Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases

In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp²−N bond forming dimerase, AspB. Overlay of the AspB structure onto C−C and C−N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C−N bond formation. MD simulations also suggest that intermolecular C−C or C−N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.     

Diastereoselective Biomimetic Synthesis of Dimeric Tetrahydrocarbazoles via a Copper(II)-Catalyzed Cycloisomerization-[3+2] Cyclodimerization Cascade

The cyclodimerization (homochiral- and heterochiral−) of monomeric units for the construction of stereodefined polycyclic systems is a powerful strategy in both biosynthesis and biomimetic synthesis. Herein we have discovered and developed a Cu^II- catalyzed, biomimetic, diastereoselective tandem cycloisomerization-[3+2] cyclodimerization of 1-(indol-2-yl)pent-4-yn-3-ol. This novel strategy operates under very mild conditions, providing access to structurally unprecedented dimeric tetrahydrocarbazoles fused to a tetrahydrofuran unit in excellent yields of the products. Several fruitful control experiments, isolation of the monomeric-cycloisomerized products and their subsequent conversion into the corresponding cyclodimeric products supported their intermediacy and the possible mechanism as a cycloisomerization-diastereoselective [3+2] cyclodimerization cascade. The cyclodimerization involves a substituent controlled, highly diastereoselective homochiral [3+2] annulation or heterochiral [3+2] annulation of in situ generated 3-hydroxytetrahydrocarbazoles. The key and important features of this strategy are: a) construction of three new C−C bonds & one new C−O bond; b) creation of two new stereocenters, and c) construction of three new rings, in a single operation; d) low catalyst loading (1–5 mol %); e) 100 % atom economy; and f) rapid construction of structurally unprecedented natural product like polycyclic frameworks. A chiral pool version using an enantio- and diastereopure substrate was also demonstrated.     

Al/P- and Ga/P-Based Frustrated Lewis Pairs and Electronically Unsaturated Substrates: Ring Cleavage and Ring Closure,C−C and C−N Bond Formation

Al/P- and Ga/P-based frustrated Lewis pairs (FLPs) reacted with an azirine under mild conditions under cleavage of the heterocycle on two different positions. Opening of the C−C bond yielded an unusual nitrile–ylide adduct in which a C−N moiety coordinated to the FLP backbone. Cleavage of a C−N bond afforded the thermodynamically favored enamine adduct with the N atom bound to P and Al or Ga atoms. Ring closure was observed upon treatment of an Al/P FLP with electronically unsaturated substrates (4-(1-cyclohexenyl)-1-aza-but-1-en-3-ynes) and yielded by C−N bond formation hexahydroquinoline derivatives, which coordinated to the FLP through P−C and Al−C bonds. Diphenylcyclopropenone showed a diverse reactivity, which depending on steric shielding and the polarizing effect of Al or Ga atoms afforded different products. An AltBu₂/P FLP yielded an adduct with the C=O group coordinated to P and Al. The dineopentyl derivative gave an equilibrium mixture consisting of a similar product and a simple adduct with O bound to Al and a three-coordinate P atom. Both compounds co-crystallize. The Ga/P FLP only formed the simple adduct with the same substrate. Rearrangement resulted in all cases in C₃-ring cleavage and migration of a mesityl group from P to a former ring C atom by C−C bond formation. Diphenylthiocyclopropenone (evidence for the presence of P=C bonds) and an imine derivative afforded similar products.     

An S=1 Iron(IV) Intermediate Revealed in a Non-Heme Iron Enzyme-Catalyzed Oxidative C−S Bond Formation

Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol-histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O₂-dependent C−S bond formation catalyzed by non-heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competent S=1 iron(IV) intermediate supported by a four-histidine ligand environment (three from the protein residues and one from the substrate) in enabling C−S bond formation in OvoA from Methyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non-heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C−S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure-function relationship of high-valent iron intermediates supported by a histidine rich ligand environment.     

