PMechDB: A Public Database of Elementary Polar Reaction Steps.

Most online chemical reaction databases are not publicly accessible or are fully downloadable. These databases tend to contain reactions in noncanonicalized formats and often lack comprehensive information regarding reaction pathways, intermediates, and byproducts. Within the few publicly available databases, reactions are typically stored in the form of unbalanced, overall transformations with minimal interpretability of the underlying chemistry. These limitations present significant obstacles to data-driven applications including the development of machine learning models. As an effort to overcome these challenges, we introduce PMechDB, a publicly accessible platform designed to curate, aggregate, and share polar chemical reaction data in the form of elementary reaction steps. Our initial version of PMechDB consists of over 100,000 such steps. In the PMechDB, all reactions are stored as canonicalized and balanced elementary steps, featuring accurate atom mapping and arrow-pushing mechanisms. As an online interactive database, PMechDB provides multiple interfaces that enable users to search, download, and upload chemical reactions. We anticipate that the public availability of PMechDB and its standardized data representation will prove beneficial for chemoinformatics research and education and the development of data-driven, interpretable models for predicting reactions and pathways. PMechDB platform is accessible online at https://deeprxn.ics.uci.edu/pmechdb.

Rhodium(II)-Catalyzed Hinsberg Dearomatization Using Trimethylsilyldiazomethane.

Rhodium(II) catalyzes carbene transfer from trimethylsilyldiazomethane to arylmethyl thioethers, generating sulfonium ylides that undergo [2,3]-sigmatropic rearrangement, punching quaternary centers into aromatic rings. The reaction works well with naphthalene, indole, and benzofuran ring systems, but the reaction is unsuccessful with the monocyclic benzene homologue. For aryl thioethers, Rh2(OAc)4 gives good results. For alkyl thioethers, the yields improve with Rh2(cap)4. Surprisingly, thioesters and thiocarbamates are also competent substrates for the reaction.

RMechDB: A Public Database of Elementary Radical Reaction Steps.

We introduce RMechDB, an open-access platform for aggregating, curating, and distributing reliable data about elementary radical reaction steps for computational radical reaction modeling and prediction. RMechDB contains over 5,300 elementary radical reaction steps, each with a single transition state at or around room temperature. These elementary step reactions are manually curated plausible arrow-pushing steps for organic radical reactions. The steps were taken from a variety of sources. Over 2,000 mechanistic steps were extracted from textbooks and/or constructed from research publications. Another 3,000 were taken from gas-phase atmospheric reactions of isoprene and other organic molecules on the MCM (Master Chemical Mechanism) Web site. Reactions are encoded in the SMIRKS format with accurate atom mapping and annotations for arrow-pushing mechanisms. At its core, RMechDB consists of a database schema with an online interactive search interface and a request portal for downloading the raw form of elementary step reactions with their metadata. It also offers an interface for submitting new reactions to RMechDB and expanding the data set through community contributions. Although there are several applications for RMechDB, it is primarily designed as a central platform of radical elementary steps with a unified and structured representation. We believe that this open access to this data and platform enables the extension of data-driven models for chemical reaction predictions and other chemoinformatics predictive tasks.

Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity.

