Positional and Geometrical Isomerisation of Alkenes: The Pinnacle of Atom Economy

Strategies to achieve spatiotemporal regulation of pre-existing alkenes via external stimuli are essential given the ubiquity of feedstock olefins in chemistry and their downstream applications. Mirroring the 1-0 switch that underpins mammalian vision through selective geometric isomerisation in retinal, strategies to manipulate 2D space by both geometric and positional isomerisation of alkenes via chemical, thermal and light-driven processes are being intensively pursued. This minireview highlights the current state of the art in activating and achieving directionality in these fundamental chemical transformations.

Structure-function studies of tetrahydroprotoberberine N-methyltransferase reveal the molecular basis of stereoselective substrate recognition

Benzylisoquinoline alkaloids (BIAs) are a structurally diverse class of plant-specialized metabolites that have been particularly well-studied in the order Ranunculales. The N-methyltransferases (NMTs) in BIA biosynthesis can be divided into three groups according to substrate specificity and amino acid sequence. Here, we report the first crystal structures of enzyme complexes from the tetrahydroprotoberberine NMT (TNMT) subclass, specifically for GfTNMT from the yellow horned poppy (Glaucium flavum). GfTNMT was co-crystallized with the cofactor S-adenosyl-l-methionine (d _min = 1.6 Å), the product S-adenosyl-l-homocysteine (d _min = 1.8 Å), or in complex with S-adenosyl-l-homocysteine and (S)-cis-N-methylstylopine (d _min = 1.8 Å). These structures reveal for the first time how a mostly hydrophobic L-shaped substrate recognition pocket selects for the (S)-cis configuration of the two central six-membered rings in protoberberine BIA compounds. Mutagenesis studies confirm and functionally define the roles of several highly-conserved residues within and near the GfTNMT-active site. The substrate specificity of TNMT enzymes appears to arise from the arrangement of subgroup-specific stereospecific recognition elements relative to catalytic elements that are more widely-conserved among all BIA NMTs. The binding mode of protoberberine compounds to GfTNMT appears to be similar to coclaurine NMT, with the isoquinoline rings buried deepest in the binding pocket. This binding mode differs from that of pavine NMT, in which the benzyl ring is bound more deeply than the isoquinoline rings. The insights into substrate recognition and catalysis provided here form a sound basis for the rational engineering of NMT enzymes for chemoenzymatic synthesis and metabolic engineering.

Selective Arene Hydrogenation for Direct Access to Saturated Carbo- and Heterocycles

Arene hydrogenation provides direct access to saturated carbo- and heterocycles and thus its strategic application may be used to shorten synthetic routes. This powerful transformation is widely applied in industry and is expected to facilitate major breakthroughs in the applied sciences. The ability to overcome aromaticity while controlling diastereo-, enantio-, and chemoselectivity is central to the use of hydrogenation in the preparation of complex molecules. In general, the hydrogenation of multisubstituted arenes yields predominantly the cis isomer. Enantiocontrol is imparted by chiral auxiliaries, Brønsted acids, or transition-metal catalysts. Recent studies have demonstrated that highly chemoselective transformations are possible. Such methods and the underlying strategies are reviewed herein, with an emphasis on synthetically useful examples that employ readily available catalysts.

Nickel-Catalyzed Stereodivergent Synthesis of E- and Z-Alkenes by Hydrogenation of Alkynes

A convenient protocol for stereodivergent hydrogenation of alkynes to E- and Z-alkenes by using nickel catalysts was developed. Simple Ni(NO3 )2 ⋅6 H2 O as a catalyst precursor formed active nanoparticles, which were effective for the semihydrogenation of several alkynes with high selectivity for the Z-alkene (Z/E>99:1). Upon addition of specific multidentate ligands (triphos, tetraphos), the resulting molecular catalysts were highly selective for the E-alkene products (E/Z>99:1). Mechanistic studies revealed that the Z-alkene-selective catalyst was heterogeneous whereas the E-alkene-selective catalyst was homogeneous. In the latter case, the alkyne was first hydrogenated to a Z-alkene, which was subsequently isomerized to the E-alkene. This proposal was supported by density functional theory calculations. This synthetic methodology was shown to be generally applicable in >40 examples and scalable to multigram-scale experiments.

