Oxyanion Hole Stabilization by C–H···O Interaction in a Transition State—A Three-Point Interaction Model for Cinchona Alkaloid-Catalyzed Asymmetric Methanolysis of meso-Cyclic Anhydrides

Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions

Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.

Interaction of low-energy electrons with radiosensitizers

We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.

The Role of Aromatic Alcohol Additives on Asymmetric Organocatalysis Reactions: Insights from Theory

The presence of an aromatic additive has been seen to enhance, often significantly, the enantioselectivity and yield in asymmetric organocatalysis. Considering their success across a dizzying range of organocatalysts and organic transformations, it would seem unlikely that a common principle exists for their functioning. However, the current investigations with DFT suggest a general principle: the phenolic additive sandwiches itself, through hydrogen bonding and π⋅⋅⋅π stacking, between the organocatalyst coordinated electrophile and nucleophile. This is seen for a wide range of experimentally reported systems. That such complex formation leads to enhanced stereoselectivity is then demonstrated for two cases: the cinchona alkaloid complex (BzCPD), catalysing thiocyanation (2-naphthol additive employed), as well as for L-pipecolicacid catalysing the asymmetric nitroaldol reaction with a range of nitro-substituted phenol additives. These findings, indicating that dual catalysis takes place when phenolic additives are employed, are likely to have a significant impact on the field of asymmetric organocatalysis.

Trialkylphosphonium Oxoborate as C(sp3 )-H Oxyanion Hole Catalyst for Diels-Alder Reaction

We have developed a catalytic protocol for Diels-Alder reaction using trialkylphosphonium oxoborates as oxyanion hole catalysts. The reaction can be operated under ambient conditions. Dienes could easily polymerize under acidic condition. Nonetheless, these acid-sensitive substrates are compatible with the catalytic protocol and the reaction scope covers a wide range of substrates.

Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii

The depolymerization of lignocellulosic biomass is facilitated by feruloyl esterases (FAEs), which hydrolyze ester bonds between lignin and polysaccharides. Fungal FAEs belonging to subfamily (SF) 6 release precursors such as ferulic acid derivatives, attractive for biochemical production. Among these, Aspergillus sydowii FAE (AsFaeE), an SF6 FAE, exhibits remarkable activity across various substrates. In this study, we conducted X-ray crystallography and kinetic analysis to unravel the molecular mechanisms governing substrate recognition and catalysis by AsFaeE. AsFaeE exhibits a typical α/β-hydrolase fold, characterized by a catalytic triad of serine, aspartate, and histidine. Comparative analysis of substrate-free, ferulic acid-bound, and sinapic acid-bound forms of AsFaeE suggests a conformational change in the loop covering the substrate-binding pocket upon binding. Notably, Pro158 and Phe159 within this loop cover the phenolic part of the substrate, forming three layers of planar rings. Our structure-based functional mutagenesis clarifies the roles of the residues involved in substrate binding and catalytic activity. Furthermore, distinct substrate-binding mechanisms between AsFaeE and other studied FAEs are identified. This investigation offers the initial structural insights into substrate recognition by SF6 FAEs, equipping us with structural knowledge that might facilitate the design of FAE variants capable of efficiently processing a wider range of substrate sizes.

Halogen bond catalysis of the [4+2] cycloaddition reaction of 2-alkenylindoles: catalytic modes and stereoselectivity

Halogen bond donor catalysts have been widely used in organic reactions because they are environmentally friendly, inexpensive and recyclable. The [4+2] cycloaddition reaction is a key reaction in organic synthesis because of its ease of use, fast speed, and wide range of applications. In this work, halogen bond catalysis in the [4+2] cycloaddition reaction between 2-alkenylindoles was investigated based on DFT calculations. There are two modes of I⋯π halogen bond catalysis: either on the ethenyl of 2-alkenylindole (mode A) or on the five-membered ring of 2-alkenylindole (mode B). Both modes involve two steps: the formation of carbon-carbon bonds and the formation of six-membered rings. Gibbs free energy barriers were determined to investigate the stereoselectivity of the endo pathway and exo pathway. For mode A, the exo products were more easily generated when the substituent R = H, and the N-H⋯π interaction promoted high endo selectivity in the case of the substituent R = Ph. For mode B, an increasing proportion of endo products can be obtained in the order of catalyst I2, IBr and ICl. The π⋯π interaction of the substituent R = Ph promotes the [4+2] cycloaddition reaction, which is consistent with the experimental observation that R = Ph has a higher yield than R = H. The study of different catalytic modes and stereoselectivity would provide new ideas for the further study of the [4+2] cycloaddition reaction.

Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5'-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.

Trialkylphosphonium oxoborates as C(sp3)-H oxyanion holes and their application in catalytic chemoselective acetalization

The use of trialkylphosphonium oxoborates (TOB) as catalysts is reported. The site-isolated borate counter anion in a TOB catalyst increases the availability of C(sp3)-H to interact with electron donor substrates. The catalytic protocol is applicable to a wide range of substrates in the acetalization reaction and provides excellent chemoselectivity in the acetalization over thioacetalization in the presence of alcohols and thiols, which is otherwise hard to achieve using typical acid catalysts. Experimental and computational studies revealed that the TOB catalysts have multiple preorganized C(sp3)-Hs that serve as a mimic of oxyanion holes, which can stabilize the oxyanion intermediates via multiple C(sp3)-H non-classical hydrogen bond interactions.

Molecular, biochemical, and toxicological characterization of two acetylcholinesterases from the Western flower thrips, Frankliniella occidentalis

We investigated the molecular and biochemical properties of two acetylcholinesterases (FoAChE1 and FoAChE2) from the Western flower thrips, Frankliniella occidentalis. Polyacrylamide gel electrophoresis and western blotting confirmed the membrane-anchored nature of both FoAChE1 and FoAChE2, which was further supported by hydrophobicity and glycophosphatidylinositol anchor predictions. High expression levels of both enzymes were observed in the head, indicating their predominant distribution in neuronal tissues. FoAChE1 exhibited significantly higher expression levels in all examined tissues compared to FoAChE2, suggesting its major role as a synaptic enzyme. Nonetheless, both recombinant enzymes displayed robust catalytic activity toward acetylthiocholine iodide, and FoAChE1 demonstrated nearly identical catalytic efficiency compared to FoAChE2. FoAChE1 exhibited slightly lower sensitivities to the cholinesterase inhibitors tested, including organophosphates (OPs) and carbamates (CBs), compared to FoAChE2. Field populations of F. occidentalis exhibited polymorphism of alanine vs. serine at position 197 of FoAChE1 within the conserved oxyanion hole. Contrary to common belief, however, functional analysis using recombinant enzymes revealed that neither A197 nor S197 residue was associated with FoAChE1 insensitivity to OPs and CBs. FoAChE2 did not exhibit any polymorphic amino acid substitutions at the positions known to be associated with resistance. Due to the absence of apparent resistance-associated mutations in field populations of F. occidentalis, the judicious use of some OPs or CBs can be suggested for controlling the highly resistant populations to other insecticides. Overall, our findings highlight the significance of both FoAChE1 and FoAChE2 as targets for toxicity assessment, while the specific contribution of each enzyme to toxicity remains unclear.

Mechanisms and Stereoselectivities in the NHC-Catalyzed [4 + 2] Annulation of 2-Bromoenal and 6-Methyluracil-5-carbaldehyde

To disclose the reaction mechanism and selectivity in the NHC-catalyzed reaction of 2-bromoenal and 6-methyluracil-5-carbaldehyde, a systematic computational study has been performed. According to DFT computations, the catalytic cycle is divided into eight elementary steps: nucleophilic attack of the NHC on 2-bromoenal, 1,2-proton transfer, C-Br bond dissociation, 1,3-proton transfer, addition to 6-methyluracil-5-carbaldehyde, [2 + 2] cycloaddition, NHC dissociation, and decarboxylation. The Bronsted acid DABCO·H+ plays a crucial role in proton transfer and decarboxylation steps. The addition to 6-methyluracil-5-carbaldehyde determines both chemoselectivity and stereoselectivity, leading to R-configured carbocycle-fused uracil, in agreement with experimental results. NCI analysis indicates that the CH···N, CH···π, and LP···π interactions should be the key factor for determining the stereoselectivity. ELF analysis shows the main role of the NHC in promoting C-Br bond dissociation. The mechanistic insights obtained in the present work may guide the rational design of potential NHC catalysts.