There is a lack of scalable quantitative measures of reactivity that cover the full range of functional groups in organic chemistry, ranging from highly unreactive C-C bonds to highly reactive naked ions. Measuring reactivity experimentally is costly and time-consuming, and no single method has sufficient dynamic range to cover the astronomical size of chemical reactivity space. In previous quantum chemistry studies, we have introduced Methyl Cation Affinities (MCA*) and Methyl Anion Affinities (MAA*), using a solvation model, as quantitative measures of reactivity for organic functional groups over the broadest range. Although MCA* and MAA* offer good estimates of reactivity parameters, their calculation through Density Functional Theory (DFT) simulations is time-consuming. To circumvent this problem, we first use DFT to calculate MCA* and MAA* for more than 2,400 organic molecules thereby establishing a large data set of chemical reactivity scores. We then design deep learning methods to predict the reactivity of molecular structures and train them using this curated data set in combination with different representations of molecular structures. Using 10-fold cross-validation, we show that graph attention neural networks applied to a relational model of molecular structures produce the most accurate estimates of reactivity, achieving over 91% test accuracy for predicting the MCA* ± 3.0 or MAA* ± 3.0, over 50 orders of magnitude. Finally, we demonstrate the application of these reactivity scores to two tasks: (1) chemical reaction prediction and (2) combinatorial generation of reaction mechanisms. The curated data sets of MCA* and MAA* scores is available through the ChemDB chemoinformatics web portal at cdb.ics.uci.edu under Chemical Reactivities data sets.

Tandem Insertion/[3,3]-Sigmatropic Rearrangement Involving the Formation of Silyl Ketene Acetals by Insertion of Rhodium Carbenes into S-Si Bonds.

Allyl 2-diazo-2-phenylacetates are shown to react with trimethylsilyl thioethers in the presence of rhodium(II) catalysts to generate α-allyl-α-thio silyl esters. The transformation involves a tandem process involving formal rhodium-catalyzed insertion of the carbene group into the S-Si bond to generate a silyl ketene acetal, followed by a spontaneous Ireland-Claisen rearrangement. The silyl ester products were isolated as the corresponding carboxylic acids after aqueous workup. Intramolecular cyclopropanation of the allyl fragment generally competes with addition of the heteroatom to the carbene center. The reaction occurs under mild conditions and in high yield, allowing for rapid entry into rearrangement tetrasubstituted products. Propargyl esters were shown to generate the corresponding α-allenyl products.

Methyl Cation Affinities of Canonical Organic Functional Groups.

Methyl cation affinities are calculated for the canonical nucleophilic functional groups in organic chemistry. These methyl cation affinities, calculated with a solvation model (MCA*), give an emprical correlation with the NsN term from the Mayr equation under aprotic conditions when they are scaled to the Mayr reference cation (4-MeOC6H4)2CH+ (Mayr E = 0). Highly reactive anionic nucleophiles were found to give a separate correlation, while some ylides and phosphorus compounds were determined to give a poor correlation. MCA*s are estimated for a broad range of simple molecules representing the canonical functional groups in organic chemistry. On the basis of a linear correlation, we estimate the range of nucleophilicities of organic functional groups, ranging from a C-C bond to a hypothetical tert-butyl carbanion, toward the reference electrophile to be about 50 orders of magnitude.

Methyl Anion Affinities of the Canonical Organic Functional Groups.

Calculated methyl anion affinities are known to correlate with experimentally determined Mayr E parameters for individual organic functional group classes but not between neutral and cationic organic electrophiles. We demonstrate that methyl anion affinities calculated with a solvation model (MAA*) give a linear correlation with Mayr E parameters for a broad range of functional groups. Methyl anion affinities (MAA*), plotted on the log scale of Mayr E, provide insights into the full range of electrophilicity of organic functional groups. On the Mayr E scale, the electrophilicity toward the methyl anion spans 180 orders of magnitude.

Total Synthesis of (±)-Brazilin Using [4 + 1] Palladium-Catalyzed Carbenylative Annulation.

Palladium-catalyzed carbene insertion was utilized in a formal synthesis of (±)-picropodophyllone and a total synthesis of (±)-brazilin. All prior syntheses of brazilin have involved a Friedel-Crafts alkylation in the key carbon-carbon bond forming events. The palladium-catalyzed [4 + 1] reaction generates a 1-arylindane with all of the functionalities needed for formation of the indano[2,1-c]chroman ring system of brazilin. The synthesis of (±)-brazilin was achieved in 11 steps (longest linear sequence) with an overall 11% yield.

