Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering.

The effective design of combinatorial libraries to balance fitness and diversity facilitates the engineering of useful enzyme functions, particularly those that are poorly characterized or unknown in biology. We introduce MODIFY, a machine learning (ML) algorithm that learns from natural protein sequences to infer evolutionarily plausible mutations and predict enzyme fitness. MODIFY co-optimizes predicted fitness and sequence diversity of starting libraries, prioritizing high-fitness variants while ensuring broad sequence coverage. In silico evaluation shows that MODIFY outperforms state-of-the-art unsupervised methods in zero-shot fitness prediction and enables ML-guided directed evolution with enhanced efficiency. Using MODIFY, we engineer generalist biocatalysts derived from a thermostable cytochrome c to achieve enantioselective C-B and C-Si bond formation via a new-to-nature carbene transfer mechanism, leading to biocatalysts six mutations away from previously developed enzymes while exhibiting superior or comparable activities. These results demonstrate MODIFY's potential in solving challenging enzyme engineering problems beyond the reach of classic directed evolution.

Synthesis of Z-gem-Cl,CF3-Substituted Alkenes by Stereoselective Cross-Metathesis and the Role of Disubstituted Mo Alkylidenes.

Stereochemically defined organofluorine compounds are central to drug discovery and development. Here, we present a catalytic cross-metathesis method for the synthesis of Z-trisubstituted olefins that contain a Cl- and a CF3-bound carbon terminus. Notably, the process is stereoselective, which is in contrast to the existing stereoretentive strategies that also involve a trisubstituted olefin as starting material. Reactions are catalyzed by a Mo monoaryloxide pyrrolide alkylidene, involve a trisubstituted alkene and gem-Cl,CF3-substituted alkene, and are fully Z-selective. Catalytic cross-coupling can be used to convert the C-Cl bond of the trisubstituted olefin to C-B, C-D, and different C-C bonds. We elucidate the role of Cl,CF3-disubstituted Mo alkylidenes. Experimental and computational (DFT) data show that in some instances a disubstituted alkylidene is formed and then transformed to a more active complex. In other cases, the Cl,CF3-disubstituted alkylidene is a direct participant in a catalytic cycle. The studies described shed new light on the chemistry of high oxidation-state disubstituted alkylidenes-scarcely investigated entities likely to be pivotal to approaches for stereocontrolled synthesis of tetrasubstituted alkenes through olefin metathesis.

Site-Selective Zn-Metalation in Poly-Triphenyl Amine-based Porous Organic Polymer for Solid-Gas Phase CO2 Photoreduction.

Harvesting solar energy to produce value-added chemicals from carbon dioxide (CO2) presents a promising route for addressing the complexities of sustainable energy systems and environmental issues. In this context, the development of metal-coordinated porous organic polymers (POPs) offers a vital avenue for improving the photocatalytic performance of organic motifs. The current study presents a metal-integrated photocatalytic system (namely, Zn@BP-POP) developed via a one-pot Friedel-Crafts (F.C.) acylation strategy, for solid-gas phase photochemical CO2 reduction to CO (CO2RR). The postsynthetic incorporation of metal (Zn) active sites on the host polymeric backbone of BP-POP significantly influences the catalytic activity. Notably, Zn@BP-POP demonstrates good photocatalytic performance in the absence of any cocatalyst and photosensitizer yielding CO while impeding the competitive hydrogen evolution reaction (HER) from water. The experimental findings collectively propose that the observed catalytic activity and selectivity arise from the synergistic interplay between the singular zinc catalytic centers and the light-harvesting capacity of the highly conjugated polymeric backbone. Further, X-ray absorption spectroscopy (XAS) analysis has significantly highlighted the prominent role played by the ZnN2O4 single sites in the polymeric framework for activating the gaseous CO2 molecules. Further, time-dependent density functional theory (DFT) analysis also reveals the thermodynamic feasibility of CO2RR over HER under optimized reaction conditions. This work cumulatively presents an effective strategy to demonstrate the importance of metal-active sites and effectively establish their structure-activity relationship during photocatalysis.

