High-Throughput Optimization of Ir-Catalyzed C–H Borylation: A Tutorial for Practical Applications

Chrysomycin A Derivatives for the Treatment of Multi-Drug-Resistant Tuberculosis

Tuberculosis (TB) is a life-threatening disease resulting in an estimated 10 million new infections and 1.8 million deaths annually, primarily in underdeveloped countries. The economic burden of TB has been estimated as approximately 12 billion USD annually in direct and indirect costs. Additionally, multi-drug-resistant (MDR) and extreme-drug-resistant (XTR) TB strains resulting in about 250 000 deaths annually are now widespread, increasing pressure on the identification of new anti-TB agents that operate by a novel mechanism of action. Chrysomycin A is a rare C-aryl glycoside first discovered over 60 years ago. In a recent high-throughput screen, we found that chrysomycin A has potent anti-TB activity, with minimum inhibitory concentration (MIC) = 0.4 μg/mL against MDR-TB strains. However, chrysomycin A is obtained in low yields from fermentation of Streptomyces, and the mechanism of action of this compound is unknown. To facilitate the mechanism of action and preclinical studies of chrysomycin A, we developed a 10-step, scalable synthesis of the isolate and its two natural congeners polycarcin V and gilvocarcin V. The synthetic sequence was enabled by the implementation of two sequential C-H functionalization steps as well as a late-stage C-glycosylation. In addition, >10 g of the advanced synthetic intermediate has been prepared, which greatly facilitated the synthesis of 33 new analogues to date. The structure-activity relationship was subsequently delineated, leading to the identification of derivatives with superior potency against MDR-TB (MIC = 0.08 μg/mL). The more potent derivatives contained a modified carbohydrate residue which suggests that further optimization is additionally possible. The chemistry we report here establishes a platform for the development of a novel class of anti-TB agents active against drug-resistant pathogens.

Machine learning dihydrogen activation in the chemical space surrounding Vaska's complex

Homogeneous catalysis using transition metal complexes is ubiquitously used for organic synthesis, as well as technologically relevant in applications such as water splitting and CO2 reduction. The key steps underlying homogeneous catalysis require a specific combination of electronic and steric effects from the ligands bound to the metal center. Finding the optimal combination of ligands is a challenging task due to the exceedingly large number of possibilities and the non-trivial ligand-ligand interactions. The classic example of Vaska's complex, trans-[Ir(PPh3)2(CO)(Cl)], illustrates this scenario. The ligands of this species activate iridium for the oxidative addition of hydrogen, yielding the dihydride cis-[Ir(H)2(PPh3)2(CO)(Cl)] complex. Despite the simplicity of this system, thousands of derivatives can be formulated for the activation of H2, with a limited number of ligands belonging to the same general categories found in the original complex. In this work, we show how DFT and machine learning (ML) methods can be combined to enable the prediction of reactivity within large chemical spaces containing thousands of complexes. In a space of 2574 species derived from Vaska's complex, data from DFT calculations are used to train and test ML models that predict the H2-activation barrier. In contrast to experiments and calculations requiring several days to be completed, the ML models were trained and used on a laptop on a time-scale of minutes. As a first approach, we combined Bayesian-optimized artificial neural networks (ANN) with features derived from autocorrelation and deltametric functions. The resulting ANNs achieved high accuracies, with mean absolute errors (MAE) between 1 and 2 kcal mol-1, depending on the size of the training set. By using a Gaussian process (GP) model trained with a set of selected features, including fingerprints, accuracy was further enhanced. Remarkably, this GP model minimized the MAE below 1 kcal mol-1, by using only 20% or less of the data available for training. The gradient boosting (GB) method was also used to assess the relevance of the features, which was used for both feature selection and model interpretation purposes. Features accounting for chemical composition, atom size and electronegativity were found to be the most determinant in the predictions. Further, the ligand fragments with the strongest influence on the H2-activation barrier were identified.