Investigation of amino acids related to Staphylococcus saprophyticus AG1 EstAG1 carboxylesterase catalytic function revealed a new family of bacterial lipolytic enzymes

Most of the lipolytic enzymes (carboxylesterases, EC 3.1.1.1 and triacylglycerol acylhydrolases, EC 3.1.1.3) originate from bacteria and form a large group of functionally important enzymes that are also well known for their use in multiple biotechnology sectors. Rapid and increasing amount of bacterial lipolytic enzymes being discovered and characterized led to a necessity to classify them. More than twenty years ago bacterial lipolytic enzymes were originally classified into eight families and six true lipase sub-families based on the differences in their amino acid sequences and biochemical properties. Later, this classification was comprehensively updated to 19 families with eight subfamilies, and more recently, employing deeper comparative analysis methods, classification expanded to 35 families and 11 subfamilies. Bacterial lipolytic enzymes that cannot be classified into currently existing families are still being discovered. This work provides site-directed mutagenesis and differential scanning fluorimetry based investigation of catalytic function-related amino acids of previously discovered and characterized EstAG1 carboxylesterase from Staphylococcus saprophyticus AG1. Experimental results obtained in this work revealed that EstAG1 carboxylesterase can be placed into a new family of bacterial lipolytic enzymes.

Unusually Large Effects of Charge-assisted C-H⋅⋅⋅F Hydrogen Bonds to Anionic Fluorine in Organic Solvents: Computational Study of 19 F NMR Shifts versus Thermochemistry

A comparison of computed ¹⁹ F NMR chemical shifts and experiment provides evidence for large specific solvent effects for fluoride-type anions interacting with the σ*(C-H) orbitals in organic solvents like MeCN or CH₂ Cl₂ . We show this for systems ranging from the fluoride ion and the bifluoride ion [FHF]^- to polyhalogen anions [ClF_x ]^- . Discrepancies between computed and experimental shifts when using continuum solvent models like COSMO or force-field-based descriptions like the 3D-RISM-SCF model show specific orbital interactions that require a quantum-mechanical treatment of the solvent molecules. This is confirmed by orbital analyses of the shielding constants, while less negatively charged fluorine atoms (e. g., in [EF₄ ]^- ) do not require such quantum-mechanical treatments to achieve reasonable accuracy. The larger ¹⁹ F solvent shift of fluoride in MeCN compared to water is due to the larger coordination number in the former. These observations are due to unusually strong charge-assisted C-H⋅⋅⋅F^- hydrogen bonds, which manifest beyond some threshold negative natural charge on fluorine of ca. < -0.6 e. The interactions are accompanied by sizable free energies of solvation, in the order F^- ≫[FHF]^- >[ClF₂ ]^- >[ClF₄ ]^- . COSMO-RS solvation free energies tend to moderately underestimate those from the micro-solvated cluster treatment. Red-shifted and intense vibrational C-H stretching bands, potentially accessible in bulk solution, are further spectroscopic finger prints.

Electrostatic vs. inductive effects in phosphine ligand donor properties and reactivity

