Broad Survey of Selectivity in the Heterogeneous Hydrogenation of Heterocycles.

A broad survey of heterogeneous hydrogenation catalysts has been conducted for the reduction of heterocycles commonly found in pharmaceuticals. The comparative reactivity of these substrates is reported as a function of catalyst, temperature, and hydrogen pressure. This analysis provided several catalysts with complementary reactivity between substrates. We then explored a series of bisheterocyclic substrates that provided an intramolecular competition of heterocycle hydrogenation reactivity. In several cases, complete selectivity could be achieved for reduction of one heterocycle and isolated yields are reported. A general trend in reactivity is inferred in which quinoline is the most reactive, followed by pyrazine, then pyrrole and with pyridine being the least reactive.

Accessing three-dimensional molecular diversity through benzylic C-H cross-coupling.

Pharmaceutical and agrochemical discovery efforts rely on robust methods for chemical synthesis that rapidly access diverse molecules1,2. Cross-coupling reactions are the most widely used synthetic methods3, but these methods typically form bonds to C(sp2)-hybridized carbon atoms (e.g., amide coupling, biaryl coupling) and lead to a prevalence of "flat" molecular structures with suboptimal physicochemical and topological properties4. Benzylic C(sp3)-H cross-coupling methods offer an appealing strategy to address this limitation by directly forming bonds to C(sp3)-hybridized carbon atoms, and emerging methods exhibit synthetic versatility that rivals conventional cross-coupling methods to access products with drug-like properties. Here, we use a virtual library of >350,000 benzylic ethers and ureas derived from benzylic C-H cross-coupling to test the widely held view that coupling at C(sp3)-hybridized carbon atoms affords products with improved three-dimensionality. The results show that the conformational rigidity of the benzylic scaffold strongly influences the product dimensionality. Products derived from flexible scaffolds often exhibit little or no improvement in three-dimensionality, unless they adopt higher energy conformations. This outcome introduces an important consideration when designing routes to topologically diverse molecular libraries. The concepts elaborated herein are validated experimentally through an informatics-guided synthesis of selected targets and the use of high-throughput experimentation to prepare a library of three-dimensional products that are broadly distributed across drug-like chemical space.

Accessing Diverse Azole Carboxylic Acid Building Blocks via Mild C-H Carboxylation: Parallel, One-Pot Amide Couplings and Machine-Learning-Guided Substrate Scope Design.

This manuscript describes a mild, functional group tolerant, and metal-free C-H carboxylation that enables direct access to azole-2-carboxylic acids, followed by amide coupling in one pot. This demonstrates a significant expansion of the accessible chemical space of azole-2-amides, compared to previously known methodologies. Key to the described reactivity is the use of silyl triflate reagents, which serve as reaction mediators in C-H deprotonation and stabilizers of (otherwise unstable) azole carboxylic acid intermediates. A diverse azole substrate scope designed via machine-learning-guided analysis demonstrates the broad utility of the sequence. Density functional theory calculations provide detailed insights into the role of silyl triflates in the reaction mechanism. Transferrable applications of the protocol are successfully established: (i) A low pressure (CO2 balloon) option for synthesizing azole-2-carboxylic acids without the need for high-pressure equipment; (ii) the use of 13CO2 for the synthesis of labeled compounds; (iii) isocyanates as alternative electrophiles for direct C-H amidation; (iv) and the use of the developed chemistry in a 24 × 12 parallel synthesis workflow with a 90% library success rate. Fundamentally, the reported protocol expands the use of heterocycle C-H functionalization from late-stage functionalization applications toward its use in library synthesis. It provides general access to densely functionalized azole-2-carboxylic acid building blocks and demonstrates their one-pot diversification.

Analysis of Laboratory-Evolved Flavin-Dependent Halogenases Affords a Computational Model for Predicting Halogenase Site Selectivity.

Flavin-dependent halogenases (FDHs) catalyze selective halogenation of electron-rich aromatic compounds without the need for harsh oxidants required by conventional oxidative halogenation reactions. Predictive models for halogenase site selectivity could greatly improve their utility for chemical synthesis. Toward this end, we analyzed the structures and selectivity of three halogenase variants evolved to halogenate tryptamine with orthogonal selectivity. Crystal structures and reversion mutations revealed key residues involved in altering halogenase selectivity. Density functional theory calculations and molecular dynamics simulations are both consistent with hypohalous acid as the active halogenating species in FDH catalysis. This model was used to accurately predict the site selectivity of halogenase variants toward different synthetic substrates, providing a valuable tool for implementing halogenases in biocatalysis efforts.