Effect of Ligand Structure on the Electron Density and Activity of Iridium Catalysts for the Borylation of Alkanes

An in-depth study of iridium catalysts for the borylation of alkyl C-H bonds is reported. Although the borylation of aryl C-H bonds can be catalyzed by iridium complexes containing phen or bpy ligands at mild temperatures and with limiting arene, the borylation of alkyl C-H bonds remains underdeveloped. We prepared a library of phenanthrolines that contain varying substitution patterns. The corresponding phen-Ir trisboryl carbon monoxide complexes were synthesized to determine the electron-donating ability of these ligands, and the initial rates for the borylation of the C-H bonds in THF and diethoxyethane β to oxygen catalyzed by Ir complexes containing these ligands were measured. For some subsets of these ligands, the donor ability correlated positively with the rate of C-H borylation catalyzed by the complexes containing ligands within a given subset. However, across subsets, ligands possessing similar donor properties to one another form catalysts for the borylation of alkyl C-H bonds with widely varying activity. This phenomenon was investigated computationally, and it was discovered that the stabilizing interactions between the phenanthroline ligand and the boryl ligands attached to Ir in the transition state for C-H oxidative addition could account for the differences in the activity of the catalysts that possess similar electron densities at Ir. The effect of these interactions on the borylation of secondary alkyl C-H bonds is larger than it is on the borylation of primary alkyl C-H bonds.

Iridium-catalysed C–H borylation of β-aryl-aminopropionic acids

Iridium-catalysed C–H borylation of β-aryl-aminopropionic acid derivatives gives 3,5-functionalised protected β-aryl-aminopropionic acid boronates. One-pot borylation–functionalisation provides diverse building blocks for medicinal chemistry.

Two-step synthesis of a red-emissive warped nanographene derivative via a ten-fold C-H borylation

The regioselective ten-fold borylation of warped nanographene (WNG: C80H30) was achieved by modifying the reaction conditions of a previously reported Ir-catalyzed C-H borylation, affording decaborylated WNG in high yield (75%) from pristine WNG. The solid-state structure of decaborylated WNG was confirmed by X-ray crystallography. Corresponding decaarylated WNGs containing electron-withdrawing and -donating groups were synthesized from decaborylated WNG using Suzuki-Miyaura cross-coupling reactions to afford the red-emissive warped nanographene derivative.

Origin of the Difference in Reactivity between Ir Catalysts for the Borylation of C-H Bonds

A mechanistic study on the origin of the difference in reactivity between Ir catalysts for C-H borylation reactions is reported. Catalytic reactions of B₂pin₂ with a series of substrates that require high temperatures and long reaction times were conducted. These reactions catalyzed by the combination of [Ir(COD)(OMe)]₂ and 3,4,7,8-tetramethylphenanthroline (tmphen) occur in yields that are substantially higher than those of reactions catalyzed by [Ir(COD)(OMe)]₂ and 4,4'-di-tert-butylbipyridine (dtbpy). The electronic properties of Ir catalysts ligated by dtbpy or tmphen and their stoichiometric reactivity were investigated. It was found that a longer lifetime rather than higher reactivity of the catalyst leads to higher yields of reactions catalyzed by Ir-tmphen. The catalyst ligated by dtbpy decomposes principally by dissociation of the ligand and rapid borylation at the positions alpha to nitrogen. Thus, the greater stability of the catalyst containing tmphen results from its greater binding constant.

Para-Selective C-H Borylation of Common Arene Building Blocks Enabled by Ion-Pairing with a Bulky Countercation

The selective functionalization of C-H bonds at the arene para position is highly challenging using transition metal catalysis. Iridium-catalyzed borylation has emerged as a leading technique for arene functionalization, but there are only a handful of strategies for para-selective borylation, which operate on specific substrate classes and use bespoke ligands or catalysts. We describe a remarkably general protocol which results in para-selectivity on some of the most common arene building blocks (anilines, benzylamines, phenols, benzyl alcohols) and uses standard borylation ligands. Our strategy hinges upon the facile conversion of the substrates into sulfate or sulfamate salts, wherein the anionic arene component is paired with a tetrabutylammonium cation. We hypothesize that the bulk of this cation disfavors meta-C-H borylation, thereby promoting the challenging para-selective reaction.

