those of theoretical calculations and the previously reported research that the active benzylic C-H would be stepwise-oxygenated in the presence of uranyl. This work deepens our understanding of the HAT mechanism of uranyl photocatalysis and provides important theoretical support for the relevant application of uranyl photocatalysts in organic transformation.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

ONIOM meets : efficient, accurate, and robust multi-layer simulations across the periodic table

The computational treatment of large molecular structures is of increasing interest in fields of modern chemistry. Accordingly, efficient quantum chemical approaches are needed to perform sophisticated investigations on such systems. This engaged the development of the well-established "Our own N-layered integrated molecular orbital and molecular mechanics" (ONIOM) multi-layer scheme [L. W. Chung et al., Chem. Rev., 2015, 115, 5678-5796]. In this work, we present the specific implementation of the ONIOM scheme into the xtb semi-empirical extended tight-binding program package and its application to challenging transition-metal complexes. The efficient and broadly applicable GFNn-xTB and -FF methods are applied in the ONIOM framework to elucidate reaction energies, geometry optimizations, and explicit solvation effects for metal-organic systems with up to several hundreds of atoms. It is shown that an ONIOM-based combination of density functional theory, semi-empirical, and force-field methods can be used to drastically reduce the computational costs and thus enable the investigation of huge systems at almost no significant loss in accuracy.

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.