Stereoselective amino acid synthesis by photobiocatalytic oxidative coupling.

Photobiocatalysis-where light is used to expand the reactivity of an enzyme-has recently emerged as a powerful strategy to develop chemistries that are new to nature. These systems have shown potential in asymmetric radical reactions that have long eluded small-molecule catalysts1. So far, unnatural photobiocatalytic reactions are limited to overall reductive and redox-neutral processes2-9. Here we report photobiocatalytic asymmetric sp3-sp3 oxidative cross-coupling between organoboron reagents and amino acids. This reaction requires the cooperative use of engineered pyridoxal biocatalysts, photoredox catalysts and an oxidizing agent. We repurpose a family of pyridoxal-5'-phosphate-dependent enzymes, threonine aldolases10-12, for the α-C-H functionalization of glycine and α-branched amino acid substrates by a radical mechanism, giving rise to a range of α-tri- and tetrasubstituted non-canonical amino acids 13-15 possessing up to two contiguous stereocentres. Directed evolution of pyridoxal radical enzymes allowed primary and secondary radical precursors, including benzyl, allyl and alkylboron reagents, to be coupled in an enantio- and diastereocontrolled fashion. Cooperative photoredox-pyridoxal biocatalysis provides a platform for sp3-sp3 oxidative coupling16, permitting the stereoselective, intermolecular free-radical transformations that are unknown to chemistry or biology.

Controlling the regioselectivity of the bromolactonization reaction in HFIP.

The halolactonization reaction provides rapid access to densely functionalized lactones from unsaturated carboxylic acids. The endo/exo regioselectivity of this cyclization reaction is primarily determined by the electronic stabilization of alkene substituents, thus making it inherently dependent on substrate structures. Therefore this method often affords one type of halolactone regioisomer only. Herein, we introduce a simple and efficient method for regioselectivity-switchable bromolactonization reactions mediated by HFIP solvent. Two sets of reaction conditions were developed, each forming endo-products or exo-products in excellent regioselectivity. A combination of computational and experimental mechanistic studies not only confirmed the crucial role of HFIP, but also revealed the formation of endo-products under kinetic control and exo-products under thermodynamic control. This study paves the way for future work on the use of perfluorinated solvents to dictate reaction outcomes in organic synthesis.

CuH-Catalyzed Regio- and Enantioselective Formal Hydroformylation of Vinyl Arenes.

A highly enantioselective formal hydroformylation of vinyl arenes enabled by copper hydride (CuH) catalysis is reported. Key to the success of the method was the use of the mild Lewis acid zinc triflate to promote the formation of oxocarbenium electrophiles through the activation of diethoxymethyl acetate. Using the newly developed protocol, a broad range of vinyl arene substrates underwent efficient hydroacetalization reactions to provide access to highly enantioenriched α-aryl acetal products in good yields with exclusively branched regioselectivity. The acetal products could be converted to the corresponding aldehydes, alcohols, and amines with full preservation of the enantiomeric purity. Density functional theory studies support that the key C-C bond-forming event between the alkyl copper intermediate and the oxocarbenium electrophile takes place with inversion of configuration of the Cu-C bond in a backside SE2-type mechanism.

Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases.

Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases to catalyse unnatural photoredox radical C-C bond formation by leveraging the strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases to facilitate decarboxylative radical cyclization with excellent chemo-, enantio- and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of fatty acid photodecarboxylases. An orthogonal set of radical photocyclases was engineered to access all four possible stereoisomers of the stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved radical photocyclases allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclization. The development of stereoselective radical photocyclases provides unnatural C-C-bond-forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free-radical-mediated reactions.

A catalytic process enables efficient and programmable access to precisely altered indole alkaloid scaffolds.