NNB-Type Tridentate Boryl Ligands Enabling a Highly Active Iridium Catalyst for C⁻H Borylation

Boryl ligands play a very important role in catalysis because of their very high electron-donating property. In this paper, NNB-type boryl anions were designed as tridentate ligands to promote aryl C-H borylation. In combination with [IrCl(COD)]₂, they generate a highly active catalyst for a broad range of (hetero)arene substrates, including highly electron-rich and/or sterically hindered ones. This work provides a new NNB-type tridentate boryl ligand to support homogeneous organometallic catalysis.

A Predictive Tool for Electrophilic Aromatic Substitutions Using Machine Learning

At the early stages of the drug development process, thousands of compounds are synthesized in order to attain the best possible potency and pharmacokinetic properties. Once successful scaffolds are identified, large libraries of analogues are made, which is a challenging and time-consuming task. Recently, late stage functionalization (LSF) has become increasingly prominent since these reactions selectively functionalize C-H bonds, allowing to quickly produce analogues. Classical electrophilic aromatic halogenations are a powerful type of reaction in the LSF toolkit. However, the introduction of an electrophile in a regioselective manner on a drug-like molecule is a challenging task. Herein we present a machine learning model able to predict the reactive site of an electrophilic aromatic substitution with an accuracy of 93% (internal validation set). The model takes as input a SMILES of a compound and uses six quantum mechanics descriptors to identify its reactive site(s). On an external validation set, 90% of all molecules were correctly predicted.

Convergent Synthesis of the NS5B Inhibitor GSK8175 Enabled by Transition Metal Catalysis

A convergent eight-stage synthesis of the boron-containing NS5B inhibitor GSK8175 is described. The previous route involves 13 steps in a completely linear sequence, with an overall 10% yield. Key issues include a multiday S_NAr arylation of a secondary sulfonamide using HMPA as solvent, multiple functional group interconversions after all of the carbon atoms are installed (including a Sandmeyer halogenation), use of carcinogenic chloromethyl methyl ether to install a protecting group late in the synthesis, and an unreliable Pd-catalyzed Miyaura borylation as the penultimate step. We have devised an orthogonal approach using a Chan-Lam coupling between a halogenated aryl pinacol boronate ester and an aryl methanesulfonamide. This reaction is performed using a cationic Cu(I) precatalyst, which can be easily generated in situ using KPF₆ as a halide abstractor. High-throughput screening revealed a new Pd catalyst system to effect the penultimate borylation chemistry using simple monodentate phosphine ligands, with PCyPh₂ identified as optimal. Reaction progress analysis of this borylation indicated likely mass-transfer rate limitations under standard conditions using KOAc as the base. We have devised a K₂CO₃/pivalic acid system as an alternative, which dramatically outperforms the standard conditions. This new synthesis proceeds in eight stages with a 20% overall yield.

Switching the Statistical C3 /C1 Ratio in the Threefold Aromatic Substitution of Tribenzotriquinacenes towards the C3 Isomer

Tribenzotriquinacene (TBTQ) is a bowl-shaped molecule that has been widely used as a molecular building block in supramolecular and materials chemistry. Especially C₃ -symmetric threefold-substituted TBTQs are interesting for these purposes. Until now a general and selective synthetic approach to those C₃ -symmetric products was lacking, mainly because the typically used electrophilic aromatic substitution reactions of the parent TBTQ hydrocarbons produce predominantly the C₁ isomer over the C₃ isomer (3:1 statistical ratio). Herein we introduce a threefold borylation of TBTQ with the C₃ isomer as the main product (2.6:1 C₃ /C₁ ratio). The borylated TBTQ can be converted in good yields into other C₃ -symmetric TBTQs, thus allowing straightforward synthetic access to new building blocks for supramolecular and materials chemistry.

Highly active, separable and recyclable bipyridine iridium catalysts for C–H borylation reactions

Iridium complexes generated from Ir(i) precursors and PIB oligomer functionalized bpy ligands efficiently catalyzed the reaction of arenes with bis(pinacolato)diboron under mild conditions to produce a variety of arylboronate compounds.

Direct regioselective C–H borylation of [5]helicene

A facile and efficient protocol for a regioselective borylation of [5]helicene was achieved via Ir-catalyzed C–H activation.