Enhanced rates and selectivity in enzymes are enabled in part by precisely tuned electric fields within active sites. Analogously, the use of charged groups to leverage electrostatics in molecular systems is a promising strategy to tune reactivity. However, separation of the through space and through bond effects of charged functional groups is a long standing challenge that limits the rational application of electric fields in molecular systems. To address this challenge we developed a method using the phosphorus selenium coupling value (J _P-Se) of anionic phosphine selenides to quantify the electrostatic contribution of the borate moiety to donor strength. In this analysis we report the synthesis of a novel anionic phosphine, PPh₂CH₂BF₃K, the corresponding tetraphenyl phosphonium and tetraethyl ammonium selenides [PPh₄][SePPh₂CH₂BF₃] and [TEA][SePPh₂CH₂BF₃], and the Rh carbonyl complex [PPh₄][Rh(acac)(CO)(PPh₂(CH₂BF₃))]. Solvent-dependent changes in J _P-Se were fit using Coulomb's law and support up to an 80% electrostatic contribution to the increase in donor strength of [PPh₄][SePPh₂CH₂BF₃] relative to SePPh₂Et, while controls with [TEA][SePPh₂CH₂BF₃] exclude convoluting ion pairing effects. Calculations using explicit solvation or point charges effectively replicate the experimental data. This J _P-Se method was extended to [PPh₄][SePPh₂(2-BF₃Ph)] and likewise estimates up to a 70% electrostatic contribution to the increase in donor strength relative to SePPh₃. The use of PPh₂CH₂BF₃K also accelerates C-F oxidative addition reactivity with Ni(COD)₂ by an order of magnitude in comparison to the comparatively donating neutral phosphines PEt₃ and PCy₃. This enhanced reactivity prompted the investigation of catalytic fluoroarene C-F borylation, with improved yields observed for less fluorinated arenes. These results demonstrate that covalently bound charged functionalities can exert a significant electrostatic influence under common solution phase reaction conditions and experimentally validate theoretical predictions regarding electrostatic effects in reactivity.

Atropselective synthesis of N-aryl pyridones via dynamic kinetic resolution enabled by non-covalent interactions

The dynamic kinetic resolution of C-N atropisomeric pyridones was achieved via asymmetric phase-transfer catalysis, exploiting a rotational barrier-lowering hydrogen bond in the starting materials. X-ray and NMR experiments revealed the presence of a barrier-raising ground state CH⋯π interaction in the product, supported by DFT calculations. A co-crystal of the quinidine-derived phase-transfer catalyst and substrate reveals key substrate-catalyst non-covalent interactions.

Cinchona alkaloid derivative modified Fe3O4 nanoparticles for enantioselective ring opening of meso-cyclic anhydrides

Making magnetic achiral surfaces chiral for asymmetric catalysis! Enantioselective meso-cyclic anhydride ring opening is demonstrated on the surface of modified-quinidine capped Fe3O4 nanoparticles.

A DFT study of NHC-catalyzed reactions between 2-bromo-2-enals and acylhydrazones: mechanisms, and chemo- and stereoselectivities

The reaction mechanisms and origins of the chemo- and stereoselectivities of NHC-catalyzed [4 + 2] annulation of 2-bromo-2-enals and acylhydrazones.

Catalytic asymmetric synthesis of α-stereogenic carboxylic acids: recent advances

Chiral carboxylic acids bearing an α-stereogenic center constitute the backbone of many natural products and therapeutic reagents as well as privileged chiral ligands and catalysts. Hence, it is not surprising that a large number of elegant catalytic asymmetric strategies have been developed toward the efficient synthesis of α-chiral carboxylic acids, such as α-hydroxy acids and α-amino acids. In this review, the recent advances in asymmetric synthesis of α-stereogenic free carboxylic acids via organocatalysis and transition metal catalysis are summarized (mainly from 2010 to 2020). The content is organized by the reaction type of the carboxyl source involved, including asymmetric functionalization of substituted carboxylic acids, cyclic anhydrides, α-keto acids, substituted α,β-unsaturated acids and so on. We hope that this review will motivate further interest in catalytic asymmetric synthesis of chiral α-substituted carboxylic acids.

Exploring the Effects of Water on the Mechanism of the Catalyst-Free Reaction between Isatin and 3-Methyl-2-pyrazolin-5-one from the Mixed Implicit/Explicit Multiple Types of Water Clusters

