Accurate Protein pKa Prediction with Physical Organic Chemistry Guided 3D Protein Representation.

Protein pKa is a fundamental physicochemical parameter that dictates protein structure and function. However, accurately determining protein site-pKa values remains a substantial challenge, both experimentally and theoretically. In this study, we introduce a physical organic approach, leveraging a protein structural and physical-organic-parameter-based representation (P-SPOC), to develop a rapid and intuitive model for protein pKa prediction. Our P-SPOC model achieves state-of-the-art predictive accuracy, with a mean absolute error (MAE) of 0.33 pKa units. Furthermore, we have incorporated advanced protein structure prediction models, like AlphaFold2, to approximate structures for proteins lacking three-dimensional representations, which enhances the applicability of our model in the context of structure-undetermined protein research. To promote broader accessibility within the research community, an online prediction interface was also established at isyn.luoszgroup.com.

Asymmetric C-H Dehydrogenative Alkenylation via a Photo-induced Chiral α­Imino Radical Intermediate.

The direct alkenylation with simple alkenes stands out as the most ideal yet challenging strategy for obtaining high-valued desaturated alkanes. Here we present a direct asymmetric dehydrogenative α-C(sp3)-H alkenylation of carbonyls based on synergistic photoredox-cobalt-chiral primary amine catalysis under visible light. The ternary catalytic system enables the direct coupling of ß-keto-carbonyls and alkenes through a cooperative radical addition-dehydrogenation process involving a chiral α-imino radical and Co(II)-metalloradical intermediate. A catalytic H-transfer process involving nitrobenzene is engaged to quench in situ generated cobalt hydride species, ensuring a chemoselective alkenylation in good yields and high enantioselectivities.

Enantioselective Transformations by "1 + x" Synergistic Catalysis with Chiral Primary Amines.

ConspectusSynergistic catalysis is a powerful tool that involves two or more distinctive catalytic systems to activate reaction partners simultaneously, thereby expanding the reactivity space of individual catalysis. As an established catalytic strategy, organocatalysis has found numerous applications in enantioselective transformations under rather mild conditions. Recently, the introduction of other catalytic systems has significantly expanded the reaction space of typical organocatalysis. In this regard, aminocatalysis is a prototypical example of synergistic catalysis. The combination of aminocatalyst and transition metal could be traced back to the early days of organocatalysis and has now been well explored as an enabling catalytic strategy. Particularly, the acid-base properties of aminocatalysis can be significantly expanded to include usually electrophiles generated in situ via metal-catalyzed cycles. Later on, aminocatalyst has also been exploited in synergistically combining with photochemical and electrochemical processes to facilitate redox transformations. However, synergistically combining one type of aminocatalyst with many different catalytic systems remains a great challenge. One of the most daunting challenges is the compatibility of aminocatalysts in coexistence with other catalytic species. As nucleophilic species, aminocatalysts may also bind with metal, which leads to mutual inhibition or even quenching of the individual catalytic activity. In addition, oxidative stability of aminocatalyst is also a non-neglectable issue, which causes difficulties in exploring oxidative enamine transformations.In 2007, we developed a vicinal diamine type of chiral primary aminocatalysts. This class of primary aminocatalysts was developed and evolved as functional and mechanistic mimics to the natural aldolase and has been widely applied in a number of enamine/iminium ion-based transformations. By following a "1 + x" synergistic strategy, the chiral primary amine catalysts were found to work synergistically or cooperatively with a number of transition metal catalysts, such as Pd, Rh, Ag, Co, and Cu, or other organocatalysts, such as B(C6F5)3, ketone, selenium, and iodide. Photocatalysis and electrochemical processes can also be incorporated to work together with the chiral primary amine catalysts. The 1 + x catalytic strategy enabled us to execute unexploited transformations by fine-tuning the acid-base and redox properties of the enamine intermediates and to achieve effective reaction and stereocontrol beyond the reach individually. During these efforts, an unprecedented excited-state chemistry of enamine was uncovered to make possible an effective deracemization process. In this Account, we describe our recent efforts since 2015 in exploring synergistic chiral primary amine catalysis, and the content is categorized according to the type of synergistic partner such that in each section the developed synergistic catalysis, reaction scopes, and mechanistic features are presented and discussed.

