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.

Bismuth-Catalyzed Amide Reduction.

In this article we report that a cationic version of Akiba's BiIII complex catalyzes the reduction of amides to amines using silane as hydride donor. The catalytic system features low catalyst loadings and mild conditions, en route to secondary and tertiary aryl- and alkylamines. The system tolerates functional groups such as alkene, ester, nitrile, furan and thiophene. Kinetic studies on the reaction mechanism result in the identification of a reaction network with an important product inhibition that is in agreement with the experimental reaction profiles.

Organocatalytic Enantioselective α-Bromination of Aldehydes with N-Bromosuccinimide.

Despite the wealth of existing organocatalytic, enantioselective transformations, the α-bromination of aldehydes remains a challenging reaction. The four examples reported to date require expensive, inconvenient brominating agents to achieve the desired products in excellent yields and enantioselectivities. The preferred brominating agent, N-bromosuccinimide (NBS), has been repeatedly discarded for these reactions because it results in low yields and relatively poor enantioselectivities. We describe a methodology that uses NBS and performs excellently with low catalyst loadings, short reaction times, and mild temperatures.

A computational tool to accurately and quickly predict 19F NMR chemical shifts of molecules with fluorine-carbon and fluorine-boron bonds.

We report the evaluation of density-functional-theory (DFT) based procedures for predicting 19F NMR chemical shifts at modest computational cost for a range of molecules with fluorine bonds, to be used as a tool for assisting the characterisation of reaction intermediates and products and as an aid to identifying mechanistic pathways. The results for a balanced learning set of molecules were then checked using two further testing sets, resulting in the recommendation of the ωB97XD/aug-cc-pvdz DFT method and basis set as having the best combination of accuracy and computational time, with a RMS error of 3.57 ppm. Cationic molecules calculated without counter-anion showed normal errors, whilst anionic molecules showed somewhat larger errors. The method was applied to the prediction of the conformationally averaged 19F chemical shifts of 2,2,3,3,4,4,5,5-octafluoropentan-1-ol, in which gauche stereoelectronic effects involving fluorine dominate and to determining the position of coordination equilibria of fluorinated boranes as an aid to verifying the relative energies of intermediate species involved in catalytic amidation reactions involving boron catalysts.

Mechanistically Guided Design of an Efficient and Enantioselective Aminocatalytic α-Chlorination of Aldehydes.

The enantioselective aminocatalytic α-chlorination of aldehydes is a challenging reaction because of its tendency to proceed through neutral intermediates in unselective pathways. Herein we report the rational shift to a highly selective reaction pathway involving charged intermediates using hexafluoroisopropanol as solvent. This change in mechanism has enabled us to match and improve upon the yields and enantioselectivities displayed by previous methods while using cheaper aminocatalysts and chlorinating agents, 80-95% less amount of catalyst, convenient temperatures, and shorter reaction times.

Use of Standard Addition to Quantify In Situ FTIR Reaction Data.

FTIR spectroscopy is a common in situ reaction monitoring technique used in modern academic and industrial environments. The FTIR signals collected during the course of a reaction are proportional to the concentration of the reaction components but not intrinsically quantitative. To make FTIR data quantitative, precalibration or offline analyses of reaction samples are required, which diminishes the unique benefits of in situ reaction monitoring techniques. Herein, we report the use of standard addition as a convenient method to obtain quantitative FTIR data.

Understanding the Diastereopreference of Intermediates in Aminocatalysis: Application to the Chiral Resolution of Lactols.

Downstream intermediates are crucial for the reactivity and selectivity of aminocatalytic reactions. We present an analysis of the stereopreference in aminocatalytic downstream intermediates, which reveals an inconspicuous mechanism of chiral recognition between the catalyst and the rest of the molecule. We delineate a stereoelectronic model to rationalize the mode of chiral transmission. We also exploit it for the resolution of chiral lactols relevant in organic synthesis as well as in the flavor and fragrance industry.

Hydroarylation of Alkenes by Protonation/Friedel-Crafts Trapping: HFIP-Mediated Access to Per-aryl Quaternary Stereocenters.

Upon treatment with a combination of HFIP and an organic sulfonic acid, alkenes behave as Brønsted bases and protonate to give carbocations which can be trapped by electron-rich arenes. The reaction constitutes a Friedel-Crafts hydroarylation which proceeds with Markovnikov selectivity and is orthogonal to traditional metal-catalyzed processes. Intermolecular transfer hydrogenation and hydrothiolation under analogous conditions are also demonstrated.

