Benzoquinone Cocatalyst Contributions to DAF/Pd(OAc)2-Catalyzed Aerobic Allylic Acetoxylation in the Absence and Presence of a Co(salophen) Cocatalyst.

Palladium(II)-catalyzed allylic acetoxylation has been the focus of extensive development and investigation. Methods that use molecular oxygen (O2) as the terminal oxidant typically benefit from the use of benzoquinone (BQ) and a transition-metal (TM) cocatalyst, such as Co(salophen), to support oxidation of Pd0 during catalytic turnover. We previously showed that Pd(OAc)2 and 4,5-diazafluoren-9-one (DAF) as an ancillary ligand catalyze allylic oxidation with O2 in the absence of cocatalysts. Herein, we show that BQ enhances DAF/Pd(OAc)2 catalytic activity, nearly matching the performance of reactions that include both BQ and Co(salophen). These observations are complemented by mechanistic studies of DAF/Pd(OAc)2 catalyst systems under three different oxidation conditions: (1) O2 alone, (2) O2 with cocatalytic BQ, and (3) O2 with cocatalytic BQ and Co(salophen). The beneficial effect of BQ in the absence of Co(salophen) is traced to synergistic roles of O2 and BQ, both of which are capable of oxidizing Pd0 to PdII The reaction of O2 generates H2O2 as a byproduct, which can oxidize hydroquinone to quinone in the presence of PdII NMR spectroscopic studies, however, show that hydroquinone is the predominant redox state of the quinone cocatalyst in the absence of Co(salophen), while inclusion of Co(salophen) maintains oxidized quinone throughout the reaction, resulting in better reaction performance.

A robotic platform for flow synthesis of organic compounds informed by AI planning.

The synthesis of complex organic molecules requires several stages, from ideation to execution, that require time and effort investment from expert chemists. Here, we report a step toward a paradigm of chemical synthesis that relieves chemists from routine tasks, combining artificial intelligence-driven synthesis planning and a robotically controlled experimental platform. Synthetic routes are proposed through generalization of millions of published chemical reactions and validated in silico to maximize their likelihood of success. Additional implementation details are determined by expert chemists and recorded in reusable recipe files, which are executed by a modular continuous-flow platform that is automatically reconfigured by a robotic arm to set up the required unit operations and carry out the reaction. This strategy for computer-augmented chemical synthesis is demonstrated for 15 drug or drug-like substances.

Operando Spectroscopic and Kinetic Characterization of Aerobic Allylic C-H Acetoxylation Catalyzed by Pd(OAc)2/4,5-Diazafluoren-9-one.

Allylic C-H acetoxylations are among the most widely studied palladium(II)-catalyzed C-H oxidation reactions. While the principal reaction steps are well established, key features of the catalytic mechanisms are poorly characterized, including the identity of the turnover-limiting step and the catalyst resting state. Here, we report a mechanistic study of aerobic allylic acetoxylation of allylbenzene with a catalyst system composed of Pd(OAc)2 and 4,5-diazafluoren-9-one (DAF). The DAF ligand is unique in its ability to support aerobic catalytic turnover, even in the absence of benzoquinone or other co-catalysts. Herein, we describe operando spectroscopic analysis of the catalytic reaction using X-ray absorption and NMR spectroscopic methods that allow direct observation of the formation and decay of a palladium(I) species during the reaction. Kinetic studies reveal the presence of two distinct kinetic phases: (1) a burst phase, involving rapid formation of the allylic acetoxylation product and formation of the dimeric PdI complex [PdI(DAF)(OAc)]2, followed by (2) a post-burst phase that coincides with evolution of the catalyst resting state from the PdI dimer into a π-allyl-PdII species. The data provide unprecedented insights into the role of ancillary ligands in supporting catalytic turnover with O2 as the stoichiometric oxidant and establish an important foundation for the development of improved catalysts for allylic oxidation reactions.