Steric,Electronic and Conformational Synergistic Effects in the Gold(I)-catalyzed α-C−H Bond Functionalization of Tertiary Amines**

Direct C−H bond functionalization is a useful strategy for the straightforward formation of C−C and C−Heteroatom bonds. In the present work, a unique approach for the challenging electrophilic Au-catalyzed α-C−H bond functionalization of tertiary amines is presented. Electronic, steric and conformational synergistic effects exerted by the use of a malonate unit in the substrate were key to the success of this transformation. This new reactivity was applied to the synthesis of tetrahydro-γ-carboline products which, under oxidative conditions, could be converted into valuable structural motifs found in bioactive alkaloid natural products.     

Steric,Electronic and Conformational Synergistic Effects in the Gold(I)-catalyzed α-C−H Bond Functionalization of Tertiary Amines**

Direct C−H bond functionalization is a useful strategy for the straightforward formation of C−C and C−Heteroatom bonds. In the present work, a unique approach for the challenging electrophilic Au-catalyzed α-C−H bond functionalization of tertiary amines is presented. Electronic, steric and conformational synergistic effects exerted by the use of a malonate unit in the substrate were key to the success of this transformation. This new reactivity was applied to the synthesis of tetrahydro-γ-carboline products which, under oxidative conditions, could be converted into valuable structural motifs found in bioactive alkaloid natural products.     

Lewis Base/Brønsted Acid Co-Catalyzed Asymmetric Thiolation of Alkenes with Acid-Controlled Divergent Regioselectivity

A divergent strategy for the facile preparation of various enantioenriched phenylthio-substituted lactones was developed based on Lewis base/Brønsted acid co-catalyzed thiolation of homoallylic acids. The acid-controlled regiodivergent cyclization (6-endo vs. 5-exo) and acid-mediated stereoselective rearrangement of phenylthio-substituted lactones were explored. Experimental and computational studies were performed to clarify the origins of the regioselectivity and enantioselectivity. The calculation results suggest that C−O and C−S bond formation might occur simultaneously, without formation of a commonly supposed catalyst-coordinated thiiranium ion intermediate and the potential π–π stacking between substrate and SPh as an important factor in the enantio-determining step. Finally, this methodology was applied in the rapid syntheses of the bioactive natural products (+)-ricciocarpin A and (R)-dodecan-4-olide.     

Actinoperylone, a novel perylenequinone-type shunt product, from a deletion mutant of the actVA-ORF5 and ORF6 genes for actinorhodin biosynthesis in Streptomyces coelicolor A3(2)

A novel shunt product, actinoperylone, has been isolated from a deletion mutant of the actVA-ORF5 and ORF6 genes involved in the biosynthesis of a benzoisochromanequinone (BIQ) antibiotic actinorhodin (ACT) in Streptomyces coelicolor A3(2). Spectroscopic analysis revealed its perylenequinone-type skeleton with the four chiral centers, obviously derived from the dimerization of an ACT intermediate. The structure of actinoperylone indicates the essential role of ActVA-ORF5 in the oxygen introduction at C-6, which is common to the formation of BIQ chromophore. The present results also agree with the distribution of the actVA-ORF5 homologues in all known BIQ biosynthetic clusters in streptomycetes.     

Divergent Total Syntheses of (+)-Vulgarisins A–E

The asymmetric total syntheses of (+)-vulgarisins A–E, which share a rare and highly oxygenated [5-6-4-5] tetracyclic core structure that were isolated from P. vulgaris Linn., have been described for the first time in a divergent manner. Key transformations include: 1) a catalytic asymmetric intramolecular cyclopropanation to forge the A ring bearing desired stereochemistry at C14; 2) a one-pot borylation/conjugate addition process for creation of the C1−C11 bond; 3) a Wolff ring contraction to assemble the bicyclo[3.2.0]heptane subunit (CD rings); and 4) a stereocontrolled pinacol cyclization for construction of the central B ring of the natural products.     