A compound's overall contour impacts its ability to elicit biological response, rendering access to distinctly shaped molecules desirable. A natural product's framework can be modified, but only if it is abundant and contains suitably modifiable functional groups. Here we introduce a programmable strategy for concise synthesis of precisely altered scaffolds of scarce bridged polycyclic alkaloids. Central to our approach is a scalable catalytic multi-component process that delivers diastereo- and enantiomerically enriched tertiary homoallylic alcohols bearing differentiable alkenyl moieties. We used one product to launch progressively divergent syntheses of a naturally occurring alkaloid and its precisely expanded, contracted and/or distorted framework analogues (average number of steps/scaffold of seven). In vitro testing showed that a skeleton expanded by one methylene in two regions is cytotoxic against four types of cancer cell line. Mechanistic and computational studies offer an account for several unanticipated selectivity trends.

Pyrolysis Free Out-of-Plane Co-Single Atomic Sites in Porous Organic Photopolymer Stimulates Solar-Powered CO2 Fixation.

Herein, a facile strategy is illustrated to develop pyrolysis-free out-of-plane coordinated single atomic sites-based M-POP via a one-pot Friedel Craft acylation route followed by a post-synthetic metalation. The optimized geometry of the Co@BiPy-POP clearly reveals the presence of out-of-plane Co-single atomic sites in the porous backbone. This novel photopolymer Co@BiPy-POP shows extensive π-conjugations followed by impressive light harvesting ability and is utilized for photochemical CO2 fixation to value-added chemicals. A remarkable conversion of styrene epoxide (STE) to styrene carbonate (STC) (≈98%) is obtained under optimized photocatalytic conditions in the existence of promoter tert-butyl ammonium bromide (TBAB). Synchrotron-based X-ray adsorption spectroscopy (XAS) analysis reveals the single atom coordination sites along with the metal (Co) oxidation number of +2.16 in the porous network. Moreover, in situ diffuse reflectance spectroscopy (DRIFTS) and electron paramagnetic resonance (EPR) investigations provide valuable information on the evolution of key reaction intermediates. Comprehensivecomputational analysis also helps to understand the overall mechanistic pathway along with the interaction between the photocatalyst and reactants. Overall, this study presents a new concept of fabricating porous photopolymers based on a pyrolysis-free out-of-plane-coordination strategy and further explores the role of single atomic sites in carrying out feasible CO2 fixation reactions.

Moisture-Assisted Hydroboration of Nitriles and Conversion Thereof to N-Heterocyles and N-Containing Derivatives.

The recent revelation of hidden-borane catalysis has revolutionized the field of catalytic hydroboration in organic synthesis. Many nucleophilic reaction promoters, previously believed to be the catalysts, in fact primarily facilitated the formation of borane (BH3), which subsequently acted as the true catalyst. This revelation prompted us to explore the untapped potential of these unexpected transformations, with a view to simplify hydroboration using more cost-effective and environmentally friendly nucleophilic precatalysts. Via computational studies, we were able to identify that water can actually undertake that role. Herein, we report a study on the simple hydroboration of nitriles, a notoriously challenging yet synthetically valuable class of substrates, using nothing more than moisture as an activating agent. This moisture-assisted nitrile hydroboration process can seamlessly integrate with a range of downstream transformations in a one-pot fashion to produce valuable N-containing products such as symmetrical imines, thioureas, and bis(alcohol)amines as well as N-heterocycles such as pyrroles, pyridines, pyridinium salts, 2-iminothiazolines, and carbazoles.

Stereoselective Synthesis of Trisubstituted Alkenes via Copper Hydride-Catalyzed Alkyne Hydroalkylation.

