Organic reaction mechanism classification using machine learning.

A mechanistic understanding of catalytic organic reactions is crucial for the design of new catalysts, modes of reactivity and the development of greener and more sustainable chemical processes1-13. Kinetic analysis lies at the core of mechanistic elucidation by facilitating direct testing of mechanistic hypotheses from experimental data. Traditionally, kinetic analysis has relied on the use of initial rates14, logarithmic plots and, more recently, visual kinetic methods15-18, in combination with mathematical rate law derivations. However, the derivation of rate laws and their interpretation require numerous mathematical approximations and, as a result, they are prone to human error and are limited to reaction networks with only a few steps operating under steady state. Here we show that a deep neural network model can be trained to analyse ordinary kinetic data and automatically elucidate the corresponding mechanism class, without any additional user input. The model identifies a wide variety of classes of mechanism with outstanding accuracy, including mechanisms out of steady state such as those involving catalyst activation and deactivation steps, and performs excellently even when the kinetic data contain substantial error or only a few time points. Our results demonstrate that artificial-intelligence-guided mechanism classification is a powerful new tool that can streamline and automate mechanistic elucidation. We are making this model freely available to the community and we anticipate that this work will lead to further advances in the development of fully automated organic reaction discovery and development.

Transition-Metal-Catalyzed C-H Bond Activation for the Formation of C-C Bonds in Complex Molecules.

Site-predictable and chemoselective C-H bond functionalization reactions offer synthetically powerful strategies for the step-economic diversification of both feedstock and fine chemicals. Many transition-metal-catalyzed methods have emerged for the selective activation and functionalization of C-H bonds. However, challenges of regio- and chemoselectivity have emerged with application to highly complex molecules bearing significant functional group density and diversity. As molecular complexity increases within molecular structures the risks of catalyst intolerance and limited applicability grow with the number of functional groups and potentially Lewis basic heteroatoms. Given the abundance of C-H bonds within highly complex and already diversified molecules such as pharmaceuticals, natural products, and materials, design and selection of reaction conditions and tolerant catalysts has proved critical for successful direct functionalization. As such, innovations within transition-metal-catalyzed C-H bond functionalization for the direct formation of carbon-carbon bonds have been discovered and developed to overcome these challenges and limitations. This review highlights progress made for the direct metal-catalyzed C-C bond forming reactions including alkylation, methylation, arylation, and olefination of C-H bonds within complex targets.

Carboxylic Acid Salts as Dual-Function Reagents for Carboxylation and Carbon Isotope Labeling.

The potassium salts of carboxylic acids are developed as efficient carboxylating agents through CO2 exchange. We describe these carboxylates as dual-function reagents because they function as a combined source of CO2 and base/metalating agent. By using the salt of a commercially available carboxylic acid, this protocol overcomes difficulties when using CO2 gas or organometallic reagents, such as pressurized containers or strictly inert conditions. The reaction proceeds under mild conditions, does not require transition metals or other additives, and shows broad substrate scope. Through the preparation of several biologically important molecules, we show how this strategy provides an opportunity for isotope labeling with low equivalents of labeled CO2 .

Sesquiterpene Lactones Potentiate Olaparib-Induced DNA Damage in p53 Wildtype Cancer Cells.

Despite notable advances in utilising PARP inhibitor monotherapy, many cancers are not PARP inhibitor-sensitive or develop treatment resistance. In this work, we show that the two structurally-related sesquiterpene lactones, a 2-bromobenzyloxy derivative of dehydrosantonin (BdS) and alantolactone (ATL) sensitise p53 wildtype, homologous recombination-proficient cancer cells to low-dose treatment with the PARP inhibitor, olaparib. Exposure to combination treatments of olaparib with BdS or ATL induces cell-cycle changes, chromosomal instability, as well as considerable increases in nuclear area. Mechanistically, we uncover that mitotic errors likely depend on oxidative stress elicited by the electrophilic lactone warheads and olaparib-mediated PARP-trapping, culminating in replication stress. Combination treatments exhibit moderately synergistic effects on cell survival, probably attenuated by a p53-mediated, protective cell-cycle arrest in the G2 cell-cycle phase. Indeed, using a WEE1 inhibitor, AZD1775, to inhibit the G2/M cell-cycle checkpoint further decreased cell survival. Around half of all cancers diagnosed retain p53 functionality, and this proportion could be expected to increase with improved diagnostic approaches in the clinic. Utilising sublethal oxidative stress to sensitise p53 wildtype, homologous recombination-proficient cancer cells to low-dose PARP-trapping could therefore serve as the basis for future research into the treatment of cancers currently refractory to PARP inhibition.