Aerobic Acyloxylation of Allylic C-H Bonds Initiated by a Pd0 Precatalyst with 4,5-Diazafluoren-9-one as an Ancillary Ligand.

Palladium-catalyzed allylic C-H oxidation has been widely studied, but most precedents use acetic acid as the coupling partner. In this study, a method compatible with diverse carboxylic acid partners has been developed. Use of a Pd0 precatalyst under aerobic reaction conditions leads to oxidation of Pd0 by O2 in the presence of the desired carboxylic acid to generate a PdII dicarboxylate that promotes acyloxylation of the allylic C-H bond. Good-to-excellent yields are obtained with a roughly 1:1 ratio of the alkene and carboxylic acid reagents. Optimized reaction conditions employ 4,5-diazafluoren-9-one (DAF) as a ligand, in combination with a quinone/iron phthalocyanine cocatalyst system to support aerobic catalytic turnover.

Detection of Palladium(I) in Aerobic Oxidation Catalysis.

Palladium(II)-catalyzed oxidation reactions exhibit broad utility in organic synthesis; however, they often feature high catalyst loading and low turnover numbers relative to non-oxidative cross-coupling reactions. Insights into the fate of the Pd catalyst during turnover could help to address this limitation. Herein, we report the identification and characterization of a dimeric PdI species in two prototypical Pd-catalyzed aerobic oxidation reactions: allylic C-H acetoxylation of terminal alkenes and intramolecular aza-Wacker cyclization. Both reactions employ 4,5-diazafluoren-9-one (DAF) as an ancillary ligand. The dimeric PdI complex, [PdI (µ-DAF)(OAc)]2 , which features two bridging DAF ligands and two terminal acetate ligands, has been characterized by several spectroscopic methods, as well as single-crystal X-ray crystallography. The origin of this PdI complex and its implications for catalytic reactivity are discussed.

Diazafluorenone-Promoted Oxidation Catalysis: Insights into the Role of Bidentate Ligands in Pd-Catalyzed Aerobic Aza-Wacker Reactions.

2,2'-Bipyridine (bpy), 1,10-phenanthroline (phen) and related bidentate ligands often inhibit homogeneous Pd-catalyzed aerobic oxidation reactions; however, certain derivatives, such as 4,5-diazafluoren-9-one (DAF), can promote catalysis. In order to gain insight into this divergent ligand behavior, eight different bpy- and phen-derived chelating ligands have been evaluated in Pd(OAc)2-catalyzed oxidative cyclization of (E)-4-hexenyltosylamide. Two of the ligands, DAF and 6,6'-dimethyl-2,2'-bipyridine (6,6'-Me2bpy), support efficient catalytic turnover, while the others strongly inhibit the reaction. DAF is especially effective and is the only ligand that exhibits "ligand-accelerated catalysis". Evidence suggests that the utility of DAF and 6,6'-Me2bpy originates from the ability of these ligands to access κ1-coordination modes via dissociation of one of the pyridyl rings. This hemilabile character is directly observed by NMR spectroscopy upon adding one equivalent of pyridine to solutions of 1:1 L/Pd(OAc)2 (L = DAF and 6,6'-Me2bpy), and is further supported by an X-ray crystal structure of Pd(py)(κ1-DAF)OAc2. DFT computational studies illuminate the influence of three different chelating ligands [DAF, 6,6'-Me2bpy, and 2,9-dimethyl-1,10-phenanthroline (2,9-Me2phen)] on the energetics of the aza-Wacker reaction pathway. The results show that DAF and 6,6'-Me2bpy destabilize the corresponding ground-state Pd(N~N)(OAc)2 complexes, while stabilizing the rate-limiting transition state for alkene insertion into a Pd-N bond. Interconversion between κ2- and κ1-coordination modes facilitate access to open coordination sites at the PdII center. The insights from these studies introduce new ligand concepts that could promote numerous other classes of Pd-catalyzed aerobic oxidation reaction.

Structurally Diverse Diazafluorene-Ligated Palladium(II) Complexes and Their Implications for Aerobic Oxidation Reactions.