Density functional theory calculations with implicit/explicit water cluster models were conducted to pursue deeper understandings about the mechanism and the water effects in the reaction of isatin with 3-methyl-2-pyrazolin-5-one. The proposed preferential mechanistic scenario here undergoes three major steps: first, 3-methyl-2-pyrazolin-5-one converts to its enol form and then, the aldol addition reaction takes place between isatin and enol to generate the intermediate INT2, followed finally by the tautomerization of INT2 to become the product 3-pyrazolone. The computed results indicate that the direct aldol reaction without the water auxiliary is feasible in the second step and the remaining tautomerization steps (steps 1, 3, and 4) assisted by tri-, tri-, and six-water cluster models, respectively, are the most favorable cases. It is further noted that more hydrogen bonding interactions in the tri-water auxiliary reaction are essential for the reduction of the free energy barrier ΔG^⧧ in the proton transfer largely than those assisted by the other types of water cluster models. The origin of the more stable transition state in the rate-determining step of the tri-water cluster model is ascribed to smaller cyclic strain and more global electron density transfer associated to its structure than the other types of water cluster models.

Plausible Pnicogen Bonding of epi-Cinchonidine as a Chiral Scaffold in Catalysis

As a non-covalent interaction of a chiral scaffold in catalysis, pnicogen bonding of epi-cinchonidine (epi-CD), a cinchona alkaloid, was simulated to consider whether the interaction can have the potential controlling enantiotopic face like hydrogen bonding. Among five reactive functional groups in epi-CD, two stable complexes of the hydroxyl group (X-epi-CD1) at C₁₇ and of the quinoline ring (X-epi-CD2) at N₁₆ with pnictide family analytes [X = substituted phosphine (PX), i.e., F, Br, Cl, CF₃, CN, HO, NO₂, and CH₃, and pnictide family analytes, i.e., PBr₃, BiI₃, SbI₃, and AsI₃] were predicted with intermolecular interaction energies, charge transfer (Q_Mulliken and Q_NBO), and band gap energies of HOMO-LUMO (Eg) at the B3LYP/6-31G(d,p) level of density functional theory. It was found that the dominant site of pnicogen bonding in epi-CD is the quinoline ring (N₁₆ atom) rather than the hydroxyl group (O₃₆ atom). In addition, the UV-Vis spectra of the complex were calculated by time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level and compared with experimental measurements. Through these calculations, two intermolecular interactions (H-bond vs. pnicogen bond) of epi-CD were compared.

Making Waxy Salts in Water: Synthetic Control of Hydrophobicity for Anion-Induced and Aggregation-Enhanced Light Emission

We show that multipodal polycationic receptors function as anion-responsive light-emitters in water. Prevailing paradigms utilize rigid holes and cavities for ion recognition. We instead built open amphiphilic scaffolds that trigger polar-to-nonpolar environment transitions around cationic fluorophores upon anion complexation. This ion-pairing and aggregation event produces a dramatic enhancement in the emission intensity, as demonstrated by perchlorate as a non-spherical hydrophobic anion model. A synergetic interplay of C-H⋅⋅⋅anion hydrogen bonding and tight anion-π⁺ contacts underpins this supramolecular phenomenon. By changing the aliphatic chain length, we demonstrate that the response profile and threshold of this signaling event can be controlled at the molecular level. With appropriate molecular design, inherently weak, ill-defined, and non-directional van der Waals interaction enables selective, sensitive, and tunable recognition in water.

Mechanism and regio- and stereoselectivity in an NHC-catalyzed Mannich/lactamization domino reaction

Density functional theory (DFT) calculations (M06-2X) have been employed to disclose the mechanisms and regio- and stereo-selectivities of the N-heterocyclic carbene (NHC)-catalyzed reaction of 2-benzothiazolimines and α-chloroaldehydes. The preferred mechanism is initiated by the nucleophilic attack of NHC on α-chloroaldehyde (first step), followed by 1,2-proton transfer which was assisted by the Brønsted acid DABCO·H+ to generate the Breslow intermediate (second step). The cleavage of the C-Cl bond (third step) and deprotonation (fourth step) form the enolate intermediate. This further reacts with 2-benzothiazolimine which leads to the formation of a new C-C bond (fifth step). Subsequent cyclization takes place via the formation of a new C-N bond (sixth step). Catalyst regeneration completes the whole catalytic cycle and affords the final product (seventh step). The DFT results indicate that the fifth step determines the stereochemistry of the reaction and leads to benzothiazolopyrimidinone with the SS configuration, which agrees well with experimental observations. Intramolecular cyclization is found to be the regioselectivity-determining step, for which the [4+2] annulation pathway is more preferred than that via [2+2] annulation, which again agrees well with experimental observations. Based on the mechanism proposed, the origins of regio- and stereoselectivities have also been investigated by performing distortion/interaction, natural bond orbital (NBO) and non-covalent interaction (NCI) analyses. The mechanistic insights gained in this work should be helpful in the rational design of potential catalysts for analogous reactions.