Enhanced liquid phase exfoliation of graphene in water using an insoluble bis-pyrene stabiliser.

Stabilisers, such as surfactants, polymers and polyaromatic molecules, offer an effective way to produce graphene dispersions in water by Liquid Phase Exfoliation (LPE) without degrading the properties of graphene. In particular, pyrene derivatives provide better exfoliation efficiency than traditional surfactants and polymers. A stabiliser is expected to be relatively soluble in order to disperse hydrophobic graphene in water. Here, we show that exfoliation can also be achieved with insoluble pyrene stabilisers if appropriately designed. In particular, bis-pyrene stabilisers (BPSs) functionalised with pyrrolidine provide a higher exfoliation efficiency and percentage of single layers compared to traditional pyrene derivatives under the same experimental conditions. This is attributed to the enhanced interactions between BPS and graphene, provided by the presence of two pyrene binding groups. This approach is therefore attractive not only to produce highly concentrated graphene, but also to use graphene to disperse insoluble molecules in water. The enhanced adsorption of BPS on graphene, however, is reflected in higher toxicity towards human epithelial bronchial immortalized cells, limiting the use of this material for biomedical applications.

Ag(I)-C-H Activation Enables Near-Room-Temperature Direct α-Arylation of Benzo[ b]thiophenes.

The first example of near-room-temperature α-arylation of benzo[ b]thiophenes is reported. The discovery rests on the observation of a switch in α-/ß-regioselectivity at different loadings of Pd2(dba)3·CHCl3 in the coupling between benzo[ b]thiophene and 4-iodotoluene. We show that this unprecedented regioselectivity switch is driven by a Ag(I)-mediated C-H activation at the α-C-H position, which becomes the dominant mode of reactivity at low concentrations of Pd. Competition experiments, kinetic studies, KIE, and D/H scrambling experiments have been carried out supporting this mechanism.

Benzoate Cyclometalation Enables Oxidative Addition of Haloarenes at a Ru(II) Center.

The first Ru(II)-catalyzed arylation of substrates without a directing group was recently developed. Remarkably, this process only worked in the presence of a benzoate additive, found to be crucial for the oxidative addition step at Ru(II). However, the exact mode of action of the benzoate was unknown. Herein, we disclose a mechanistic study that elucidates the key role of the benzoate salt in the C-H arylation of fluoroarenes with aryl halides. Through a combination of rationally designed stoichiometric experiments and DFT studies, we demonstrate that the aryl-Ru(II) species arising from initial C-H activation of the fluoroarene undergoes cyclometalation with the benzoate to generate an anionic Ru(II) intermediate. The enhanced lability of this intermediate, coupled with the electron-rich anionic Ru(II) metal center renders the oxidative addition of the aryl halide accessible. The role of an additional (NMe4)OC(CF3)3 additive in facilitating the overall arylation process is also shown to be linked to a shift in the C-H pre-equilibrium associated with benzoate cyclometalation.

Transition-Metal-Free Decarboxylative Iodination: New Routes for Decarboxylative Oxidative Cross-Couplings.

Constructing products of high synthetic value from inexpensive and abundant starting materials is of great importance. Aryl iodides are essential building blocks for the synthesis of functional molecules, and efficient methods for their synthesis from chemical feedstocks are highly sought after. Here we report a low-cost decarboxylative iodination that occurs simply from readily available benzoic acids and I2. The reaction is scalable and the scope and robustness of the reaction is thoroughly examined. Mechanistic studies suggest that this reaction does not proceed via a radical mechanism, which is in contrast to classical Hunsdiecker-type decarboxylative halogenations. In addition, DFT studies allow comparisons to be made between our procedure and current transition-metal-catalyzed decarboxylations. The utility of this procedure is demonstrated in its application to oxidative cross-couplings of aromatics via decarboxylative/C-H or double decarboxylative activations that use I2 as the terminal oxidant. This strategy allows the preparation of biaryls previously inaccessible via decarboxylative methods and holds other advantages over existing decarboxylative oxidative couplings, as stoichiometric transition metals are avoided.