Alkenes are ubiquitous in organic chemistry, yet many classes of alkenes remain challenging to access by current synthetic methodology. Herein, we report a copper hydride-catalyzed approach for the synthesis of Z-configured trisubstituted alkenes with high stereo- and regioselectivity via alkyne hydroalkylation. A DTBM-dppf-supported Cu catalyst was found to be optimal, providing a substantial increase in product yield compared to reactions conducted with dppf as the ligand. DFT calculations show that the DTBM substitution leads to the acceleration of alkyne hydrocupration through combined ground and transition state effects related to preventing catalyst dimerization and enhancing catalyst-substrate dispersion interactions, respectively. Alkyne hydroalkylation was successfully demonstrated with methyl and larger alkyl tosylate electrophiles to produce a variety of (hetero)aryl-substituted alkenes in moderate to high yields with complete selectivity for the Z stereochemically configured products. In the formation of the key C-C bond, computational studies revealed a direct SN2 pathway for alkylation of the vinylcopper intermediate with in situ-formed alkyl iodides.

Stereoselective amino acid synthesis by synergistic photoredox-pyridoxal radical biocatalysis.

Developing synthetically useful enzymatic reactions that are not known in biochemistry and organic chemistry is an important challenge in biocatalysis. Through the synergistic merger of photoredox catalysis and pyridoxal 5'-phosphate (PLP) biocatalysis, we developed a pyridoxal radical biocatalysis approach to prepare valuable noncanonical amino acids, including those bearing a stereochemical dyad or triad, without the need for protecting groups. Using engineered PLP enzymes, either enantiomeric product could be produced in a biocatalyst-controlled fashion. Synergistic photoredox-pyridoxal radical biocatalysis represents a powerful platform with which to discover previously unknown catalytic reactions and to tame radical intermediates for asymmetric catalysis.

Photochemically Driven Nickel-Catalyzed Carboxylative C-N Coupling: Scope and Mechanism.

Herein we disclosed an unprecedented photochemically driven nickel-catalyzed carboxylative Buchwald-Hartwig amination to access a wide range of aryl carbamate derivatives. This reaction is performed under mild condition of temperature and atmospheric pressure of CO2 starting from commercially available (hetero)aryl iodides/bromides derivatives and alkyl amines preventing the formation of hazardous and/or toxic waste. Moreover, preliminary mechanistic investigations including stochiometric experiments as well as DFT calculations allow us to shed light on the reaction mechanism.

Experimental Validation and Computational Predictions Join Forces to Map Catalytic C-H Activation in Ferrocene Metalated Porous Organic Polymers.

In recent times, a self-complementary balanced characteristic feature with the combination of both covalent bonds (structural stability) and open metal sites (single-site catalysis) introduced an advanced emerging functional nanoarchitecture termed metalated porous organic polymers (M-POPs). However, the development of M-POPs in view of the current interest in catalysis has been realized still in its infancy and remains a challenge for the years to come. In this work, we built benzothiazole-linked Fe-metalated porous organic polymer (Fc-Bz-POP) using ferrocene dicarboxaldehyde (FDC), 1,3,5-tris(4-aminophenyl) benzene (APB), and elemental sulfur (S8) via a template-free, multicomponent, cost-effective one-pot synthetic approach. This Fc-Bz-POP is endowed with unique features including an extended network unit, isolated active sites, and catalytic pocket with a possible local structure, in which convergent binding sites are positioned in such a way that substrate molecules can be held in close proximity. Prospective catalytic application of this Fc-Bz-POP has been explored in executing catalytic allylic "C-H" bond functionalization of cyclohexene (CHX) in water at room temperature. Catalytic screening results identified that a superior performance with a CHX conversion of 95% and a 2-cyclohexene-1-ol selectivity (COL) of 80.8% at 4 h and 25 °C temperature has been achieved over Fc-Bz-POP, thereby addressing previous shortcomings of the other conventional catalytic systems. Comprehensive characterization understanding with the aid of synchrotron-based extended X-ray absorption fine structure (EXAFS) analysis manifested that the Fe atom with an oxidation state of +2 in our Fc-Bz-POP catalytic system encompasses a sandwich structural environment with the two symmetrical eclipsed cyclopentadienyl (Cp) rings, featuring nearest-neighbor (NN) Fe-C (≈2.05 Å) intramolecular bonds, as validated by the Fe L3-edge EXAFS fitting result. Furthermore, in situ attenuated total reflection-infrared spectroscopy (ATR-IR) analysis data for liquid-phase oxidation of cyclohexene allow for the formulation of a molecular-level reaction mechanistic pathway with the involvement of specific reaction intermediates, which is initiated by the radical functionalization of the allyl hydrogen. A deep insight investigation from density functional theory (DFT) calculations unambiguously revealed that the dominant pathway from cyclohexene to 2-cyclohexene-1-ol is initiated by an allyl-H functionalization step accompanied by the formation of 2-cyclohexene-1-hydroperoxide species as the key reaction intermediate. Electronic properties obtained from DFT simulations via the charge density difference plot, Bader charge, and density of state (DOS) demonstrate the importance of the organic polymer frame structure in altering the electronic properties of the Fe site in Fc-Bz-POP, resulting in its high activity. Our contribution has great implications for the precise design of metalated porous organic polymer-based robust catalysts, which will open a new avenue to get a clear image of surface catalysis.