Enantioselective synthesis of chiral tetrasubstituted allenes: harnessing electrostatic and noncovalent interactions in a bifunctional activation model for N-triflylphosphoramide catalysis

DFT calculation reveals that the oxygen activation model is preferred than the nitrogen activation model due to the preferred chiral electrostatic environment.

Mechanistic study on the NHC-catalyzed [3+4] annulation of enals and thiazolones

Reaction mechanisms and origins of regio- and stereo-selectivities of NHC catalyzed [3+4] annulation of enals and thiazolones.

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.

Bicyclic Guanidine-Catalyzed Asymmetric Cycloaddition Reaction of Anthrones-Bifunctional Binding Modes and Origin of Stereoselectivity

We report a computational analysis of the [5,5] bicyclic guanidine-catalyzed asymmetric cycloaddition reaction of anthrones. Based on extensive conformational search of key intermediates and transition states on the potential energy surface and density functional theory calculations, we studied five plausible binding modes between the guanidine catalyst and substrates for this reaction. Our results indicate that the most favorable pathway is a stepwise conjugate addition-Aldol sequence via the dual hydrogen-bond binding mode. The predicted level of enantioselectivity is in good agreement with experimental values. Trends in variation of substrates and catalysts have also been reproduced by our calculations. Decomposition analysis revealed the significance of aromatic interactions in stabilizing the key enantioselectivity-determining transition state structures.

New Mechanism for Cinchona Alkaloid-Catalysis Allows for an Efficient Thiophosphorylation Reaction

An efficient synthesis of nucleoside 5'-monothiophosphates under mild reaction conditions using commercially available thiophosphoryl chloride was achieved with a cinchona alkaloid catalyst. A detailed mechanistic study of the reaction was undertaken, employing a combination of reaction kinetics, NMR spectroscopy, and computational modeling, to better understand the observed reactivity. Taken collectively, the results support an unprecedented mechanism for this class of organocatalyst.

2-Aminobenzothiazole-Containing Copper(II) Complex as Catalyst in Click Chemistry: An Experimental and Theoretical Study

The reaction of copper(II) acetate with the 2-aminobenzothiazole (abt) heterocycle affords the new copper(II) complex of formula [Cu(abt)2(OOCCH3)2] (1) in a straightforward manner. Compound 1 served as a precatalyst for azide/alkyne cycloaddition reactions (CuAAC) in water, leading to 1,4-disubstituted-1,2,3-triazole derivatives in a regioselective manner and with excellent yields at room temperature. The main advantages of the coordination of such a heterocyclic ligand in 1 are its strong σ-donating ability (N-Cu), nontoxicity and biological properties. In addition, the click chemistry reaction conditions using 1 allow the formation of a great variety of 1,2,3-triazole-based heterocyclic compounds that make this protocol potentially relevant from biological and sustainable viewpoints. A molecular electron density theory (MEDT) study was performed by using density functional theory (DFT) calculations at the B3LYP/6-31G(d,p) (LANL2DZ for Cu) level to understand the observed regioselectivity in the CuAAC reaction. The intramolecular nature of this reaction accounts for the regioselective formation of the 1,4-regioisomeric triazole derivatives. The ionic nature of the starting copper-acetylide precludes any type of covalent interaction throughout the reaction, as supported by the electron localization function (ELF) topological analysis, reaffirming the zwitterionic-type (zw-type) mechanism of the copper(I)/aminobenzothiazole-catalysed azide-alkyne cycloaddition reactions.