A Direct Arylation-Cyclisation Reaction for the Construction of Medium-Sized Rings.

A strategy for assembling biaryls linked through a medium-sized ring is herein presented. π-Complexation of fluoroarenes to chromium tricarbonyl activates the molecule towards both C-H activation and nucleophilic aromatic substitution without covalently altering the molecular connectivity of the arene. The construction of bridged biaryl molecules with 6-10-membered core rings is achieved through a one-pot C-H arylation/nucleophilic aromatic substitution sequence. The methodology is applicable to the synthesis of heterocyclic as well as fully carbocyclic rings.

Ruthenium-Catalyzed C-H Arylation of Benzoic Acids and Indole Carboxylic Acids with Aryl Halides.

Herein we report the first Ru-catalyzed C-H arylation of benzoic acids with readily available aryl (pseudo)halides. The reaction, which does not require the use of silver salt additives, allows the arylation of previously challenging hindered benzoic acids and the use of generally unreactive ortho-substituted halorarenes. Furthermore, our new protocol can efficiently be applied to indole carboxylic acids, thus allowing access to C7-, C6-, C5- and C4-arylated indole compounds, a departure from the classical enhanced reactivity of the C2 and C3 positions of indole.

Recent Progress in Decarboxylative Oxidative Cross-Coupling for Biaryl Synthesis.

The beginning of the 21st century has seen tremendous growth in the field of decarboxylative activation. Benzoic acid derivatives are now recognised as atom-economic alternatives to traditional cross-coupling partners, and they also benefit from being inexpensive, readily available and shelf-stable reagents. In this microreview we discuss recent developments in the coupling of benzoic acid derivatives either with an arene or with a second benzoic acid derivative, a process often termed decarboxylative oxidative cross-coupling. These procedures offer great promise for the development of highly selective and atom-economic cross-couplings.

Ag(I)-Catalyzed C-H Activation: The Role of the Ag(I) Salt in Pd/Ag-Mediated C-H Arylation of Electron-Deficient Arenes.

The use of stoichiometric Ag(I)-salts as additives in Pd-catalyzed C-H functionalization reactions is widespread. It is commonly proposed that this additive acts as an oxidant or as a halide scavenger promoting Pd-catalyst turnover. We demonstrate that, contrary to current proposals, phosphine ligated Ag(I)-carboxylates can efficiently carry out C-H activation on electron-deficient arenes. We show through a combination of stoichiometric and kinetic studies that a (PPh3)Ag-carboxylate is responsible for the C-H activation step in the Pd-catalyzed arylation of Cr(CO)3-complexed fluorobenzene. Furthermore, the reaction rate is controlled by the rate of Ag(I)-C-H activation, leading to an order zero on the Pd-catalyst. H/D scrambling studies indicate that this Ag(I) complex can carry out C-H activation on a variety of aromatic compounds traditionally used in Pd/Ag-mediated C-H functionalization methodologies.

Room-Temperature Direct ß-Arylation of Thiophenes and Benzo[b]thiophenes and Kinetic Evidence for a Heck-type Pathway.

The first example of a regioselective ß-arylation of benzo[b]thiophenes and thiophenes at room temperature with aryl iodides as coupling partners is reported. This methodology stands out for its operational simplicity: no prefunctionalization of either starting material is required, the reaction is insensitive to air and moisture, and it proceeds at room temperature. The mild conditions afford wide functional group tolerance, often with complete regioselectivity and high yields, resulting in a highly efficient catalytic system. Initial mechanistic studies, including (13)C and (2)H KIEs, suggest that this process occurs via a concerted carbo-palladation across the thiophene double bond, followed by a base-assisted anti-elimination.

Ru-Catalyzed C-H Arylation of Fluoroarenes with Aryl Halides.