Phase-Transfer Catalysis for Electrochemical Chlorination and Nitration of Arenes.

A biphasic anodic oxidation method for aromatic halogenation process was developed, where aqueous metal salts were directly used as halogen source. Ammonium salts serve as both electrolytes and phase transfer catalysis to facilitate anion transport and oxidative transformation. This design allows for chlorination or nitration of multiple types of arenes using NaCl or KNO2.

Aerobic Asymmetric Allylic C-H Alkylation by Synergistic Chiral Primary Amine-Palladium-Hydroquinone Catalysis.

A synergistic chiral primary amine/palladium /p-hydroquinone catalysis was developed to facilitate oxidative asymmetric allylic C-H alkylation under aerobic conditions. The ternary synergistic catalysis enables a facile allylic C-H activation and alkylation with oxygen so that stoichiometric utilization of benzoquinone can be avoided. The identified optimal catalytic system allows for terminal addition to allyl arenes with α-branched ß-ketocarbonyls to afford allylic adducts bearing all-carbon quaternary centers with high regio- and enantioselectivity. This work provides new insights for further studies on the aerobically oxidative C-H alkylation reaction.

Catalytic Asymmetric Visible-Light de Mayo Reaction by ZrCl4-Chiral Phosphoric Acid Complex.

Catalytic asymmetric de Mayo reaction was achieved for the first time under visible light using asymmetric binary acid catalysis (ABC) involving zirconium chloride and chiral phosphoric acid (CPA). The chiral zirconium catalysis enables effective reactions over a broad range of 1,3-diketones and alkenes with up to >99% yield and 98% ee. The key chiral zirconium enolate was isolated and characterized to account for the observed catalysis and stereoselectivity.

Catalytic Deracemization Reactions.

Deracemization, which converts a racemate into its single enantiomer without separation of the intermediate, has gained renewed interest in asymmetric synthesis with its inherent atomic economy and high efficiency. However, this ideal process requires selective energy input and delicate reaction design to surmount the thermodynamical and kinetical constraints. With the rapid development of asymmetric catalysis, many catalytic strategies in concert with exogenous energy input have been exploited to facilitate this nonspontaneous enantioenrichment. In this perspective, we will discuss the basic ideas to accomplish catalytic deracemization, categorized by the three major exogenous energy sources including chemical (redox)-, photo- and mechanical energy from attrition. Emphasis will be given to the catalytic features and the underlying deracemization mechanism together with perspectives on future development.

Asymmetric α-allylic allenylation of ß-ketocarbonyls and aldehydes by synergistic Pd/chiral primary amine catalysis.

We herein describe an asymmetric α-allylic allenylation of ß-ketocarbonyls and aldehydes with 1,3-enynes. A synergistic chiral primary amine/Pd catalyst was identified to facilitate the utilization of 1,3-enynes as atom-economic and achiral allene precursors. The synergistic catalysis enables the construction of all-carbon quaternary centers-tethered allenes bearing non-adjacent 1,3-axial central stereogenic centers in high level of diastereo- and enantio-selectivity. By switching the configurations of ligands and aminocatalysts, diastereodivergence can be achieved and any of the four diastereoisomers can be accessed in high diastereo- and enantio- selectivity.

Prediction of Nucleophilicity and Electrophilicity Based on a Machine-Learning Approach.

Nucleophilicity and electrophilicity dictate the reactivity of polar organic reactions. In the past decades, Mayr et al. established a quantitative scale for nucleophilicity (N) and electrophilicity (E), which proved to be a useful tool for the rationalization of chemical reactivity. In this study, a holistic prediction model was developed through a machine-learning approach. rSPOC, an ensemble molecular representation with structural, physicochemical and solvent features, was developed for this purpose. With 1115 nucleophiles, 285 electrophiles, and 22 solvents, the dataset is currently the largest one for reactivity prediction. The rSPOC model trained with the Extra Trees algorithm showed high accuracy in predicting Mayr's N and E parameters with R2 of 0.92 and 0.93, MAE of 1.45 and 1.45, respectively. Furthermore, the practical applications of the model, for instance, nucleophilicity prediction of NADH, NADPH and a series of enamines showed potential in predicting molecules with unknown reactivity within seconds. An online prediction platform (http://isyn.luoszgroup.com/) was constructed based on the current model, which is available free to the scientific community.