Electrochemical Glycosylation as an Enabling Tool for the Stereoselective Synthesis of Cyclic Oligosaccharides

Electrochemical glycosylation of a linear oligosaccharide with a protecting-group-free primary hydroxyl group afforded cyclic oligo-saccharides, up to hexasaccharides, in high yields. Precursors of the cyclic oligosaccharides were prepared by automated electro-chemical assembly-a method for the automated electrochemical solution-phase synthesis of oligosaccharides. We demonstrated that electrochemical glycosylation is useful not only for intermolecular glycosylation but also for intramolecular glycosylation to synthesize cyclic oligosaccharides.

Pd-Catalyzed Stereodivergent Allylic Amination of α-Tertiary Allylic Alcohols towards α,β-Unsaturated γ-Amino Acids

Tertiary allylic alcohols were conveniently converted into either (Z)- or (E)-configured α,β-unsaturated γ-amino acids by treatment with secondary amines under Pd catalysis at ambient conditions. The key to control the stereochemical course of these formal allylic aminations was the presence of a suitable diphosphine ligand, with dppp [1,3-bis(diphenylphosphino)propane, L12] providing high yields and selectivities for the (Z) isomers, whereas the bis[(2-diphenylphosphino)phenyl]ether (DPEPhos) derivative L1' allowed for selective formation of the corresponding (E) isomeric products. This ligand-controlled, stereodivergent protocol thus shows promise for the stereoselective preparation of allylic amine products from a common substrate precursor.

Towards a better understanding of the electrosynthesis of 2,5-dicarboxy-2,5-dihydrofurans: structure, mechanism and influence over stereochemistry

2,5-Dicarboxy-2,5-dihydrofurans are key constituents of a number of natural products and have roles as intermediates in the formation of other such compounds of interest. Typically, these species are synthesized using toxic Pb(IV) salts. Electrochemical syntheses of 2,5-diacetoxy-2,5-dihydrofuran that do not require the use of lead have been reported, but a general lack of experimental detail has prevented these procedures from being more widely adopted. Moreover, no electrochemical study has yet reported the ratio of cis and trans isomers produced. Herein, we compare the chemical, lead-based route to 2,5-diacetoxy-2,5-dihydrofuran with a fully described electrosynthesis method. In doing so, we have discovered that the cis and trans isomers of this compound were previously incorrectly assigned in the literature, an error that we correct by obtaining the crystal structure of cis-2,5-diacetoxy-2,5-dihydrofuran. This allows the ratios of the isomers as prepared by the chemical (2 : 1 cis : trans) and electrochemical (7 : 5 cis : trans) methods to be obtained. Through experimental and computational insights, we propose a mechanism for the electrochemical synthesis of 2,5-dicarboxy-2,5-dihydrofurans and go some way towards validating this mechanism by synthesizing 2,5-dibutoxy-2,5-dihydrofuran electrochemically for the first time. We hope that these findings will provide some greater clarity to the literature surrounding the electrosynthesis and potential applications of 2,5-dicarboxy-2,5-dihydrofurans.

New dicationic DABCO-based ionic liquids: a scalable metal-free one-pot synthesis of bis-2-amino-5-arylidenethiazol-4-ones

Herein, a novel DABCO-based dicationic ionic liquid (bis-DIL) was easily prepared from the sonication of DABCO with 1,3-dichloro-2-propanol and then characterized by several techniques. Thereafter, under the ultimate green conditions, the performance of the bis-DIL was examined for the sono-synthesis of a new library of bis-2-amino-5-arylidenethiazol-4-ones via one-pot pseudo-five-component Knoevenagel condensation reaction of appropriate dialdehydes, rhodanine and amines. This protocol is tolerant towards several mono- and dialdehydes, excellently high yielding and affording access to the desired products in a single step within a short reaction time. Compared with the conventional methodologies, the proposed method displayed several remarkable merits such as milder reaction conditions without any side product, green solvent media, recording well in a variety of green metrics and applicability in gram-scale production. The recyclability of the bis-DIL was also investigated with an average recovered yield of 97% for six sequential cycles without any significant loss of the activity.