4,5-Diazafluoren-9-one (DAF) has been identified as a highly effective ligand in a number of Pd-catalyzed oxidation reactions, but the mechanistic basis for its utility has not been elucidated. Here, we present the complex coordination chemistry of DAF and palladium(II) carboxylate salts. Multiple complexes among an equilibrating mixture of species have been characterized by (1)H and (15)N NMR spectroscopy and X-ray crystallography. These complexes include monomeric and dimeric Pd(II) species, with monodentate (κ(1)), bidentate (κ(2)), and bridging (µ:κ(1):κ(1)) DAF coordination modes. Titration studies of DAF and Pd(OAc)2 reveal the formation of two dimeric DAF/Pd(OAc)2 complexes at low [DAF] and four monomeric species at higher [DAF]. The dimeric complexes feature two bridging acetate ligands together with either a bridging or nonbridging (κ(1)) DAF ligand coordinated to each Pd(II) center. The monomeric structures consist of three isomeric Pd(κ(1)-DAF)2(OAc)2 complexes, together with Pd(κ(2)-DAF)(OAc)2 in which the DAF exhibits a traditional bidentate coordination mode. Replacing DAF with the structurally related, but more-electron-rich derivative 9,9-dimethyl-4,5-diazafluorene (Me2DAF) simplifies the equilibrium mixture to two complexes: a dimeric species in which the Me2DAF bridges the two Pd centers and a monomeric species with a traditional κ(2)-Me2DAF coordination mode. The use of DAF in combination with other carboxylate ligands (CF3CO2(-) or tBuCO2(-)) also results in a simplified collection of equilibrating Pd(II)-DAF complexes. Collectively, the results highlight the ability of DAF to equilibrate rapidly among multiple coordination modes, and provide valuable insights into the utility of DAF as a ligand in Pd-catalyzed oxidation reactions.

De novo structure prediction and experimental characterization of folded peptoid oligomers.

Peptoid molecules are biomimetic oligomers that can fold into unique three-dimensional structures. As part of an effort to advance computational design of folded oligomers, we present blind-structure predictions for three peptoid sequences using a combination of Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement. We correctly predicted the structure of a N-aryl peptoid trimer to within 0.2 Å rmsd-backbone and a cyclic peptoid nonamer to an accuracy of 1.0 Å rmsd-backbone. X-ray crystallographic structures are presented for a linear N-alkyl peptoid trimer and for the cyclic peptoid nonamer. The peptoid macrocycle structure features a combination of cis and trans backbone amides, significant nonplanarity of the amide bonds, and a unique "basket" arrangement of (S)-N(1-phenylethyl) side chains encompassing a bound ethanol molecule. REMD simulations of the peptoid trimers reveal that well folded peptoids can exhibit funnel-like conformational free energy landscapes similar to those for ordered polypeptides. These results indicate that physical modeling can successfully perform de novo structure prediction for small peptoid molecules.

Hierarchical self-assembly of a biomimetic diblock copolypeptoid into homochiral superhelices.

The aqueous self-assembly of a sequence-specific bioinspired peptoid diblock copolymer into monodisperse superhelices is demonstrated to be the result of a hierarchical process, strongly dependent on the charging level of the molecule. The partially charged amphiphilic diblock copolypeptoid 30-mer, [N-(2-phenethyl)glycine](15)-[N-(2-carboxyethyl)glycine](15), forms superhelices in high yields, with diameters of 624 ± 69 nm and lengths ranging from 2 to 20 µm. Chemical analogs coupled with X-ray scattering and crystallography of a model compound have been used to develop a hierarchical model of self-assembly. Lamellar stacks roll up to form a supramolecular double helical structure with the internal ordering of the stacks being mediated by crystalline aromatic side chain-side chain interactions within the hydrophobic block. The role of electrostatic and hydrogen bonding interactions in the hydrophilic block is also investigated and found to be important in the self-assembly process.