Organic & Biomolecular Chemistry (v.10, #34)

Front cover (6805-6805).

Inside front cover (6806-6806).

Contents list (6807-6816).

The Negishi coupling has been widely applied in organic synthesis, while relevant mechanistic studies are relatively rare. To obtain an understanding of the fundamental steps in the Negishi coupling, oxidative addition, transmetalation and reductive elimination, the kinetic investigation has served as one of the most important strategies. In this review, insights into the elementary steps in the Negishi coupling through kinetic investigations are summarized.

We report the palladium-catalyzed, pyrrolidine-mediated α-benzylation of enamines generated from aldehydes and ketones. The method allows for direct coupling of medicinally relevant coumarin moieties with aldehydes and ketones in good yield under mild conditions. The reaction is believed to proceed via a Pd–π-benzyl complex generated from (coumarinyl)methyl acetates.

Diverted organic synthesis (DOS): accessing a new, natural product inspired, neurotrophically active scaffold through an intramolecular Pauson–Khand reaction by Goverdhan Mehta; Ramesh Samineni; Pabbaraja Srihari; R. Gajendra Reddy; Sumana Chakravarty (6830-6833).
Drawing inspiration from the impressive neurotrophic activity exhibited by the natural product paecilomycine A, we have designed a new natural product-like scaffold employing an intramolecular Pauson–Khand reaction. Several compounds based on the new designer scaffold exhibited promising neurotrophic activity and are worthy of further biological evaluation. Our findings also highlight the importance of a DOS strategy in creating useful therapeutical leads.

Regioselective synthesis of 2-(2-hydroxyaryl)pyridines from the reactions of benzynes with pyridine N-oxides by Balagopal S. Shaibu; Rahul Kisan Kawade; Rai-Shung Liu (6834-6839).
By modifying the conditions from those in Larock's reported synthesis of 3-(2-hydroxyaryl)pyridines from benzynes, and pyridine N-oxides, we altered the regioselectivity of the reaction toward an efficient synthesis of 2-substituted pyridines. The presence of ethyl propiolate altered the regioselectivity to afford 3-substituted pyridine products instead. We conducted appropriate control experiments that enable a full understanding of the mechanism.

π-Fused bis-BODIPY as a candidate for NIR dyes by Mitsunori Nakamura; Hiroyuki Tahara; Kohtaro Takahashi; Toshi Nagata; Hiroki Uoyama; Daiki Kuzuhara; Shigeki Mori; Tetsuo Okujima; Hiroko Yamada; Hidemitsu Uno (6840-6849).
Benzene-fused bis-(borondipyrromethene)s (bis-BODIPYs) were synthesized by retro-Diels–Alder reaction of the corresponding bicyclo[2.2.2]octadiene-fused (BCOD-fused) bis-BODIPYs, which were, in turn, prepared from 4,8-ethano-4,8-dihydropyrrolo[3,4-f]isoindole derivatives. The π-fused bis-BODIPY chromophores were designed to show intensive absorption and strong fluorescence in the near-infrared region and not to have any strong absorption in the visible region. A 6,10-dibora-5a,6a,9a,10a-tetraaza-s-indaceno[2,3-b:6,5-b′]difluorene derivative (syn-bis-benzoBODIPY) obtained by a thermal retro-Diels–Alder reaction of the corresponding BCOD-fused BODIPY dimer has strong absorption and emission bands at 775 and 781 nm, respectively. The absolute quantum yield is 0.36. The absorption is more than 5.0 times stronger than other absorptions observed in the visible region. In the case of 6,15-dibora-5a,6a,14a,15a-tetraaza-s-indaceno[2,3-b:6,7-b′]difluorene derivatives (anti-bis-benzoBODIPY), the absorption and emission maxima exceed 840 nm.

A 2-fluoro-substituted pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimer with a 1,4-di-n-propyl piperazine linker was studied with respect to its binding and crosslinking capability towards double-helical DNA targets. Duplex thermal stabilizations upon drug binding as measured by UV melting experiments suggest that two guanine bases separated by four AT base pairs constitute the favorable binding site for the PBD dimer. Large stabilizations were observed for the self-complementary duplex d(AACAATTGTT)2 as well as for the non-self-complementary duplex d(AAGAATTGTT)·d(AACAATTCTT) with both guanines located on the same strand. Formation of interstrand and intrastrand crosslinks by the covalent binding of both PBD moieties of the dimer to the exocyclic 2-amino group of the two guanine bases within the duplex minor groove was confirmed by NMR structural studies. In both the symmetric and non-symmetric DNA–PBD adducts the newly created stereogenic center at C11 of the tricyclic PBD subunits favors an S configuration. Different orientations of the PBD aromatic A-ring with respect to the covalently modified guanine as observed in the non-symmetric complex are shown to result in characteristic changes of PBD H11 and H11a proton chemical shifts. Based on a compilation of available NMR data on various PBD complexes, these differences may be used as valuable probes for the identification of PBD orientational preferences in DNA–PBD adducts.