Development of a catalytic enantioselective synthesis of the guanacastepene and heptemerone tricyclic core

For nearly two decades, synthetic chemists have been fascinated by the structural complexity and synthetic challenges afforded by the guanacastepene and heptemerone diterpenoids.Numerous synthetic approaches to these compounds have been reported, but to date the application of enantioselective catalysis to this problem has not been realized. Herein we report an enantioselective synthesis of an advanced intermediate corresponding to the tricyclic core common to the guanacastepenes and heptemerones. Highlights of this work include sequential Pd-catalyzed decarboxylative allylic alkylation reactions to generate the two all carbon quaternary stereocenters, the use of ring-closing metathesis to close the A ring in the presence of a distal allyl sidechain, and a region and diastereoselective oxidation of an trienol ether to introduce oxygenation on the A ring.

Copper-Catalyzed Cascade Cyclization of Indolyl Homopropargyl Amides: Stereospecific Construction of Bridged Aza-[n.2.1] Skeletons

Catalytic cycloisomerization-initiated cascade cyclizations of terminal alkynes have received tremendous interest, and been widely used in the facile synthesis of a diverse array of valuable complex heterocycles. However, these tandem reactions have been mostly limited to noble-metal catalysis, and are initiated by an exo-cyclization pathway. Reported herein is an unprecedented copper-catalyzed endo-cyclization-initiated tandem reaction of indolyl homopropargyl amides, where copper catalyzes both the hydroamination and Friedel-Crafts alkylation process. This method allows the practical and atom-economical synthesis of valuable bridged aza-[n.2.1] skeletons (n=3-6) with wide substrate scope, and excellent diastereoselectivity and enantioselectivity by a chirality-transfer strategy. Moreover, the mechanistic rationale for this novel cascade cyclization is also strongly supported by control experiments, and is distinctively different from the related gold catalysis.

Role of Water in the Reaction Mechanism and endo/exo Selectivity of 1,3-Dipolar Cycloadditions Elucidated by Quantum Chemistry and Machine Learning

Asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are among the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the role of water molecules in the reactivity and endo/exo selectivity remains unclear. To explore how water accelerates the reactions and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide (1) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules was used. It is demonstrated that not only the nature of both the dipolarophile and the 1,3-dipole, but also the solvent medium, can perturb or even alter the reaction mechanism. An extreme case was found for the reaction of 1,3-dipole 1 with methyl vinyl ketone, in which the reaction mechanism changes from a concerted to a stepwise mode on going from MeCN to H₂ O as solvent, with formation of a zwitterionic intermediate that is a very shallow minimum on the energy surface. Thus, high stereocontrol can still be expected despite the stepwise nature of the mechanism. The results indicate that water can induce global polarization along the reaction coordinate and highlight the role of microsolvation effects and bulk-phase effects in reproducing the experimentally observed aqueous acceleration and enhanced endo/exo selectivity.

Synthesis of oxidized phospholipids by sn-1 acyltransferase using 2-15-HETE lysophospholipids

Recently, oxidized phospholipid species have emerged as important signaling lipids in activated immune cells and platelets. The canonical pathway for the synthesis of oxidized phospholipids is through the release of arachidonic acid by cytosolic phospholipase A₂α (cPLA₂α) followed by its enzymatic oxidation, activation of the carboxylate anion by acyl-CoA synthetase(s), and re-esterification to the sn-2 position by sn-2 acyltransferase activity (i.e. the Lands cycle). However, recent studies have demonstrated the unanticipated significance of sn-1 hydrolysis of arachidonoyl-containing choline and ethanolamine glycerophospholipids by other phospholipases to generate the corresponding 2-arachidonoyl-lysolipids. Herein, we identified a pathway for oxidized phospholipid synthesis comprising sequential sn-1 hydrolysis by a phospholipase A₁ (e.g. by patatin-like phospholipase domain-containing 8 (PNPLA8)), direct enzymatic oxidation of the resultant 2-arachidonoyl-lysophospholipids, and the esterification of oxidized 2-arachidonoyl-lysophospholipids by acyl-CoA-dependent sn-1 acyltransferase(s). To circumvent ambiguities associated with acyl migration or hydrolysis, we developed a synthesis for optically active (d- and l-enantiomers) nonhydrolyzable analogs of 2-arachidonoyl-lysophosphatidylcholine (2-AA-LPC). sn-1 acyltransferase activity in murine liver microsomes stereospecifically and preferentially utilized the naturally occurring l-enantiomer of the ether analog of lysophosphatidylcholine. Next, we demonstrated the high selectivity of the sn-1 acyltransferase activity for saturated acyl-CoA species. Importantly, we established that 2-15-hydroxyeicosatetraenoic acid (HETE) ether-LPC sn-1 esterification is markedly activated by thrombin treatment of murine platelets to generate oxidized PC. Collectively, these findings demonstrate the enantiomeric specificity and saturated acyl-CoA selectivity of microsomal sn-1 acyltransferase(s) and reveal its participation in a previously uncharacterized pathway for the synthesis of oxidized phospholipids with cell-signaling properties.