Kinetic Treatments for Catalyst Activation and Deactivation Processes based on Variable Time Normalization Analysis.

Progress reaction profiles are affected by both catalyst activation and deactivation processes occurring alongside the main reaction. These processes complicate the kinetic analysis of reactions, often directing researchers toward incorrect conclusions. We report the application of two kinetic treatments, based on variable time normalization analysis, to reactions involving catalyst activation and deactivation processes. The first kinetic treatment allows the removal of induction periods or the effect of rate perturbations associated with catalyst deactivation from kinetic profiles when the quantity of active catalyst can be measured. The second treatment allows the estimation of the activation or deactivation profile of the catalyst when the order of the reactants for the main reaction is known. Both treatments facilitate kinetic analysis of reactions suffering catalyst activation or deactivation processes.

Intermediacy of Ni-Ni Species in sp2 C-O Bond Cleavage of Aryl Esters: Relevance in Catalytic C-Si Bond Formation.

Monodentate phosphine ligands are frequently employed in the Ni-catalyzed C-O functionalization of aryl esters. However, the extensive body of preparative work on such reactions contrasts with the lack of information concerning the structure and reactivity of the relevant nickel intermediates. In fact, experimental evidence for a seemingly trivial oxidative addition into the C-O bond of aryl esters with monodentate phosphines and low-valent nickel complexes still remains elusive. Herein, we report a combined experimental and theoretical study on the Ni(0)/PCy3-catalyzed silylation of aryl pivalates with CuF2/CsF additives that reveals the involvement of unorthodox dinickel oxidative addition complexes in C-O bond cleavage and their relevance in C-Si bond formation. We have obtained a mechanistic picture that clarifies the role of the additives and demonstrates that dinickel complexes act as reservoirs of the propagating monomeric nickel complexes by disproportionation. We believe this study will serve as a useful entry point to unravelling the mechanistic underpinnings of other related Ni-catalyzed C-O functionalization reactions employing monodentate phosphines.

Distribution of Catalytic Species as an Indicator To Overcome Reproducibility Problems.

Irreproducibility is a common issue in catalysis. The ordinary way to minimize it is by ensuring enhanced control over the factors that affect the reaction. When control is insufficient, some parameters can be used as indicators of the reaction performance. Herein we describe the use of the distribution of catalytic species as an indicator to map, track, and fine-tune the performance of catalytic reactions. This indicator is very sensitive and presents a quick response to variations in the reaction conditions. We have applied this new strategy to the conjugate addition of C-nucleophiles to enals via iminium intermediates, consistently achieving maximum turnover frequencies (TOF) regardless of the quality of the starting materials used. In addition, the present method has allowed us to efficiently reduce the catalyst loading to as little as 0.1 mol %, the lowest one described for this kind of reaction.

Explaining Anomalies in Enamine Catalysis: "Downstream Species" as a New Paradigm for Stereocontrol.

Enantioselective organocatalysis by diarylprolinol ethers is remarkably selective and efficient for a wide range of transformations involving a number of different activation modes, including HOMO activation via enamines. A simple steric model based on facial discrimination in the attack of an enamine on an electrophile has been invoked to rationalize high enantioselectivity. In a number of reactions, however, experimental observations have persistently left us with mechanistic puzzles that fail to fit neatly into this simple picture. Further studies involving both kinetic profiling of reaction networks and NMR spectroscopic characterization of the structures of intermediate species helped us to address these puzzles. This work led to the proposal of a new paradigm for stereocontrol in asymmetric aminocatalysis, demonstrating that the ultimate stereochemical outcome may not, in fact, be determined solely in the stereogenic bond-forming step between enamine and electrophile. The identification of stable species occurring downstream from the addition of an electrophile to an enamine, and the discovery of kinetic features that are diagnostic of the presence of such species, allows development of a new mechanistic framework that reveals a hierarchical selection. Both kinetic and thermodynamic processes associated with downstream intermediates can exert an influence on the ultimate enantioselectivity. Interestingly, the role of these species may be either to enhance or to erode selectivity established at the enamine-electrophile step. The reversibility of steps preceding and subsequent to the stereogenic bond-forming step is an important factor, as are reaction parameters that may stabilize or destabilize intermediates, including the nature of the electrophile counterion and the solvent. These concepts hold implications for the future design and optimization of asymmetric catalytic processes, because such design does not necessarily feature the same parameters at the second hierarchical level as it does at the first. Examples presented to highlight these issues include the conjugate addition of aldehydes to nitroalkenes and the α-chlorination and α-selenylation of aldehdyes using diarylprolinol ether catalysts commonly assumed to follow a steric model for enantioselectivity. While the new paradigm for stereocontrol involving downstream intermediates is developed here for enamine catalysis, the same concepts may hold for other organocatalytic modes of activation.