Weak Intermolecular CH···N Hydrogen Bonding: Determination of 13CH-15N Hydrogen-Bond Mediated J Couplings by Solid-State NMR Spectroscopy and First-Principles Calculations

Weak hydrogen bonds are increasingly hypothesized to play key roles in a wide range of chemistry from catalysis to gelation to polymer structure. Here, ¹⁵N/¹³C spin-echo magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) experiments are applied to "view" intermolecular CH···N hydrogen bonding in two selectively labeled organic compounds, 4-[¹⁵N] cyano-4'-[¹³C₂] ethynylbiphenyl (1) and [¹⁵N₃,¹³C₆]-2,4,6-triethynyl-1,3,5-triazine (2). The synthesis of 2-¹⁵N₃,¹³C₆ is reported here for the first time via a multistep procedure, where the key element is the reaction of [¹⁵N₃]-2,4,6-trichloro-1,3,5-triazine (5) with [¹³C₂]-[(trimethylsilyl)ethynyl]zinc chloride (8) to afford its immediate precursor [¹⁵N₃,¹³C₆]-2,4,6-tris[(trimethylsilyl)ethynyl]-1,3,5-triazine (9). Experimentally determined hydrogen-bond-mediated ^2hJ_CN couplings (4.7 ± 0.4 Hz (1) and 4.1 ± 0.3 Hz (2)) are compared with density functional theory (DFT) gauge-including projector augmented wave (GIPAW) calculations, whereby species-independent coupling values ^2hK_CN (29.0 × 10¹⁹ kg m^-2 s^-2 A^-2 (1) and 27.9 × 10¹⁹ kg m^-2 s^-2 A^-2 (2)) quantitatively demonstrate the J couplings for these "weak" CH···N hydrogen bonds to be of a similar magnitude to those for conventionally observed NH···O hydrogen-bonding interactions in uracil (^2hK_NO: 28.1 and 36.8 × 10¹⁹ kg m^-2 s^-2 A^-2). Moreover, the GIPAW calculations show a clear correlation between increasing ^2hJ_CN (and ^3hJ_CN) coupling and reducing C(H)···N and H···N hydrogen-bonding distances, with the Fermi contact term accounting for at least 98% of the isotropic ^2hJ_CN coupling.

Installation of internal electric fields by non-redox active cations in transition metal complexes

Local electric fields contribute to the high selectivity and catalytic activity in enzyme active sites and confined reaction centers in zeolites by modifying the relative energy of transition states, intermediates and/or products. Proximal charged functionalities can generate equivalent internal electric fields in molecular systems but the magnitude of their effect and impact on electronic structure has been minimally explored. To generate quantitative insight into installing internal fields in synthetic systems, we report an experimental and computational study using transition metal (M1) Schiff base complexes functionalized with a crown ether unit containing a mono- or dicationic alkali or alkaline earth metal ion (M2). The synthesis and characterization of the complexes M1 = Ni(ii) and M2 = Na+ or Ba2+ are reported. The electronic absorption spectra and density functional theory (DFT) calculations establish that the cations generate a robust electric field at the metal, which stabilizes the Ni-based molecular orbitals without significantly changing their relative energies. The stabilization is also reflected in the experimental Ni(ii/i) reduction potentials, which are shifted 0.12 V and 0.34 V positive for M2 = Na+ and Ba2+, respectively, compared to a complex lacking a proximal cation. To compare with the cationic Ni complexes, we also synthesized a series of Ni(salen) complexes modified in the 5' position with electron-donating and -withdrawing functionalities (-CF3, -Cl, -H, -tBu, and -OCH3). Data from this series of compounds provides further evidence that the reduction potential shifts observed in the cationic complexes are not due to inductive ligand effects. DFT studies were also performed on the previously reported monocationic and dicatonic Fe(ii)(CH3CN) and Fe(iii)Cl analogues of this system to analyze the impact of an anionic chloride on the electrostatic potential and electronic structure of the Fe site.