Lithium Binaphtholate-Catalyzed Michael Reaction of Malonates with Maleates and Its Application to the Enantioselective Synthesis of Tricarboxylic Acid Derivatives

The Michael reaction of malonates with maleates afforded the corresponding adducts in high yields with high enantioselectivities (up to 98% enantiomeric excess (ee)) by using dilithium 3,3'-dichlorobinaphtholate as a catalyst. The obtained Michael adducts could be converted to optically active tricarboxylic acid (TCA) derivatives via the Krapcho reaction.

Stereoselectivity Switch in the Reduction of α-Alkyl-β-Arylenones by Structure-Guided Designed Variants of the Ene Reductase OYE1

Ene reductases from the Old Yellow Enzyme (OYE) family are industrially interesting enzymes for the biocatalytic asymmetric reduction of alkenes. To access both enantiomers of the target reduced products, stereocomplementary pairs of OYE enzymes are necessary, but their natural occurrence is quite limited. A library of wild type ene reductases from different sources was screened in the stereoselective reduction of a set of representative α-alkyl-β-arylenones to investigate the naturally available biodiversity. As far as the bioreduction of the ethyl ketone derivatives concerns, the results confirmed the distinctiveness of the OYE3 enzyme in affording the reduced product in the (S) configuration, while all the other tested ene reductases from the Old Yellow Enzymes family showed the same stereoselectivity toward the formation of corresponding (R) enantiomer. A possible determinant role of the "hot spot" residue in position 296 for the stereoselectivity control of these reactions was confirmed by the replacement of Phe296 of OYE1 with Ser as found in OYE3. Further investigations showed that the same stereoselectivity switch in OYE1 could be achieved also by the replacement of Trp116 with Ala and Val, these experimental results being rationalized by structural and docking studies. Moreover, an additive effect on the stereoselectivity of OYE1 was observed when coupling the selected mutations in position 296 and 116, thus providing two extremely enantioselective variants of OYE1 (W116A-F296S, W116V-F296S) showing the opposite stereoselectivity of the wild type enzyme. Lastly, the effects of the mutations on the bioreduction of carvone enantiomers were investigated as well.

Diastereo- and enantioselective preparation of cyclopropanol derivatives

The diastereoselective carbocupration reaction of alkoxy-functionalized cyclopropene derivatives, followed by a subsequent trapping of the resulting cyclopropylmetal species with an electrophilic source of oxygen (oxenoid) afforded various tetrasubstituted cyclopropanol derivatives in high diastereo- and enantiomeric ratios. Similarly, the enantioselective copper-catalyzed carbomagnesiation/oxidation (or amination) sequence on achiral nonfunctionalized cyclopropenes provided the desired cyclopropanol (and cyclopropylamine) derivatives in excellent diastereo- and enantiomeric excesses.