Ligand libraries for high throughput screening of homogeneous catalysts

This review describes different approaches to construct ligand libraries towards high throughput screening of homogeneous metal catalysts.

Dinuclear tethered pyridine, diimine complexes

Synthesis and structures of aryl tethered pyridine, diimine complexes.

The Evolution of Chemical High-Throughput Experimentation To Address Challenging Problems in Pharmaceutical Synthesis

The structural complexity of pharmaceuticals presents a significant challenge to modern catalysis. Many published methods that work well on simple substrates often fail when attempts are made to apply them to complex drug intermediates. The use of high-throughput experimentation (HTE) techniques offers a means to overcome this fundamental challenge by facilitating the rational exploration of large arrays of catalysts and reaction conditions in a time- and material-efficient manner. Initial forays into the use of HTE in our laboratories for solving chemistry problems centered around screening of chiral precious-metal catalysts for homogeneous asymmetric hydrogenation. The success of these early efforts in developing efficient catalytic steps for late-stage development programs motivated the desire to increase the scope of this approach to encompass other high-value catalytic chemistries. Doing so, however, required significant advances in reactor and workflow design and automation to enable the effective assembly and agitation of arrays of heterogeneous reaction mixtures and retention of volatile solvents under a wide range of temperatures. Associated innovations in high-throughput analytical chemistry techniques greatly increased the efficiency and reliability of these methods. These evolved HTE techniques have been utilized extensively to develop highly innovative catalysis solutions to the most challenging problems in large-scale pharmaceutical synthesis. Starting with Pd- and Cu-catalyzed cross-coupling chemistry, subsequent efforts expanded to other valuable modern synthetic transformations such as chiral phase-transfer catalysis, photoredox catalysis, and C-H functionalization. As our experience and confidence in HTE techniques matured, we envisioned their application beyond problems in process chemistry to address the needs of medicinal chemists. Here the problem of reaction generality is felt most acutely, and HTE approaches should prove broadly enabling. However, the quantities of both time and starting materials available for chemistry troubleshooting in this space generally are severely limited. Adapting to these needs led us to invest in smaller predefined arrays of transformation-specific screening "kits" and push the boundaries of miniaturization in chemistry screening, culminating in the development of "nanoscale" reaction screening carried out in 1536-well plates. Grappling with the problem of generality also inspired the exploration of cheminformatics-driven HTE approaches such as the Chemistry Informer Libraries. These next-generation HTE methods promise to empower chemists to run orders of magnitude more experiments and enable "big data" informatics approaches to reaction design and troubleshooting. With these advances, HTE is poised to revolutionize how chemists across both industry and academia discover new synthetic methods, develop them into tools of broad utility, and apply them to problems of practical significance.

Regioselective Diversification of 2,1-Borazaronaphthalenes: Unlocking Isosteric Space via C-H Activation

Methods for the regioselective C–H borylation and subsequent cross-coupling of the 2,1-borazaronaphthalene core are reported. Azaborines are dependent on B–N/C=C isosterism when employed in strategies for developing diverse heterocyclic scaffolds. Although 2,1-borazaronaphthalene is closely related to naphthalene in terms of structure, the argument is made that the former has electronic similarities to indole. Based on that premise, iridium-mediated C–H activation has enabled facile installation of a versatile, nucleophilic coupling handle at a previously inaccessible site of 2,1-borazaronaphthalenes. A variety of substituted 2,1-borazaronaphthalene cores can be successfully borylated and further cross-coupled in a facile manner to yield diverse C(8)-substituted 2,1-borazaronaphthalenes.

Convenient and General Zinc-Catalyzed Borylation of Aryl Diazonium Salts and Aryltriazenes under Mild Conditions

A convenient and general zinc‐catalyzed borylation of aryl diazonium salts and aryltriazenes has been developed. With bis‐ (pinacolato)diboron as the borylation reagent, aryldiazonium tetrafluoroborate salts and aryltriazenes were transformed into the corresponding arylboronates in moderate to excellent yields under mild conditions. As a convenient and practical methodology, no additional ligands, base, or any other additives are required here.