A bis(pyridyl)-N-alkylamine/Cu(i) catalyst system for aerobic alcohol oxidation.

Herein a bis(pyridyl)-N-alkylamine/CuI/TEMPO/NMI catalyst system is reported for aerobic oxidation of a variety of primary alcohols to the corresponding aldehydes using readily available reagents, at room temperature and ambient air as the oxidant. ESI-MS analysis of the reaction showed the formation of a [(L1)(NMI)CuII-OOH]+ species, which is a key intermediate in the alcohol oxidation reaction. Evaluation of the effect of reaction parameters on the initial rate of the reaction allowed us to obtain the optimum conditions for catalytic activity. The careful choice of reaction solvent allowed for the oxidation of 4-hydroxybenzyl alcohol, a substrate which proved problematic in previous studies. In the case of 2-pyridinemethanol as substrate, experimental evidence shows that catalytic activity is diminished due to competitive inhibition of the catalyst by the alcohol substrate.

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.

Variable Time Normalization Analysis: General Graphical Elucidation of Reaction Orders from Concentration Profiles.

The recent technological evolution of reaction monitoring techniques has not been paralleled by the development of modern kinetic analyses. The analyses currently used disregard part of the data acquired, thus requiring an increased number of experiments to obtain sufficient kinetic information for a given chemical reaction. Herein, we present a simple graphical analysis method that takes advantage of the data-rich results provided by modern reaction monitoring tools. This analysis uses a variable normalization of the time scale to enable the visual comparison of entire concentration reaction profiles. As a result, the order in each component of the reaction, as well as kobs , is determined with just a few experiments using a simple and quick mathematical data treatment. This analysis facilitates the rapid extraction of relevant kinetic information and will be a valuable tool for the study of reaction mechanisms.

A Simple Graphical Method to Determine the Order in Catalyst.

A graphical analysis to elucidate the order in catalyst is presented. This analysis uses a normalized time scale, t [cat]T (n) , to adjust entire reaction profiles constructed with concentration data. The method is fast and simple to perform because it directly uses the concentration data, therefore avoiding the data handling that is usually required to extract rates. Compared to methods that use rates, the normalized time scale analysis requires fewer experiments and minimizes the effects of experimental errors by using information on the entire reaction profile.

Rationalization of an unusual solvent-induced inversion of enantiomeric excess in organocatalytic selenylation of aldehydes.

An unusual solvent-induced inversion of the sense of enantioselectivity observed in the α-selenylation of aldehydes catalyzed by a diphenylprolinol silyl ether catalyst is correlated to the presence of intermediates formed subsequent to the highly selective C-Se bond-forming step in the catalytic cycle. This work provides support for a mechanistic concept for enamine catalysis and includes a general role for "downstream intermediates" in selectivity outcomes in organocatalysis.

Mechanistic interpretation of orders in catalyst greater than one.

Orders in catalyst greater than one can be attributed to several different reaction mechanisms. Differentiating among these possibilities requires careful analysis of their rate laws, rational experiment design and accurate measurement of the progress of the reactions. We have compiled the most popular mechanisms proposed for reactions with an order in catalyst greater than one and derived their steady-state rate laws. We have analysed the rate laws and proposed experiments to discern between mechanisms. Finally, we have examined 100 case studies that showcase good practices to propose robust mechanisms and to avoid common pitfalls.

Curtin-Hammett paradigm for stereocontrol in organocatalysis by diarylprolinol ether catalysts.

Detailed mechanistic study of two reactions catalyzed by diarylprolinol ether catalysts, the conjugate addition of aldehydes to nitro-olefins and the α-chlorination of aldehydes, leads to the proposal that the stereochemical outcome in these cases is not determined by the transition state of the step in which the stereogenic center is formed from enamine attack on the electrophile but instead is correlated with the relative stability and reactivity of diastereomeric intermediates downstream in the catalytic cycle. This combination of kinetic and thermodynamic factors illustrates a remarkable Curtin-Hammett scenario that can result in either an enhancement or an erosion of the selectivity that would be predicted by the transition state for enamine attack on the electrophile. Evidence is offered to suggest that this concept may represent a general phenomenon for pyrrolidine-based catalysts lacking an acidic directing proton. Implications for catalyst and reaction design are discussed.