Chiral Graphs: Reduced Representations of Ligand Scaffolds for Stereoselective Biomolecular Recognition, Drug Design, and Enhanced Exploration of Chemical Structure Space

Rational structure-based drug design relies on a detailed, atomic-level understanding of protein-ligand interactions. The chiral nature of drug binding sites in proteins has led to the discovery of predominantly chiral drugs. A mechanistic understanding of stereoselectivity (which governs how one stereoisomer of a drug might bind stronger than the others to a protein) depends on the topology of stereocenters in the chiral molecule. Chiral graphs and reduced chiral graphs, introduced here, are new topological representations of chiral ligands using graph theory, to facilitate a detailed understanding of chiral recognition of ligands/drugs by proteins. These representations are demonstrated by application to all ≈14 000+ chiral ligands in the Protein Data Bank (PDB), which will facilitate an understanding of protein-ligand stereoselectivity mechanisms. Ligand modifications during drug development can be easily incorporated into these chiral graphs. In addition, these chiral graphs present an efficient tool for a deep dive into the enormous chemical structure space to enable sampling of unexplored structural scaffolds.

Phenanthroline-Catalyzed Stereoretentive Glycosylations

Carbohydrates are essential moieties of many bioactive molecules in nature. However, efforts to elucidate their modes of action are often impeded by limitations in synthetic access to well-defined oligosaccharides. Most of the current methods rely on the design of specialized coupling partners to control selectivity during the formation of glycosidic bonds. Reported herein is the use of a commercially available phenanthroline to catalyze stereoretentive glycosylation with glycosyl bromides. The method provides efficient access to α-1,2-cis glycosides. This protocol has been performed for the large-scale synthesis of an octasaccharide adjuvant. Density-functional theory calculations, together with kinetic studies, suggest that the reaction proceeds by a double S_N 2 mechanism.

Enantioselective capillary electrophoresis for pharmacokinetic analysis of methadone and 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine in equines anesthetized with ketamine and isoflurane

An enantioselective assay for the determination of methadone and its main metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine in equine plasma based on capillary electrophoresis with highly sulfated γ-cyclodextrin as chiral selector and electrokinetic analyte injection is described. The assay is based on liquid/liquid extraction of the analytes at alkaline pH from 0.1 mL plasma followed by electrokinetic sample injection of the analytes from the extract across a buffer plug without chiral selector. Separation occurs cationically at normal polarity in a pH 3 phosphate buffer containing 0.16% (w/v) of highly sulfated γ-cyclodextrin. The developed assay is precise (intra- and interday RSD < 4% and < 7%, respectively), is capable to determine enantiomer levels of methadone and 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine in plasma down to 2.5 ng/mL, and was successfully applied to monitor enantiomer drug and metabolite levels in plasma of a pony that was anesthetized with racemic ketamine and isoflurane and received a bolus of racemic methadone and a bolus followed by constant rate infusion of racemic methadone. The data suggest that the assay is well suited for pharmacokinetic purposes.

Stereoselective β-Mannosylation with 2,6-Lactone-bridged Thiomannosyl Donor by Remote Acyl Group Participation

Stereoselective β-mannosylation has been recognized as one of the greatest challenges of carbohydrate chemistry. Herein, we described a practical method for stereoselective construction of β-mannosides by using a 2,6-lactone-bridged thiomannosyl donor through the remote acyl-group participation as well as the steric effect of O-4 substituent. The two effects are enabled through the conversion of a regular mannopyranosyl ⁴ C₁ conformation into a 2,6-lactone bridged conformation. The lactone donor could be readily prepared in three steps on a gram scale and the β-mannosylation proceeded smoothly with high stereoselectivity for primary, secondary and tertiary alcohol acceptors. In addition, this strategy was successfully applied to the synthesis of a naturally occurring trisaccharide.

Traceless Protection for More Broadly Applicable Olefin Metathesis

An operationally simple in situ protection/deprotection strategy that significantly expands the scope of kinetically controlled catalytic Z- and E-selective olefin metathesis is introduced. Prior to the addition of a sensitive Mo- or Ru-based complex, treatment of a hydroxy- or a carboxylic-acid-containing olefin with commercially available HB(pin) or readily accessible HB(trip)₂ (pin=pinacolato, trip=2,4,6-tri(isopropyl)phenyl) for 15 min is sufficient for efficient generation of a desired product. Routine workup leads to quantitative deprotection. A range of stereochemically defined Z- and E-alkenyl chlorides, bromides, fluorides, and boronates or Z-trifluoromethyl-substituted alkenes with a hydroxy or carboxylic acid group were thus prepared in 51-97 % yield with 93 to >98 % stereoselectivity. We also show that, regardless of whether a polar functional unit is present or not, a small amount of HB(pin) may be used to remove residual water, significantly enhancing efficiency.