Total Synthesis of (±)-Pestalachloride C and (±)-Pestalachloride D through a Biomimetic Knoevenagel/Hetero-Diels-Alder Cascade.

A concise total synthesis of (±)-pestalachloride C and (±)-pestalachloride D was achieved through a Knoevenagel/hetero-Diels-Alder cascade reaction to test the nonenzymatic biosynthetic hypothesis of Shao, Wang, and co-workers. The cascade reaction generates a mixture of racemic indano[2,1- c]chromans like those found in the natural products.

Enantioselective Palladium-Catalyzed Carbene Insertion into the N-H Bonds of Aromatic Heterocycles.

C3-substituted indoles and carbazoles react with α-aryl-α-diazoesters under palladium catalysis to form α-(N-indolyl)-α-arylesters and α-(N-carbazolyl)-α-arylesters. The products result from insertion of a palladium-carbene ligand into the N-H bond of the aromatic N-heterocycles. Enantioselection was achieved using a chiral bis(oxazoline) ligand, in many cases with high enantioselectivity (up to 99 % ee). The method was applied to synthesize the core of a bioactive carbazole derivative in a concise manner.

Potent Antifungal Synergy of Phthalazinone and Isoquinolones with Azoles Against Candida albicans.

Four phthalazinones (CIDs 22334057, 22333974, 22334032, 22334012) and one isoquinolone (CID 5224943) were previously shown to be potent enhancers of antifungal activity of fluconazole against Candida albicans. Several even more potent analogues of these compounds were identified, some with EC50 as low as 1 nM, against C. albicans. The compounds exhibited pharmacological synergy (FIC < 0.5) with fluconazole. The compounds were also shown to enhance the antifungal activity of isavuconazole, a recently FDA approved azole antifungal. Isoquinolone 15 and phthalazinone 24 were shown to be active against several resistant clinical isolates of C. albicans.

Carbenylative Amination and Alkylation of Vinyl Iodides via Palladium Alkylidene Intermediates.

Most palladium-catalyzed reactions involving insertion of alkylidenes with α-hydrogens undergo ß-hydride elimination from alkylpalladium(II) intermediates to form alkenes. Vinyl iodides were shown to generate η(3)-allylpalladium intermediates that resist ß-hydride elimination, preserving the sp(3) center adjacent to the carbene moiety. Acyclic stereocontrol (syn/anti) for carbenylative amination and alkylation reactions was low, suggesting a lack of control in the migratory insertion step. Highly hindered carbene precursors inexplicably led to formation of Z-alkenes with high levels of stereocontrol.

Potent Synergy between Spirocyclic Pyrrolidinoindolinones and Fluconazole against Candida albicans.

A spiroindolinone, (1S,3R,3aR,6aS)-1-benzyl-6'-chloro-5-(4-fluorophenyl)-7'-methylspiro[1,2,3a,6a-tetrahydropyrrolo[3,4-c]pyrrole-3,3'-1H-indole]-2',4,6-trione, was previously reported to enhance the antifungal effect of fluconazole against Candida albicans. A diastereomer of this compound was synthesized, along with various analogues. Many of the compounds were shown to enhance the antifungal effect of fluconazole against C. albicans, some with exquisite potency. One spirocyclic piperazine derivative, which we have named synazo-1, was found to enhance the effect of fluconazole with an EC50 value of 300 pM against a susceptible strain of C. albicans and going as low as 2 nM against some resistant strains. Synazo-1 exhibits true synergy with fluconazole, with an FIC index below 0.5 in the strains tested. Synazo-1 exhibited low toxicity in mammalian cells relative to the concentrations required for antifungal synergy.

Cyclization of η3-benzylpalladium intermediates derived from carbene insertion.

Migratory insertion of benzylidene carbene ligands into arylpalladium(II) species generates η(3)-benzylpalladium intermediates that can cyclize to generate five- and six-membered rings with new sp(3) centers. The reaction tolerates a range of arene functional groups and stabilized enolates. The products generated through this reaction are 1-arylindanes and 1-aryltetralins that are common to a range of natural products.

