Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.

Improving Protein Expression, Stability, and Function with ProteinMPNN.

Natural proteins are highly optimized for function but are often difficult to produce at a scale suitable for biotechnological applications due to poor expression in heterologous systems, limited solubility, and sensitivity to temperature. Thus, a general method that improves the physical properties of native proteins while maintaining function could have wide utility for protein-based technologies. Here, we show that the deep neural network ProteinMPNN, together with evolutionary and structural information, provides a route to increasing protein expression, stability, and function. For both myoglobin and tobacco etch virus (TEV) protease, we generated designs with improved expression, elevated melting temperatures, and improved function. For TEV protease, we identified multiple designs with improved catalytic activity as compared to the parent sequence and previously reported TEV variants. Our approach should be broadly useful for improving the expression, stability, and function of biotechnologically important proteins.

Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site.

The catalytic versatility of pentacoordinated iron is highlighted by the broad range of natural and engineered activities of heme enzymes such as cytochrome P450s, which position a porphyrin cofactor coordinating a central iron atom below an open substrate binding pocket. This catalytic prowess has inspired efforts to design de novo helical bundle scaffolds that bind porphyrin cofactors. However, such designs lack the large open substrate binding pocket of P450s, and hence, the range of chemical transformations accessible is limited. Here, with the goal of combining the advantages of the P450 catalytic site geometry with the almost unlimited customizability of de novo protein design, we design a high-affinity heme-binding protein, dnHEM1, with an axial histidine ligand, a vacant coordination site for generating reactive intermediates, and a tunable distal pocket for substrate binding. A 1.6 Å X-ray crystal structure of dnHEM1 reveals excellent agreement to the design model with key features programmed as intended. The incorporation of distal pocket substitutions converted dnHEM1 into a proficient peroxidase with a stable neutral ferryl intermediate. In parallel, dnHEM1 was redesigned to generate enantiocomplementary carbene transferases for styrene cyclopropanation (up to 93% isolated yield, 5000 turnovers, 97:3 e.r.) by reconfiguring the distal pocket to accommodate calculated transition state models. Our approach now enables the custom design of enzymes containing cofactors adjacent to binding pockets with an almost unlimited variety of shapes and functionalities.

Selective ortho-Functionalization of Adamantylarenes Enabled by Dispersion and an Air-Stable Palladium(I) Dimer.

Contrary to the general belief that Pd-catalyzed cross-coupling at sites of severe steric hindrance are disfavored, we herein show that the oxidative addition to C-Br ortho to an adamantyl group is as favored as the corresponding adamantyl-free system due to attractive dispersion forces. This enabled the development of a fully selective arylation and alkylation of C-Br ortho to an adamantyl group, even if challenged with competing non-hindered C-OTf or C-Cl sites. The method makes use of an air-stable PdI dimer and enables straightforward access to diversely substituted therapeutically important adamantylarenes in 5-30 min.

Site-Selective, Modular Diversification of Polyhalogenated Aryl Fluorosulfates (ArOSO2 F) Enabled by an Air-Stable PdI Dimer.

Since 2014, the interest in aryl fluorosulfates (ArOSO2 F) as well as their implementation in powerful applications has continuously grown. In this context, the enabling capability of ArOSO2 F will strongly depend on the substitution pattern of the arene, which ultimately dictates its overall function as drug candidate, material, or bio-linker. This report showcases the modular, substrate-independent, and fully predictable, selective functionalization of polysubstituted arenes bearing C-OSO2 F, C-Br, and C-Cl sites, which makes it possible to diversify the arene in the presence of OSO2 F or utilize OSO2 F as a triflate surrogate. Sequential and triply selective arylations and alkylations were realized within minutes at room temperature, using a single and air-stable PdI dimer.

Direct α-alkylation of primary aliphatic amines enabled by CO2 and electrostatics.

Primary aliphatic amines are important building blocks in organic synthesis due to the presence of a synthetically versatile NH2 group. N-functionalization of primary amines is well established, but selective C-functionalization of unprotected primary amines remains challenging. Here, we report the use of CO2 as an activator for the direct transformation of abundant primary aliphatic amines into valuable γ-lactams under photoredox and hydrogen atom transfer (HAT) catalysis. Experimental and computational studies suggest that CO2 not only inhibits undesired N-alkylation of primary amines, but also promotes selective intermolecular HAT by an electrostatically accelerated interaction between the in situ-generated negatively charged carbamate and the positively charged quinuclidinium radical. This electrostatic attraction overwhelms the inherent bond dissociation energies which suggest that HAT should occur unselectively. We anticipate that our findings will open up new avenues for amine functionalizations as well as selectivity control in HAT reactions.

Divergent Reactivity of a Dinuclear (NHC)Nickel(I) Catalyst versus Nickel(0) Enables Chemoselective Trifluoromethylselenolation.