Enantiomeric Tartaric Acid Production Using cis-Epoxysuccinate Hydrolase: History and Perspectives

Tartaric acid is an important chiral chemical building block with broad industrial and scientific applications. The enantioselective synthesis of l(+)- and d(−)-tartaric acids has been successfully achieved using bacteria presenting cis-epoxysuccinate hydrolase (CESH) activity, while the catalytic mechanisms of CESHs were not elucidated clearly until very recently. As biocatalysts, CESHs are unique epoxide hydrolases because their substrate is a small, mirror-symmetric, highly hydrophilic molecule, and their products show very high enantiomeric purity with nearly 100% enantiomeric excess. In this paper, we review over forty years of the history, process and mechanism studies of CESHs as well as our perspective on the future research and applications of CESH in enantiomeric tartaric acid production.

Characterization of the recombinant (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases: A case study to augment the teaching of enzyme kinetics and stereoselectivity

A homologous pair of stereospecific NAD-dependent enzymes, (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenase, are part of a bacterial pathway of short-chain alkene and epoxide metabolism. Their discovery and study, which spans multiple publications over more than a decade, is a data rich story that combines both classical and contemporary experimental biochemistry. A subset of the data for characterization of the recombinant enzymes was used as a case study to augment the teaching of enzyme kinetics and stereoselectivity in an undergraduate biochemistry course at California State University-Chico. © 2018 International Union of Biochemistry and Molecular Biology, 47(2): 124-132, 2019.

Synthesis of Novel N-Heterocyclic Compounds Containing 1,2,3-Triazole Ring System via Domino, "Click" and RDA Reactions

An uncomplicated, high-yielding synthetic route has been developed to constitute complicated heterocycles, applying domino, click and retro-Diels–Alder (RDA) reaction sequences. Starting from 2-aminocarboxamides, a new set of isoindolo[2,1-a]quinazolinones was synthesized with domino ring closure. A click reaction was performed to create the 1,2,3-triazole heterocyclic ring, followed by an RDA reaction resulting in dihydropyrimido[2,1-a]isoindole-2,6-diones. The absolute configuration, concluded by the norbornene structure that served as a chiral source, remained constant throughout the transformations. The structure of the synthesized compounds was examined by ¹H and ¹³C Nuclear Magnetic Resonance (NMR) methods.

Selective Emergence of the Halogen Bond in Ground and Excited States of Noble-Gas-Chlorine Systems

Molecular-beam scattering experiments and theoretical calculations prove the nature, strength, and selectivity of the halogen bonds (XB) in the interaction of halogen molecules with the series of noble gas (Ng) atoms. The XB, accompanied by charge transfer from the Ng to the halogen, is shown to take place in, and measurably stabilize, the collinear conformation of the adducts, which thus becomes (in contrast to what happens for other Ng-molecule systems) approximately as bound as the T-shaped form. It is also shown how and why XB is inhibited when the halogen molecule is in the ³ Π_u excited state. A general potential formulation fitting the experimental observables, based on few physically essential parameters, is proposed to describe the interaction accurately and is validated by ab initio computations.

Asymmetric Synthesis of Cα-Substituted Prolines through Curtin-Hammett-Controlled Diastereoselective N-Alkylation

Asymmetric synthesis of α-substituted proline derivatives has been accomplished by an efficient chirality-transfer method. High diastereoselectivity of the N-alkylation of the proline ester (C→N chirality transfer) was achieved when a 2,3-disubstituted benzyl group was used as the N-substituent. DFT calculations provided a mechanistic rationale for the high degree of stereoselectivity. The generated N-chirality of the quaternary ammonium salt was transferred back to the α-carbon through a stereoselective [2,3]-Stevens rearrangement (N→C chirality transfer) to give α-substituted proline ester.