Electrophotochemical Metal-Catalyzed Enantioselective Decarboxylative Cyanation.

In contrast to the rapid growth of electrophotocatalysis in recent years, enantioselective catalytic reactions powered by this unique methodology remain rare. In this work, we report an electrophotochemical metal-catalyzed protocol for direct asymmetric decarboxylative cyanation of aliphatic carboxylic acids. The synergistic merging of electrophotochemical cerium catalysis and asymmetric electrochemical copper catalysis permits mild reaction conditions for the formation and utilization of the key carbon centered radicals by combining the power of light and electrical energy. Electrophotochemical cerium catalysis enables radical decarboxylation to produce alkyl radicals, which could be effectively intercepted by asymmetric electrochemical copper catalysis for the construction of C-CN bonds in a highly stereoselective fashion. This environmentally benign method smoothly converts a diverse array of arylacetic acids into the corresponding alkyl nitriles in good yields and enantioselectivities without using chemical oxidants or pre-functionalization of the acid substrates and can be readily scaled up.

Visible-light promoted de Mayo reaction by zirconium catalysis.

Zirconium catalysis with ZrCl4 was developed to facilitate a de Mayo reaction under visible light conditions without any external photosensitizer and additive.

Chiral Primary Amine Catalyzed α-Arylation of Simple Ketones via Asymmetric Retro-Claisen Cleavage.

Highly enantioselective α-arylation of simple ketones has been achieved by chiral primary amine catalyzed asymmetric retro-Claisen cleavage of ß-diketones. This mild organocatalytic strategy enables the construction of α-aryl tertiary carbon stereocenters in good yields and excellent enantioselectivities (up to 98 % ee) with the para-quinone monoimines as aryl sources. Furthermore, oxidative catalytic asymmetric α-arylation has also been realized with free p-aminophenols.

Electrophotochemical Metal-Catalyzed Decarboxylative Coupling of Aliphatic Carboxylic Acids.

An electrophotochemical dual metal-catalyzed protocol for decarboxylative arylation of simple aliphatic carboxylic acids with aryl halides is reported. The relative stabilities of catalytically active metal complexes simultaneously generated at anode and cathode are the key design elements for the success of this convergent paired electrolysis. This new electrophotocatalytic method is mild, robust, and most importantly, capable of accommodating simple primary aliphatic acids including acetic acid - ubiquitous and variegated structural motifs yet remain oddly challenging substrates - directly as native functional groups for decarboxylative C(sp2 )-C(sp3 ) bond formation.

Catalytic Asymmetric α-Alkylsulfenylation with a Disulfide Reagent.

The use of alkylthio electrophiles in synthesis has remained elusive because of the lack of a suitable reagent that is practical and of excellent enantioselectivity and appropriate reactivity. In this work we introduce a novel alkylthio reagent based on the 2-mercapto-5-methyl-1,3,4-thiadiazole (MMTD) fragment for direct alkylsulfenylation of ketones and aldehydes. It can be readily prepared by the oxidative coupling between thiadiazole and other alkylthio reagents and be combined with chiral primary aminocatalysis. This protocol provides facile access to diverse α-alkylthio quaternary carbon centers with good stereoselectivities.

Asymmetric C-H Dehydrogenative Allylic Alkylation by Ternary Photoredox-Cobalt-Chiral Primary Amine Catalysis under Visible Light.

We report herein an asymmetric C-H dehydrogenative allylic alkylation by a synergistic catalytic system involving a chiral primary amine, a photoredox catalyst, and a cobaloxime cocatalyst. The ternary catalytic system enables the coupling of ß-ketocarbonyls and olefins with good yields and high enantioselectivities. Mechanism studies disclosed a cooperative radical addition process with a chiral α-imino radical and Co(II)-metalloradical wherein the chiral primary aminocatalyst and the cobaloxime catalyst work in concert to control the stereoinduction.

An Ensemble Structure and Physicochemical (SPOC) Descriptor for Machine-Learning Prediction of Chemical Reaction and Molecular Properties.