Catalytic Cross-Metathesis Reactions That Afford E- and Z-Trisubstituted Alkenyl Bromides: Scope, Applications, and Mechanistic Insights.

Stereochemically defined trisubstituted alkenes with a bromide and a methyl group at a terminus can be readily and stereoretentively derivatized through catalytic cross-coupling, affording unsaturated fragments found in many bioactive natural products. A direct method for generating such entities would be by stereocontrolled catalytic cross-metathesis (CM). Such methods are scarce however. Here, we present a stereoretentive strategy for CM between tri-, Z- or E-di, or monosubstituted olefins and Z- or E-2-bromo-2-butene, affording an assortment of E- or Z-trisubstituted alkenyl bromides. The majority of the transformations were catalyzed by two Mo monoaryloxide pyrrolide (MAP) complexes, one purchasable and the other accessible by well-established protocols. Substrates, such as feedstock trisubstituted olefins, can be purchased; the alkenyl bromide reagents are commercially available or can be prepared in two steps in a multigram scale. The catalytic process can be used to generate products that contain polar moieties, such as an amine or an alcohol, or sterically hindered alkenes that are α- or ß-branched. The utility of the approach is highlighted by a brief and stereocontrolled synthesis of an unsaturated fragment of phomactin A and a concise total synthesis of ambrein. An unexpected outcome of these investigations was the discovery of a new role for the presence of a small-molecule alkene in an olefin metathesis reaction. DFT studies indicate that this additive swiftly reacts with a short-lived Mo alkylidene and probably helps circumvent the formation of catalytically inactive square pyramidal metallacyclobutanes, enhancing the efficiency of a transformation.

Correction: Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches.

Correction for 'Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches' by Son Tung Ngo et al., Phys. Chem. Chem. Phys., 2022, https://doi.org/10.1039/d2cp04476e.

Enantioselective Synthesis of Quaternary Oxindoles: Desymmetrizing Staudinger-Aza-Wittig Reaction Enabled by a Bespoke HypPhos Oxide Catalyst.

This paper describes a catalytic asymmetric Staudinger-aza-Wittig reaction of (o-azidoaryl)malonates, allowing access to chiral quaternary oxindoles through phosphine oxide catalysis. We designed a novel HypPhos oxide catalyst to enable the desymmetrizing Staudinger-aza-Wittig reaction through the PIII/PV═O redox cycle in the presence of a silane reductant and an IrI-based Lewis acid. The reaction occurs under mild conditions, with good functional group tolerance, a wide substrate scope, and excellent enantioselectivity. Density functional theory revealed that the enantioselectivity in the desymmetrizing reaction arose from the cooperative effects of the IrI species and the HypPhos catalyst. The utility of this methodology is demonstrated by the (formal) syntheses of seven alkaloid targets: (-)-gliocladin C, (-)-coerulescine, (-)-horsfiline, (+)-deoxyeseroline, (+)-esermethole, (+)-physostigmine, and (+)-physovenine.

Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches.