Pd-catalyzed bis-cyclization/dimerization reactions of ω-aminovinyl halides.

Palladium is shown to catalyze the dimerization and cyclization of vinyl halides to generate pyrrolidine and piperidine dimers connected by a trans-ethylene bridge. The reaction tolerates a variety of N-alkyl substituents, including adamantyl. This remarkable dimerization reaction generates the skeleton of the alkaloid hyalbidone in a single step. A crossover experiment with a vinyl halide and a vinyl bromide is consistent with a Michael-type addition to a vinylpalladium cation to generate a Pd(0) alkylidene intermediate.

Palladium-catalyzed Catellani aminocyclopropanation reactions with vinyl halides.

Palladium is shown to catalyze an intramolecular aminocyclopropanation of norbornenes with aliphatic vinyl halides in good yields. The reaction tolerates a variety of amine substituents and gives good results with a variety of carbocyclic and oxabicyclic [2.2.1] alkene acceptors. Notably, stabilized enolate nucleophiles were also employed in cyclopropanation reactions.

Carbenylative amination with N-tosylhydrazones.

A Pd-catalyzed reaction of vinyl iodides and N-tosylhydrazones that assembles η(3)-allyl ligands through carbene insertion is demonstrated. Intramolecular trapping with nitrogen nucleophiles generates good yields of cinnamyl and pentadienyl amines like those found in alkaloid natural products. Carbenylative amination was the key reaction to complete the synthesis of the alkaloid caulophyllumine B. Migratory insertion was biased to provide allylamines with optical purity up to 64% ee, but in a lower yield.

Palladium-catalyzed insertion of alpha-diazoesters into vinyl halides to generate alpha,beta-unsaturated gamma-amino esters.

As easy as 1, 2, 3: A palladium-catalyzed three-component coupling generates alpha,beta-unsaturated gamma-amino acids in a single step (see scheme). The reaction is believed to involve migration of a vinyl substituent to a highly electrophilic palladium carbene. Unlike previous synthetic approaches, this synthesis provides access to gamma-amino acids with non-natural side chains.

Synthesis, screening, and sequencing of cysteine-rich one-bead one-compound peptide libraries.

Cysteine-rich peptides are valued as tags for biarsenical fluorophores and as environmentally important reagents for binding toxic heavy metals. Due to the inherent difficulties created by cysteine, the power of one-bead one-compound (OBOC) libraries has never been applied to the discovery of short cysteine-rich peptides. We have developed the first method for the synthesis, screening, and sequencing of cysteine-rich OBOC peptide libraries. First, we synthesized a heavily biased cysteine-rich OBOC library, incorporating 50% cysteine at each position (Ac-X8-KM-TentaGel). Then, we developed conditions for cysteine alkylation, cyanogen bromide cleavage, and direct MS/MS sequencing of that library at the single bead level. The sequencing efficiency of this library was comparable to a traditional cysteine-free library. To validate screening of cysteine-rich OBOC libraries, we reacted a library with the biarsenical FlAsH and identified beads bearing the known biarsenical-binding motif (CCXXCC). These results enable OBOC libraries to be used in high-throughput discovery of cysteine-rich peptides for protein tagging, environmental remediation of metal contaminants, or cysteine-rich pharmaceuticals.

Palladium-catalyzed carbene insertion and trapping with carbon nucleophiles.

Palladium catalysts are shown to catalyze the three-component coupling of vinyl halides, trimethylsilyldiazomethane, and stabilized carbon nucleophiles. The reaction is believed to proceed through a palladium-carbene intermediate LX(R)PdCHSiMe 3 that undergoes migration of the vinyl substituent to the electrophilic carbene center to generate an eta 3-allylpalladium intermediate. The allylpalladium intermediate is attacked by the carbon nucleophile to generate a vinylsilane product.