We herein showcase the ability of NHC-coordinated dinuclear NiI -NiI complexes to override fundamental reactivity limits of mononuclear (NHC)Ni0 catalysts in cross-couplings. This is demonstrated with the development of a chemoselective trifluoromethylselenolation of aryl iodides catalyzed by a NiI dimer. A novel SeCF3 -bridged NiI dimer was isolated and shown to selectively react with Ar-I bonds. Our computational and experimental reactivity data suggest dinuclear NiI catalysis to be operative. The corresponding Ni0 species, on the other hand, suffers from preferred reaction with the product, ArSeCF3 , over productive cross-coupling and is hence inactive.

Atropisomerism in Tertiary Biaryl 2-Amides: A Study of Ar-CO and Ar-Ar' Rotational Barriers.

A rotational barrier study was performed on eight tertiary biaryl 2-amides using variable-temperature (VT) NMR and exchange (EXSY) spectroscopy experiments. Seven out of the eight 2-amido-2'-methylbiphenyls with additional 3- and 6-substitution patterns (1-7) were found to have approximately similar rotational barriers (ΔG⧧Tc = 56.5-67.5 kJ/mol). However, for both 3- and 6-substitution (8), the rotational barrier was found to be significantly higher (ΔG⧧ = 102.6-103.8 kJ/mol). Computational studies performed on all eight compounds gave results in good agreement with the experimental rotational barriers. A transition state in which atropisomerism occurs by a cooperative rotation of the Ar-CO and Ar-Ar' bonds depending on substituent location is proposed.

Palladium(I) Dimer Enabled Extremely Rapid and Chemoselective Alkylation of Aryl Bromides over Triflates and Chlorides in Air.

Disclosed herein is the first general chemo- and site-selective alkylation of C-Br bonds in the presence of COTf, C-Cl and other potentially reactive functional groups, using the air-, moisture-, and thermally stable dinuclear PdI catalyst, [Pd(µ-I)PtBu3 ]2 . The bromo-selectivity is independent of the substrate and the relative positioning of the competing reaction sites, and as such fully predictable. Primary and secondary alkyl chains were introduced with extremely high speed (<5 min reaction time) at room temperature and under open-flask reaction conditions.

Mild and selective base-free C-H arylation of heteroarenes: experiment and computation.

A mild and selective C-H arylation strategy for indoles, benzofurans and benzothiophenes is described. The arylation method engages aryldiazonium salts as arylating reagents in equimolar amounts. The protocol is operationally simple, base free, moisture tolerant and air tolerant. It utilizes low palladium loadings (0.5 to 2.0 mol% Pd), short reaction times, green solvents (EtOAc/2-MeTHF or MeOH) and is carried out at room temperature, providing a broad substrate scope (47 examples) and excellent selectivity (C-2 arylation for indoles and benzofurans, C-3 arylation for benzothiophenes). Mechanistic experiments and DFT calculations support a Heck-Matsuda type coupling mechanism.

When Weaker Can Be Tougher: The Role of Oxidation State (I) in P- vs N-Ligand-Derived Ni-Catalyzed Trifluoromethylthiolation of Aryl Halides.

The direct introduction of the valuable SCF3 moiety into organic molecules has received considerable attention. While it can be achieved successfully for aryl chlorides under catalysis with Ni0(cod)2 and dppf, this report investigates the Ni-catalyzed functionalization of the seemingly more reactive aryl halides ArI and ArBr. Counterintuitively, the observed conversion triggered by dppf/Ni0 is ArCl > ArBr > ArI, at odds with bond strength preferences. By a combined computational and experimental approach, the origin of this was identified to be due to the formation of (dppf)NiI, which favors ß-F elimination as a competing pathway over the productive cross-coupling, ultimately generating the inactive complex (dppf)Ni(SCF2) as a catalysis dead end. The complexes (dppf)NiI-Br and (dppf)NiI-I were isolated and resolved by X-ray crystallography. Their formation was found to be consistent with a ligand-exchange-induced comproportionation mechanism. In stark contrast to these phosphine-derived Ni complexes, the corresponding nitrogen-ligand-derived species were found to be likely competent catalysts in oxidation state I. Our computational studies of N-ligand derived NiI complexes fully support productive NiI/NiIII catalysis, as the competing ß-F elimination is disfavored. Moreover, N-derived NiI complexes are predicted to be more reactive than their Ni0 counterparts in catalysis. These data showcase fundamentally different roles of NiI in carbon-heteroatom bond formation depending on the ligand sphere.

Rapid Room-Temperature, Chemoselective Csp2 -Csp2 Coupling of Poly(pseudo)halogenated Arenes Enabled by Palladium(I) Catalysis in Air.

While chemoselectivities in Pd0 -catalyzed coupling reactions are frequently non-intuitive and a result of a complex interplay of ligand/catalyst, substrate, and reaction conditions, we herein report a general method based on PdI that allows for an a priori predictable chemoselective Csp2 -Csp2 coupling at C-Br in preference to C-OTf and C-Cl bonds, regardless of the electronic or steric bias of the substrate. The C-C bond formations are extremely rapid (<5 min at RT) and are catalyzed by an air- and moisture-stable PdI dimer under open-flask conditions.

Lewis Acid Assisted Nickel-Catalyzed Cross-Coupling of Aryl Methyl Ethers by C-O Bond-Cleaving Alkylation: Prevention of Undesired ß-Hydride Elimination.