Selenocysteine as a Substrate,an Inhibitor and a Mechanistic Probe for Bacterial and Fungal Iron-Dependent Sulfoxide Synthases

Sulfoxide synthases are non-heme iron enzymes that participate in the biosynthesis of thiohistidines, such as ergothioneine and ovothiol A. The sulfoxide synthase EgtB from Chloracidobacterium thermophilum (CthEgtB) catalyzes oxidative coupling between the side chains of N-α-trimethyl histidine (TMH) and cysteine (Cys) in a reaction that entails complete reduction of molecular oxygen, carbon–sulfur (C−S) and sulfur–oxygen (S−O) bond formation as well as carbon–hydrogen (C−H) bond cleavage. In this report, we show that CthEgtB and other bacterial sulfoxide synthases cannot efficiently accept selenocysteine (SeCys) as a substrate in place of cysteine. In contrast, the sulfoxide synthase from the filamentous fungus Chaetomium thermophilum (CthEgt1) catalyzes C−S and C−Se bond formation at almost equal efficiency. We discuss evidence suggesting that this functional difference between bacterial and fungal sulfoxide synthases emerges from different modes of oxygen activation.     

Fragmentation Mechanism of White Phosphorus: A Theoretical Insight into Multiple Cleavage/Formation of P−P and P−C Bonds

Molecular-level understanding of metal-mediated white phosphorus (P₄) activation is meaningful but challenging because of its direct relevance to the conversion of P₄ into useful organophosphorus compounds as well as the complicated and unforeseeable cleavage process of P−P bonds. The related study, however, has still rarely been achieved to date. Here, a theoretical insight into the step-by-step process of three P−P bond cleavage/four P−C bond formation for [P₃+P₁]-fragmentation of P₄ mediated by lutetacyclopentadienes is reported. The unique charge-separated intermediate and the intermolecular cooperation between two lutetacyclopentadienes play a vital role in the subsequent P−P/P−C bond breaking/forming. It is found that, although the first P−C formation is involved in the assembly of the cyclo-P₃ [R₄C₄P₃]⁻ unit, the construction of the aromatic five-membered P₁ heterocycle [R₄C₄P]⁻ is completed prior to the cyclo-P₃ formation. The reaction mechanism has been carefully elucidated by analyses of the geometric structure, frontier molecular orbitals, bond index, and natural charge, which greatly broaden and enrich the general knowledge of the direct functionalization of P₄.     

New Reactivity Patterns in 3H-Phosphaallene Chemistry [Aryl-P=C=C(H)-tBu]: Hydroboration of the C=C Bond,Deprotonation and Trimerisation

3H-Phosphaallenes, R−P=C=C(H)C−R’ ( 3 ), are accessible in a multigram scale on a new and facile route and show a fascinating chemical reactivity. BH₃(SMe₂) and 3 a (R=Mes*, R’=tBu) afforded by hydroboration of the C=C bonds of two phosphaallene molecules an unprecedented borane ( 7 ) with the B atom bound to two P=C double bonds. This compound represents a new FLP based on a B and two P atoms. The increased Lewis acidity of the B atom led to a different reaction course upon treatment of 3 a with H₂B-C₆F₅(SMe₂). Hydroboration of a C=C bond of a first phosphaallene is followed in a typical FLP reaction by the coordination of a second phosphaallene molecule via B−C and P−B bond formation to yield a BP₂C₂ heterocycle ( 8 ). Its B−P bond is short and the B-bound P atom has a planar surrounding. Treatment of 3 a with tBuLi resulted in deprotonation of the β-C atom of the phosphaallene ( 9 ). The Li atom is bound to the P atom as demonstrated by crystal structure determination, quantum chemical calculations and reactions with HCl, Cl-SiMe₃ or Cl-PtBu₂. The thermally unstable phosphaallene Ph−P=C=C(H)-tBu gave a unique trimeric secondary product by P−P, P−C and C−C bond formation. It contains a P₂C₄ heterocycle and was isolated as a W(CO)₄ complex with two P atoms coordinated to W ( 15 ).     