Computational approaches, including physics- and knowledge-based methods, have commonly been used to determine the ligand-binding affinity toward SARS-CoV-2 main protease (Mpro or 3CLpro). Strong binding ligands can thus be suggested as potential inhibitors for blocking the biological activity of the protease. In this context, this paper aims to provide a short review of computational approaches that have recently been applied in the search for inhibitor candidates of Mpro. In particular, molecular docking and molecular dynamics (MD) simulations are usually combined to predict the binding affinity of thousands of compounds. Quantitative structure-activity relationship (QSAR) is the least computationally demanding and therefore can be used for large chemical collections of ligands. However, its accuracy may not be high. Moreover, the quantum mechanics/molecular mechanics (QM/MM) method is most commonly used for covalently binding inhibitors, which also play an important role in inhibiting the activity of SARS-CoV-2. Furthermore, machine learning (ML) models can significantly increase the searching space of ligands with high accuracy for binding affinity prediction. Physical insights into the binding process can then be confirmed via physics-based calculations. Integration of ML models into computational chemistry provides many more benefits and can lead to new therapies sooner.

Diastereo- and enantioselective synthesis of compounds with a trifluoromethyl- and fluoro-substituted carbon centre.

Molecules that contain one or more fluorine atoms are crucial to drug discovery. There are protocols available for the selective synthesis of different organofluorine compounds, including those with a fluoro-substituted or a trifluoromethyl-substituted stereogenic carbon centre. However, approaches for synthesizing compounds with a trifluoromethyl- and fluoro-substituent stereogenic carbon centre are far less common. This potentially impactful set of molecules thus remains severely underdeveloped. Here we introduce a catalytic regio-, diastereo- and enantioselective strategy for the preparation of homoallylic alcohols bearing a stereogenic carbon centre bound to a trifluoromethyl group and a fluorine atom. The process, which involves a polyfluoroallyl boronate and is catalysed by an in situ-formed organozinc complex, can be used for diastereodivergent preparation of tetrafluoro-monosaccharides, including ribose core analogues of the antiviral drug sofosbuvir (Sovaldi). Unexpected reactivity/selectivity profiles, probably originating from the trifluoromethyl- and fluoro-substituted carbon site, are discovered, foreshadowing other unique chemistries that remain unknown.

Kinetic, ESI-CID-MS and Computational Studies of π-Allyliridium C,O-Benzoate-Catalyzed Allylic Amination: Understanding the Effect of Cesium Ion.

The mechanism of π-allyliridium C,O-benzoate-catalyzed allylic amination was studied by (a) reaction progress kinetic analysis (RPKA), (b) tandem ESI-MS analysis, and (c) computational studies involving density functional theory (DFT) calculations. Reaction progress kinetic analysis (RPKA) reveals a zero-order dependence on allyl acetate, first-order dependence on catalyst and fractional-order dependence on amine. These data corroborate rapid ionization of the allylic acetate followed by turnover limiting C-N bond formation. To illuminate the origins of the 0.4 kinetic order dependence on amine, ESI-MS analyses of quaternary ammonium-labelled piperazine with multistage collision induced dissociation (CID) were conducted that corroborate intervention of cesium-bridged amine dimers that dissociate to form monomeric cesium amide nucleophiles. Computational data align with RPKA and ESI-CID-MS analyses and suggest early transition states mitigate the impact of steric factors, thus enabling formation of highly substituted C-N bonds with complete levels of branched regioselectivity. Specifically, trans-effects of the iridium complex facilitate nucleophilic attack at the more substituted allyl terminus trans to phosphorus with enantioselectivity governed by steric repulsions between the chiral bisphosphine ligand and the π-allyl of a dominant diastereomer of the stereogenic-at-metal complex. Beyond defining aspects of the mechanism of π-allyliridium C,O-benzoate-catalyzed allylic amination, these data reveal that a key feature of cesium carbonate not only lies in its enhanced basicity, but also its capacity for Lewis-acid enhanced Brønsted acidification of amines.