Although the ruthenium-catalyzed C-H arylation of arenes bearing directing groups with haloarenes is well-known, this process has never been achieved in the absence of directing groups. We report the first example of such a process and show that unexpectedly the reaction only takes place in the presence of catalytic amounts of a benzoic acid. Furthermore, contrary to other transition metals, the arylation site selectivity is governed by both electronic and steric factors. Stoichiometric and NMR mechanistic studies support a catalytic cycle that involves a well-defined η(6)-arene-ligand-free Ru(II) catalyst. Indeed, upon initial pivalate-assisted C-H activation, the aryl-Ru(II) intermediate generated is able to react with an aryl bromide coupling partner only in the presence of a benzoate additive. In contrast, directing-group-containing substrates (such as 2-phenylpyridine) do not require a benzoate additive. Deuterium labeling and kinetic isotope effect experiments indicate that C-H activation is both reversible and kinetically significant. Computational studies support a concerted metalation-deprotonation (CMD)-type ruthenation mode and shed light on the unusual arylation regioselectivity.

Carboxylation of Phenols with CO2 at Atmospheric Pressure.

A convenient and efficient method for the ortho-carboxylation of phenols under atmospheric CO2 pressure has been developed. This method provides an alternative to the previously reported Kolbe-Schmitt method, which requires very high pressures of CO2 . The addition of a trisubstituted phenol has proved essential for the successful carboxylation of phenols with CO2 at standard atmospheric pressure, allowing the efficient preparation of a broad variety of salicylic acids.

Au-Catalyzed Cross-Coupling of Arenes via Double C-H Activation.

The first methodology for Au(I/III)-catalyzed oxidative cross-coupling of arenes via double C-H activation has been developed. The reaction is fully selective for the cross-coupling between electron-rich hetero-/carbocyclic arenes and electron-poor arenes bearing relatively acidic C-H bonds. The inherently high cross-selectivity of the system obviates the need for directing groups or a large excess of one of the coupling partners.

Overriding ortho-para selectivity via a traceless directing group relay strategy: the meta-selective arylation of phenols.

The direct functionalization of phenols at the ortho and para position is generally facilitated by the electron-donating nature of the hydroxyl group. Accessing meta-functionalized phenols from the parent phenols, on the other hand, generally requires lengthy synthetic sequences. Here, we report the first methodology for the one-pot direct meta-selective arylation of phenols. This methodology is based on a traceless directing group relay strategy. In this process carbon dioxide is used as a transient directing group which facilitates a palladium catalyzed arylation meta to the phenol hydroxyl group with iodoarenes. This transformation proceeds with complete meta-selectivity and is compatible with a variety of functional groups both in the phenol and in the iodoarene coupling partner.

Tuning reactivity and site selectivity of simple arenes in C-H activation: ortho-arylation of anisoles via arene-metal π-complexation.

Current approaches to achieve site selectivity in the C-H activation of arenes involve the use of directing groups or highly electron-poor arenes. In contrast, simple arenes, such as anisole, are characterized by poor reactivity and selectivity. We report that π-complexation to a Cr(CO)3 unit enhances the reactivity of anisoles providing an unprecedented ortho-selective arylation. This mild methodology can be used for the late stage functionalization of bioactive compounds containing the anisole motif, allowing the construction of novel organic scaffolds with few synthetic steps.

The ortho-substituent effect on the Ag-catalysed decarboxylation of benzoic acids.

A combined experimental and computational investigation on the Ag-catalysed decarboxylation of benzoic acids is reported herein. The present study demonstrates that a substituent at the ortho position exerts dual effects in the decarboxylation event. On one hand, ortho-substituted benzoic acids are inherently destabilised starting materials compared to their meta- and para-substituted counterparts. On the other hand, the presence of an ortho-electron-withdrawing group results in an additional stabilisation of the transition state. The combination of both effects results in an overall reduction of the activation energy barrier associated with the decarboxylation event. Furthermore, the Fujita-Nishioka linear free energy relationship model indicates that steric bulk of the substituent can also exert a negative effect by destabilising the transition state of decarboxylation.

Unlocking regioselective meta-alkylation with epoxides and oxetanes via dynamic kinetic catalyst control.

Regioselective arene C-H bond alkylation is a powerful tool in synthetic chemistry, yet subject to many challenges. Herein, we report the meta-C-H bond alkylation of aromatics bearing N-directing groups using (hetero)aromatic epoxides as alkylating agents. This method results in complete regioselectivity on both the arene as well as the epoxide coupling partners, cleaving exclusively the benzylic C-O bond. Oxetanes, which are normally unreactive, also participate as alkylating reagents under the reaction conditions. Our mechanistic studies reveal an unexpected reversible epoxide ring opening process undergoing catalyst-controlled regioselection, as key for the observed high regioselectivities.