Feature representations, or descriptors, are machines' chemical language that largely shapes the prediction capability, generalizability and interpretability of machine learning models. To develop a generally applicable descriptor is highly warranted for chemists to deal with conventional prediction tasks in the context of sparsely distributed and small datasets. Inspired by the chemist's vision on molecules, we presented herein an ensemble descriptor, SPOC, curated on the principles of physical organic chemistry that integrates Structure and Physicochemical property (SPOC) of a molecule. SPOC could be readily constructed by combining molecular fingerprints, representing the structure of a given molecule, and molecular physicochemical properties extracted from RDKit or Mordred molecular descriptors. The applicability of SPOC was fully surveyed in a range of well-structured chemical databases with machine learning tasks varying from regression to classifications.

Bond Energies of Enamines.

Energetics of reactive intermediates underlies their reactivity. The availability of these data provides a rational basis for understanding and predicting a chemical reaction. We reported here a comprehensive computational study on the energetics of enamine intermediates that are fundamental in carbonyl chemistry. Accurate density functional theory (DFT) calculations were performed to determine the bond energies of enamines and their derived radical intermediates. These efforts led to the compilation of a database of enamine energetics including a thermodynamic index such as free-energy stability, bond dissociation energy (BDE), and acid dissociation constant (pK a) as well as a kinetic index such as nucleophilicity and electrophilicity. These data were validated by relating to experimentally determined parameters and their relevance and utility were discussed in the context of modern enamine catalysis. It was found that pK a values of enamine radical cations correlated well with redox potentials of their parent enamines, the former could be used to rationalize the proton-transfer behavior of enamine radical cations. An analysis of the BDE of enamine radical cations indicated that these species underwent facile ß-C-H hydrogen transfer, in line with the known oxidative enamine catalysis. The enamine energetics offers the possibility of a systematic evaluation of the reactivities of enamines and related radicals, which would provide useful guidance in exploring new enamine transformations.

Deracemization through photochemical E/Z isomerization of enamines.

Catalytic deracemization of α-branched aldehydes is a direct strategy to construct enantiopure α-tertiary carbonyls, which are essential to pharmaceutical applications. Here, we report a photochemical E/Z isomerization strategy for the deracemization of α-branched aldehydes by using simple aminocatalysts and readily available photosensitizers. A variety of racemic α-branched aldehydes could be directly transformed into either enantiomer with high selectivity. Rapid photodynamic E/Z isomerization and highly stereospecific iminium/enamine tautomerization are two key factors that underlie the enantioenrichment. This study presents a distinctive photochemical E/Z isomerization strategy for externally tuning enamine catalysis.

Highly Stereoselective Construction of ß,ß-Diaryl-α-Branched Ketones by the Chiral Primary Amine-Catalyzed Asymmetric Retro-Claisen Reaction.

Highly diastereo- and enantioselective retro-Claisen reaction of ß-diketones with o-quinone methides has been developed by chiral primary amine catalysis. This reaction allows for efficient synthesis of chiral ß,ß-diaryl-α-branched ketones in moderate to good yields with excellent stereoselectivities. The reaction occurs via a tandem sequence of benzylic C-C bond formation, C-C bond cleavage, and stereospecific enamine protonation. This strategy uses o-quinone methides as diaryl precursors and features a broad substrate scope, mild conditions, and a high degree of stereocontrol.

Bio-inspired lanthanum-ortho-quinone catalysis for aerobic alcohol oxidation: semi-quinone anionic radical as redox ligand.

Oxidation reactions are fundamental transformations in organic synthesis and chemical industry. With oxygen or air as terminal oxidant, aerobic oxidation catalysis provides the most sustainable and economic oxidation processes. Most aerobic oxidation catalysis employs redox metal as its active center. While nature provides non-redox metal strategy as in pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenases (MDH), such an effective chemical version is unknown. Inspired by the recently discovered rare earth metal-dependent enzyme Ln-MDH, here we show that an open-shell semi-quinone anionic radical species in complexing with lanthanum could serve as a very efficient aerobic oxidation catalyst under ambient conditions. In this catalyst, the lanthanum(III) ion serves only as a Lewis acid promoter and the redox process occurs exclusively on the semiquinone ligand. The catalysis is initiated by 1e--reduction of lanthanum-activated ortho-quinone to a semiquinone-lanthanum complex La(SQ-.)2, which undergoes a coupled O-H/C-H (PCHT: proton coupled hydride transfer) dehydrogenation for aerobic oxidation of alcohols with up to 330 h-1 TOF.