Driving to a Better Understanding of Acyl Glucuronide Transformations Using NMR and Molecular Modeling.

Acyl glucuronide (AG) metabolites of carboxylic acid-containing drugs and products of their transformations have long been implicated in drug-induced liver injury (DILI). To inform on the DILI risk arising from AG reactive intermediates, a comprehensive mechanistic study of enzyme-independent AG rearrangements using nuclear magnetic resonance (NMR) and density functional theory (DFT) was undertaken. NMR spectroscopy was utilized for structure elucidation and kinetics measurements of nine rearrangement and hydrolysis products of 1ß-O-acyl glucuronide of ibufenac. To extract rate constants of rearrangement, mutarotation, and hydrolysis from kinetic data, 11 different kinetic models were examined. Model selection and estimated rate constant verification were supported by measurements of H/D kinetic isotope effects. DFT calculations of ground and transition states supported the proposed kinetic mechanisms and helped to explain the unusually fast intramolecular transacylation rates found for some of the intermediates. The findings of the current study reinforce the notion that the short half-life of parent AG and slow hydrolysis rates of AG rearrangement products are the two key factors that can influence the in vivo toxicity of AGs.

Lewis acid mediated, mild C-H aminoalkylation of azoles via three component coupling.

This manuscript reports the development of a mild, highly functional group tolerant and metal-free C-H aminoalkylation of azoles via a three-component coupling approach. This method enables the C-H functionalization of diverse azole substrates, such as oxazoles, benzoxazoles, thiazoles, benzothiazoles, imidazoles, and benzimidazoles. DFT calculations identify a key deprotonation equilibrium in the mechanism of the reaction. Using DFT as a predictive tool, the C-H aminoalkylation of initially unreactive substrates (imidazoles/benzimidazoles) can be enabled through an in situ protecting/activating group strategy. The DFT-supported mechanistic pathway proposes key interactions between the azole substrate and the Lewis acid/base pair TBSOTf/EtNiPr2 that lead to azole activation by deprotonation, followed by C-C bond formation between a carbene intermediate and an iminium electrophile. Two diverse approaches are demonstrated to explore the amine substrate scope: (i) a DFT-guided predictive analysis of amine components that relates reactivity to distortion of the iminium intermediates in the computed transition state structures; and (ii) a parallel medicinal chemistry workflow enabling synthesis and isolation of several diversified products at the same time. Overall, the presented work enables a metal-free approach to azole C-H functionalization via Lewis acid mediated azole C-H deprotonation, demonstrating the potential of a readily available, Si-based Lewis acid to mediate new C-C bond formations.

Catalytic Effects of Ammonium and Sulfonium Salts and External Electric Fields on Aza-Diels-Alder Reactions.

The mechanism of the aza-Diels-Alder reaction catalyzed by tetraalkylammonium or trialkylsulfonium salts is explored with density functional theory. Favorable electrostatic interactions between the dienophile and the charged catalyst stabilize the highly polar transition state, leading to lower free energy barriers and higher dipole moments. Endo selectivity is predicted for both uncatalyzed and catalyzed systems. We also computationally evaluate the effects of oriented external electric fields (EEFs) on the same aza-Diels-Alder reaction, demonstrating that very strong EEFs would be needed to achieve the catalytic strength of these cationic catalysts.

Thermodynamic consequences of Tyr to Trp mutations in the cation-π-mediated binding of trimethyllysine by the HP1 chromodomain.