Long‐Chain Alkyl Cyanides: Unprecedented Volatile Compounds Released by Pseudomonas and Micromonospora Bacteria

The analysis of volatiles from bacterial cultures revealed long‐chain aliphatic nitriles, a new class of natural products. Such nitriles are produced by both Gram‐positive Micromonospora echinospora and Gram‐negative Pseudomonas veronii bacteria, although the structures differ. A variable sequence of chain elongation and dehydration in the fatty acid biosynthesis leads to either unbranched saturated or unsaturated nitriles with an ω−7 double bond, such as (Z )‐11‐octadecenenitrile, or methyl‐branched unsaturated nitriles with the double bond located at C‐3, such as (Z )‐13‐methyltetradec‐3‐enenitrile. The nitrile biosynthesis starts from fatty acids, which are converted into their amides and finally dehydrated. The structures and biosyntheses of the 19 naturally occurring compounds were elucidated by mass spectrometry, synthesis, and feeding experiments with deuterium‐labeled precursors. Some of the nitriles showed antimicrobial activity, for example, against multiresistant Staphylococcus aureus strains.     

Asymmetric Total Syntheses of Di- and Sesquiterpenoids by Catalytic C−C Activation of Cyclopentanones

To show the synthetic utility of the catalytic C−C activation of less strained substrates, described here are the collective and concise syntheses of the natural products (−)-microthecaline A, (−)-leubehanol, (+)-pseudopteroxazole, (+)-seco-pseudopteroxazole, pseudopterosin A–F and G—J aglycones, and (+)-heritonin. The key step in these syntheses involve a Rh-catalyzed C−C/C−H activation cascade of 3-arylcyclopentanones, which provides a rapid and enantioselective route to access the polysubstituted tetrahydronaphthalene cores presented in these natural products. Other important features include 1) the direct C−H amination of the tetralone substrate in the synthesis of (−)-microthecaline A, 2) the use of phosphoric acid to enhance efficiency and regioselectivity for problematic cyclopentanone substrates in the C−C activation reactions, and 3) the direct conversion of serrulatane into amphilectane diterpenes by an allylic cyclodehydrogenation coupling.     

Enantioselective Copper(I)/Chiral Phosphoric Acid Catalyzed Intramolecular Amination of Allylic and Benzylic C−H Bonds

Radical-involved enantioselective oxidative C−H bond functionalization by a hydrogen-atom transfer (HAT) process has emerged as a promising method for accessing functionally diverse enantioenriched products, while asymmetric C(sp³)−H bond amination remains a formidable challenge. To address this problem, described herein is a dual Cu^I/chiral phosphoric acid (CPA) catalytic system for radical-involved enantioselective intramolecular C(sp³)−H amination of not only allylic positions but also benzylic positions with broad substrate scope. The use of 4-methoxy-NHPI (NHPI=N-hydroxyphthalimide) as a stable and chemoselective HAT mediator precursor is crucial for the fulfillment of this transformation. Preliminary mechanistic studies indicate that a crucial allylic or benzylic radical intermediate resulting from a HAT process is involved.     

Exploiting a C–N Bond Forming Cytochrome P450 Monooxygenase for C–S Bond Formation

C–S bond formation reactions are widely distributed in the biosynthesis of biologically active molecules, and thus have received much attention over the past decades. Herein, we report intramolecular C–S bond formation by a P450 monooxygenase, TleB, which normally catalyzes a C−N bond formation in teleocidin biosynthesis. Based on the proposed reaction mechanism of TleB, a thiol-substituted substrate analogue was synthesized and tested in the enzyme reaction, which afforded the unprecedented sulfur-containing thio-indolactam V, in addition to an unusual indole-fused 6/5/8-tricyclic product whose structure was determined by the crystalline sponge method. Interestingly, conformational analysis revealed that the SOFA conformation is stable in thio-indolactam V, in sharp contrast to the major TWIST form in indolactam V, resulting in differences in their biological activities.     