Mechanism and stereoselectivity in NHC-catalyzed β-functionalization of saturated carboxylic ester

To understand the mechanism and origin of the stereoselectivity of the [3 + 2] annulation reaction between a carboxylic ester and an isatin generating spirooxindole lactone catalyzed by N-heterocyclic carbene (NHC), density functional theory (DFT) calculations have been carried out. DFT results indicate that the catalytic cycle begins with the coupling of the catalyst with benzotriazole ester, followed by α-deprotonation to produce the enolate intermediate. The subsequent 1,4-proton transfer affords the homoenolate intermediate. The next crucial step is the stereoselective C-C bond formation. Then proton transfer takes place leading to the formation of the lactone intermediate. Finally, the elimination of the catalyst furnishes the final product. The presence of 1-hydroxybenzotriazole (HOBt) dramatically accelerates the proton transfer step. More importantly, HOBt has a non-negligible impact on stereoselective C-C bond formation, and the SR-configured product is the major stereoisomer of the annulation product, which is in good agreement with the experimental observations. The differential π⋯π stacking, C-H⋯π, lone pair (LP)⋯π and repulsion interactions are found to be responsible for the stereoselectivity. The obtained mechanistic insights should provide valuable information for understanding the important roles of the NHC catalyst and HOBt additive and be helpful for designing better NHC catalysts for this kind of reaction.

Understanding the mechanism and stereoselectivity of NHC-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines

The mechanism and origin of stereoselectivities in N-heterocyclic carbine (NHC)-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines have been studied using density functional theory (DFT) calculations. Various possible reaction pathways were examined and analyzed. Our calculation results reveal that the catalytic cycle can be characterized by six steps: nucleophilic attack of a catalyst on 3-bromoenal (step I); [1,2]-proton transfer (step II); addition to the other reactant isatin N-Boc ketimine (step III); debromination (step IV); intramolecular cycloaddition concerted with hydrogen-elimination (step V) and elimination of the NHC catalyst (step VI). For step II, besides the direct [1,2]-proton transfer, the mediator (base and water)-assisted proton transfer has been investigated, and the DFT results show that the 2H2O cluster-mediated proton transfer is most energy favorable. The carbon-carbon bond formation step (step III) is calculated to be the stereoselectivity-determining step and the S-configuration product is the predominant product, which are in good agreement with the experimental observations. The mechanistic insights gained in this work should be helpful for other NHC-catalyzed reactions.

Theoretical investigations of Rh-catalyzed asymmetric 1,4-addition to enones using planar-chiral phosphine-olefin ligands

Recently, planar-chiral phosphine-olefin ligands based on (η⁶ -arene)chromium(0) and (η⁵ -cyclopentadienyl)manganese(I), which are known as first- and second-generation, respectively, have been developed. These ligands were employed for Rh-catalyzed asymmetric 1,4-addition to enones. First-generation ligands involve high enantioselectivity for cyclic enones (>98% ee). Second-generation ligands involve high enantioselectivity for not only cyclic enones but also for acyclic enones (>98% ee). In this study, we have performed DFT calculations to investigate the origin of enantioselectivity. The theoretical values of enantioselectivities were found to be in good agreement with the experimental values obtained for a cyclic enone, 2-cyclopenten-1-one, using both the first- and second-generation ligands. Regarding an acyclic enone, 3-penten-2-one, it was found that the s-cis type decreases the enantioselectivity because the transition states in the s-cis type have a large steric repulsion. Energy decomposition analysis (EDA) and natural bond orbital (NBO) analysis indicate that it is important to study the orbital interactions in the transition states of the insertion step for the acyclic enone attacked from si-face with the second-generation ligand. © 2018 Wiley Periodicals, Inc.

Development of a new bicyclic imidazole nucleophilic organocatalyst for direct enantioselective C-acylation

A new chiral nucleophilic organocatalyst bearing a 5,6,7,8-tetrahydroimidazo[1,2-a]pyridine skeleton has been developed.

Mechanisms of phosphine-catalyzed [3+3] cycloaddition of ynones and azomethine imines: a DFT study

Mechanisms of PPh₃-catalyzed [3+3] cycloaddition between a ynone and an azomethine imine.

The control effects of different scaffolds in chiral phosphoric acids: a case study of enantioselective asymmetric arylation

DFT calculations disclosed that the sign of enantioselectivity in chiral-phosphoric-acid catalyzed reactions can be tuned by BINOL- or SPINOL-derived backbones.