Evolution has converged on cation-π interactions for recognition of quaternary alkyl ammonium groups such as trimethyllysine (Kme3). While computational modelling indicates that Trp provides the strongest cation-π interaction of the native aromatic amino acids, there is limited corroborative data from measurements within proteins. Herein we investigate a Tyr to Trp mutation in the binding pocket of the HP1 chromodomain, a reader protein that recognizes Kme3. Binding studies demonstrate that the Trp-mediated cation-π interaction is about -5 kcal mol-1 stronger, and the Y24W crystal structure shows that the mutation is not perturbing. Quantum mechanical calculations indicate that greater enthalpic binding is predominantly due to increased cation-π interactions. NMR studies indicate that differences in the unbound state of the Y24W mutation lead to enthalpy-entropy compensation. These results provide direct experimental quantification of Trp versus Tyr in a cation-π interaction and afford insight into the conservation of aromatic cage residues in Kme3 reader domains.

Mechanism and Regioselectivity of an Unsymmetrical Hexadehydro-Diels-Alder (HDDA) Reaction.

Hoye reported intramolecular hexadehydro-Diels-Alder (HDDA) reactions to generate arynes that functionalize natural product phenols and amines. In their studies, Hoye found that unsymmetrical tetraynes selectively form a single aryne. We report density functional theory (DFT) calculations that reveal the factors controlling the regioselectivity.

Origins of Selectivities in the Stork Diels-Alder Cycloaddition for the Synthesis of (±)-4-Methylenegermine.

The remarkably high  stereoselectivity of  a Diels-Alder cycloaddition  designed by  Stork for the synthesis of germine has been examined with theory. We conceived a collaboration with Gilbert Stork, the great synthetic chemist and collaborator. We wished to complement Stork's insights with computations to explain the extraordinary selectivity he designed to introduce four new stereocenters in one step. Stork passed away on October 21, 2017, at age 95, sadly before we finished this work.

Organocatalytic [6+4] Cycloadditions via Zwitterionic Intermediates: Chemo-, Regio-, and Stereoselectivities.

The mechanisms and origins of chemo- and stereoselectivities of the organocatalytic [6+4] cycloaddition between 2-cyclopentenone and tropone have been investigated by a combined computational and experimental study. In the presence of a cinchona alkaloid primary amine catalyst and an acid additive, 2-cyclopentenone forms a cross-dienamine intermediate that subsequently undergoes a stepwise [6+4] cycloaddition reaction via a zwitterionic intermediate. The rate-determining transition state features a strong hydrogen-bonding interaction between the tropone oxygen atom and the protonated quinuclidine directing the reaction course leading to a highly periselective [6+4] cycloaddition. The importance of the strong hydrogen-bonding interaction is also demonstrated by the influence of the concentration of the acid additive on the yields and enantioselectivities of the reaction. The corresponding [4+2] cycloaddition reaction has a much higher energy barrier. The enantioselectivity of the [6+4] cycloaddition originates from different repulsive hydrogen-hydrogen interactions that distinguish the diastereomeric transition states.

Biosynthesis of thiocarboxylic acid-containing natural products.

Thiocarboxylic acid-containing natural products are rare and their biosynthesis and biological significance remain unknown. Thioplatensimycin (thioPTM) and thioplatencin (thioPTN), thiocarboxylic acid congeners of the antibacterial natural products platensimycin (PTM) and platencin (PTN), were recently discovered. Here we report the biosynthetic origin of the thiocarboxylic acid moiety in thioPTM and thioPTN. We identify a thioacid cassette encoding two proteins, PtmA3 and PtmU4, responsible for carboxylate activation by coenzyme A and sulfur transfer, respectively. ThioPTM and thioPTN bind tightly to ß-ketoacyl-ACP synthase II (FabF) and retain strong antibacterial activities. Density functional theory calculations of binding and solvation free energies suggest thioPTM and thioPTN bind to FabF more favorably than PTM and PTN. Additionally, thioacid cassettes are prevalent in the genomes of bacteria, implicating that thiocarboxylic acid-containing natural products are underappreciated. These results suggest that thiocarboxylic acid, as an alternative pharmacophore, and thiocarboxylic acid-containing natural products may be considered for future drug discovery.

Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis.

Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.

Origins of Stereoselectivity in Chiral Aminoalcohol Catalysis of Oxyallyl Cation-Indole Reactions.

The enantioselective coupling of indoles with racemic α-tosyloxy ketones mediated by a chiral amino alcohol catalyst is studied with density functional theory (DFT) calculations. The addition of indole to an oxyallyl cation intrinsically favors the (S,S) and (R,R) stereoisomeric products through electrostatic interactions in the transition state. Our model shows that the enantioselectivity is controlled by the cyclohexane moiety of the catalyst; selectivity diminishes upon removal of the cyclohexane ring. Substitution to enhance the enantioselectivity of this reaction is proposed.