A Copper‐Catalyzed Aerobic [1,3]‐Nitrogen Shift through Nitrogen‐Radical 4‐exo‐trig Cyclization

A novel radical [1,3]‐nitrogen shift catalyzed by copper diacetate under an oxygen atmosphere (1 atm) has been developed for the construction of a diverse range of indole derivatives from α,α‐disubstituted benzylamine. In this reaction, oxygen was used as a clean terminal oxidant, and water was produced as the only by‐product. Five inert bonds were cleaved, and two C−N bonds and one C−C double bond were constructed in one pot during this transformation. This unique method demonstrated broad application protential for the late‐stage modification of biologically active natural products and drugs. Mechanistic investigations indicate that a unique 4‐exo ‐trig cyclization of an aminyl radical onto a phenyl ring is involved in the catalytic cycle.     

Weak Interactions Initiate C−H and C−C Bond Dissociation of Ethane on Nbn+ Clusters

The conversion of ethane into value-added chemicals under ambient conditions has attracted much attention but the mechanisms remain not fully understood. Here we report a study on the reaction of ethane with thermalized Nb_n⁺ clusters based on a multiple-ion laminar flow tube reactor combined with a triple quadrupole mass spectrometer (MIFT-TQMS). It is found that ethane reacts with Nb_n⁺ clusters to form both products of dehydrogenation and methane-removal (odd-carbon products). Combined with density functional theory (DFT) calculations, we studied the reaction mechanisms of the C−C bond activation and C−H bond cleavage on the Nb_n⁺ clusters. It is unveiled that hydrogen atom transfer (HAT) initiates the reaction process, giving rise to the formation of Nb−C bonds and an elongated C−C distance in the HNb_n⁺CH₂CH₃ motif. Subsequent reactions allow for C−C bond activation and a competitive HAT process which is associated with CH₄ removal or H₂ release, resulting in the production of the observed carbides.     

One‐Step Multigram‐Scale Biomimetic Synthesis of Psiguadial B

A gram‐scale synthesis of psiguadial B, a purported inhibitor of human hepatoma cell growth, has been achieved in one step by a biomimetic three‐component coupling of caryophyllene, benzaldehyde, and diformylphloroglucinol. This cascade reaction is catalyzed by N,N′‐dimethylethylenediamine, and proceeds at ambient temperature to generate four stereocenters, two rings, one C−O bond, and three C−C bonds. Combined computational and experimental investigations suggest the biosynthesis of the natural product is non‐enzyme mediated, and is the result of a Michael addition between caryophyllene and a reactive ortho‐quinone methide, followed by two sequential intramolecular cationic cyclization events.     

Tuning Ruthenium Carbene Complexes for Selective P−H Activation through Metal-Ligand Cooperation

The use of iminophosphoryl-tethered ruthenium carbene complexes to activate secondary phosphine P−H bonds is reported. Complexes of type [(p-cymene)-RuC(SO₂Ph)(PPh₂NR)] (with R = SiMe₃ or 4-C₆H₄−NO₂) were found to exhibit different reactivities depending on the electronics of the applied phosphine and the substituent at the iminophosphoryl moiety. Hence, the electron-rich silyl-substituted complex undergoes cyclometallation or shift of the imine moiety after cooperative activation of the P−H bond across the M=C linkage, depending on the electronics of the applied phosphine. Deuteration experiments and computational studies proved that cyclometallation is initiated by the activation process at the M=C bond and triggered by the high electron density at the metal in the phosphido intermediates. Consistently, replacement of the trimethylsilyl (TMS) group by the electron-withdrawing 4-nitrophenyl substituent allowed the selective cooperative P−H activation to form stable activation products.