In the presence of trialkylaluminum reagents, diverse aryl methyl ethers can be transformed into valuable products by C-O bond-cleaving alkylation, for the first time without the limiting ß-hydride elimination. This new nickel-catalyzed dealkoxylative alkylation method enables powerful orthogonal synthetic strategies for the transformation of a variety of naturally occurring and easily accessible anisole derivatives. The directing and/or activating properties of aromatic methoxy groups are utilized first, before they are replaced by alkyl chains in a subsequent coupling process.

Nickel-catalyzed trifluoromethylthiolation of Csp2-O bonds.

While nickel catalysts have previously been shown to activate even the least reactive Csp2-O bonds, i.e. aryl ethers, in the context of C-C bond formation, little is known about the reactivity limits and molecular requirements for the introduction of valuable functional groups under homogeneous nickel catalysis. We identified that due to the high reactivity of Ni-catalysts, they are also prone to react with existing or installed functional groups, which ultimately causes catalyst deactivation. The scope of the Ni-catalyzed coupling protocol will therefore be dictated by the reactivity of the functional groups towards the catalyst. Herein, we showed that the application of computational tools allowed the identification of matching functional groups in terms of suitable leaving groups and tolerated functional groups. This allowed for the development of the first efficient protocol to trifluoromethylthiolate Csp2-O bonds, giving the mild and operationally simple C-SCF3 coupling of a range of aryl, vinyl triflates and nonaflates. The novel methodology was also applied to biologically active and pharmaceutical relevant targets, showcasing its robustness and wide applicability.

Trifluoromethylthiolation of aryl iodides and bromides enabled by a bench-stable and easy-to-recover dinuclear palladium(I) catalyst.

While palladium catalysis is ubiquitous in modern chemical research, the recovery of the active transition-metal complex under routine laboratory applications is frequently challenging. Described herein is the concept of alternative cross-coupling cycles with a more robust (air-, moisture-, and thermally-stable) dinuclear Pd(I) complex, thus avoiding the handling of sensitive Pd(0) species or ligands. Highly efficient C-SCF3 coupling of a range of aryl iodides and bromides was achieved, and the recovery of the Pd(I) complex was accomplished via simple open-atmosphere column chromatography. Kinetic and computational data support the feasibility of dinuclear Pd(I) catalysis. A novel SCF3-bridged Pd(I) dimer was isolated, characterized by X-ray crystallography, and verified to be a competent catalytic intermediate.

Fundamental studies and development of nickel-catalyzed trifluoromethylthiolation of aryl chlorides: active catalytic species and key roles of ligand and traceless MeCN additive revealed.

A catalytic protocol to convert aryl and heteroaryl chlorides to the corresponding trifluoromethyl sulfides is reported herein. It relies on a relatively inexpensive Ni(cod)2/dppf (cod = 1,5-cyclooctadiene; dppf = 1,1'-bis(diphenylphosphino)ferrocene) catalyst system and the readily accessible coupling reagent (Me4N)SCF3. Our computational and experimental mechanistic data are consistent with a Ni(0)/Ni(II) cycle and inconsistent with Ni(I) as the reactive species. The relevant intermediates were prepared, characterized by X-ray crystallography, and tested for their catalytic competence. This revealed that a monomeric tricoordinate Ni(I) complex is favored for dppf and Cl whose role was unambiguously assigned as being an off-cycle catalyst deactivation product. Only bidentate ligands with wide bite angles (e.g., dppf) are effective. These bulky ligands render the catalyst resting state as [(P-P)Ni(cod)]. The latter is more reactive than Ni(P-P)2, which was found to be the resting state for ligands with smaller bite angles and suffers from an initial high-energy dissociation of one ligand prior to oxidative addition, rendering the system unreactive. The key to effective catalysis is hence the presence of a labile auxiliary ligand in the catalyst resting state. For more challenging substrates, high conversions were achieved via the employment of MeCN as a traceless additive. Mechanistic data suggest that its beneficial role lies in decreasing the energetic span, therefore accelerating product formation. Finally, the methodology has been applied to synthetic targets of pharmaceutical relevance.

Kinetic and computational studies on Pd(I) dimer-mediated halogen exchange of aryl iodides.

Building on our previous discovery and reactivity explorations of the Pd(I) dimer [(PtBu3)PdBr]2-mediated halogen exchange of aryl iodides [Chem. Sci. 2013, 4, 4434], this report presents kinetic studies of this process, giving first-order kinetic dependence in the Pd(I) dimer and aryl iodide. An activation free energy barrier of ΔG(‡) = 24.9 ± 3.3 kcal/mol was experimentally determined. Extensive computational studies on the likely reaction pathway were subsequently carried out. A variety of DFT methods were assessed, ranging from dispersion-free methods to those that better account for dispersion (M06L, ωB97XD, D3-DFT). While significant discrepancies in the quantitative prediction of activation barriers were observed, all computational methods consistently predicted the analogous qualitative reactivity that is in agreement with all spectroscopic and reactivity data collected. Overall, these data provide compelling additional support of the direct reactivity of Pd(I)-Pd(I) with aryl iodides.