Chirality Sensing of α-Hydroxyphosphonates by N-tert-Butyl Sulfinyl Squaramide.

N-tert-Butyl sulfinyl squaramides were used for chiral discrimination of α-hydroxyphosphonates using 31P NMR. A free energy relationship study indicates that both steric and the electronic effects influence the chiral recognition of the donors.

Model for the Enantioselectivity of Asymmetric Intramolecular Alkylations by Bis-Quaternized Cinchona Alkaloid-Derived Catalysts.

A model for the stereoselectivity of intramolecular alkylations by N,N'-disubstituted cinchona alkaloids reported by Xiang et al. was established using density functional theory (DFT) calculations. The stereocontrol is based on the minimal distortion of the transition state (TS) and catalyst required to achieve favorable electrostatic interactions in the favored TS. Counterions must be included in computational modeling of ion-paired catalysis in order to reproduce experimental enantioselectivity.

Mechanisms and Origins of Periselectivity of the Ambimodal [6 + 4] Cycloadditions of Tropone to Dimethylfulvene.

The mechanisms and selectivities of the cycloadditions of tropone to dimethylfulvene have been investigated with M06-2X and B3LYP-D3 density functional theory (DFT) calculations and quasi-classical direct molecular dynamics simulations. The originally proposed reaction mechanism (Houk) involves a highly peri-, regio-, and stereoselective [6F + 4T] cycloaddition of tropone [4π] to dimethylfulvene [6π], followed by a [1,5] hydrogen shift, and, finally, a second [6 + 4] cycloaddition of tropone [6π] to the cyclopentadiene moiety [4π]. Paddon-Row and Warrener proposed an alternative mechanism: the initial cycloaddition involves a different [6T + 4F] cycloaddition in which fulvene acts as the 4π component, and a subsequent Cope rearrangement produces the formal [6F + 4T] adduct. Computations now demonstrate that the initial cycloaddition proceeds via an ambimodal transition state that can lead to both of the proposed [6 + 4] adducts. These adducts can interconvert through a [3,3] sigmatropic shift (Cope rearrangement). Molecular dynamics simulations reveal the initial distribution of products and provide insights into the time-resolved mechanism of this ambimodal cycloaddition. Competing [4 + 2] cycloadditions and various sigmatropic shifts are also explored.

Design and Applications of N-tert-Butyl Sulfinyl Squaramide Catalysts.

A new chiral HBD system, N-tert-butyl sulfinyl squaramide, was designed and synthesized. The core N-tert-butyl sulfinyl squaramide with an 1-aminoindan-2-ol skeleton was found to be an efficient catalyst in the enantioselective Friedel-Crafts alkylation of indoles and acyl phosphonates.

Origins of regioselectivity in 1,3-dipolar cycloadditions of nitrile oxides with alkynylboronates.

Density functional theory (M06-2X) studies of the regioselectivity of 1,3-dipolar cycloaddition reactions of benzo and mesitonitrile oxides with alkynyl pinacol and MIDA boronates are reported. Calculated relative free energies of activation reproduce the experimentally observed product ratios. The electronic energies of activation are found to be mainly controlled by distortion energies required to achieve the transition states. Both electronic and steric effects influence regioselectivities.

Distortion, Tether, and Entropy Effects on Transannular Diels-Alder Cycloaddition Reactions of 10-18-Membered Rings.

Density functional theory calculations were performed on a set of 13 transannular Diels-Alder (TADA) reactions with 10-18-membered rings. The results were compared with those for bimolecular and intramolecular Diels-Alder reactions in order to investigate the controlling factors of the high TADA reactivities. The effects of tether length, heteroatoms, and alkynyl dienophiles on reactivity were analyzed. We found a correlation between tether length and reactivity, specifically with 12-membered macrocycles undergoing cycloaddition most readily. Furthermore, modifying 12-membered macrocycles by heteroatom substitution and utilizing alkynyl dienophiles enhances the reaction rates up to 10(5)-fold.