A NIR BODIPY dye bearing 3,4,4a-trihydroxanthene moieties by Xin-Dong Jiang; Ruina Gao; Yi Yue; Guo-Tao Sun; Weili Zhao (6861-6865).
A novel 3,4,4a-trihydroxanthene-fused pyrrole 2 was synthesized by the reaction of 2,3,4,4a-tetrahydro-1H-xanthen-1-one with 3-phenyl-2H-azirine in the presence of LDA. Utilizing this pyrrole 2, a NIR BODIPY 1 (λabs = 732 nm, λem = 747 nm) has been prepared. The new BODIPY 1 was stable, non-cytotoxic, and suited to labeling living cells for imaging assay in the NIR region.

Enantioselective, protecting group-free synthesis of 1S-ethyl-4-substituted quinolizidines by Mercedes Amat; Vladislav Semak; Carmen Escolano; Elies Molins; Joan Bosch (6866-6875).
A practical enantioselective protecting group-free four-step route to the key quinolizidinone 6 from phenylglycinol-derived bicyclic lactam 1 is reported. The Grignard addition reaction to 6 takes place stereoselectively to give 1-ethyl-4-substituted quinolizidines 4-epi-207I and 7–9. Following a similar synthetic sequence, 9a-epi-6 is also accessed. However, the addition of Grignard reagents to 9a-epi-6 proceeds in a non-stereoselective manner. In order to gain insight into the different stereochemical outcome in the two series, theoretical calculations on the iminium salts A and B have been performed. The study concludes that the addition of the hydride, which is the step that determines the configuration of the final products, occurs in a stereoelectronic controlled manner. The theoretical study is in agreement with the experimental results.

A highly enantio- and diastereoselective sulfa-Michael addition of thioacetic acid to α,β-disubstituted nitroalkenes catalysed by a chiral squaramide organocatalyst has been described. This organocatalytic reaction at an extremely low catalyst loading (0.2 mol%) furnished synthetically useful β-nitro sulfides in excellent yields with good diastereoselectivities and high enantioselectivities (up to 94 : 6 dr, 95% ee). In addition, the catalytic reaction can be performed on a 10 gram scale, and facile transformation into taurine derivative is also presented.

The binding of a series of indole-derived hosts to various ammonium cations in pure, buffered water is investigated using both solution phase 1H NMR studies and computational modeling. These hosts can engage their targets via the cation–pi interaction, electrostatic attraction, and the hydrophobic effect. The hydrophobic effect is shown to be a dominant influence in the strength of the binding interactions, both in terms of the hydrophobicity of the host and of the guest. Our findings show that small changes that reduce the host hydrophobic surface area without reducing either the number of negative charges or amount of aromatic surface area are found to significantly decrease binding. Additionally, the position of solubilizing charges is also shown to influence the preferred host geometry and resulting binding constants.

The emerging functional versatility of cellular glycans makes research on the design of synthetic inhibitors a timely topic. In detail, the combination of ligand (or headgroup or contact site) structure with spatial parameters that depend on topological and geometrical factors underlies the physiological selectivity of glycan-protein (lectin) recognition. We herein tested a panel of bi-, tri- and tetravalent compounds against two plant agglutinins and adhesion/growth-regulatory lectins (galectins). In addition, we examined the impact of headgroup tailoring (converting lactose to 2′-fucosyllactose) in combination with valency increase in two assay types of increasing biorelevance (from solid-phase binding to cell binding). Compounds were prepared using copper-catalysed azide alkyne cycloaddition from peracetylated lactosyl or 2′-fucosyllactosyl azides. Significant inhibition was achieved for the plant toxin with a tetravalent compound. Different levels of sensitivity were noted for the three groups of the galectin family. The headgroup extension to 2′-fucosyllactose led to a selectivity gain, especially for the chimera-type galectin-3. Valency increase established discrimination against the homodimeric proteins, whereas the combination of valency with the headgroup extension led to discrimination against the tandem-repeat-type galectin-8 for chicken galectins but not human galectins-3 and -4. Thus, detailed structure–activity profiling of glycoclusters combined with suitably modifying the contact site for the targeted lectin will help minimize cross-reactivity among this class of closely related proteins.

An efficient allylic amination of Morita–Baylis–Hillman acetates with simple aromatic amines provided good yields with excellent α-regioselectivity (up to exclusive α-product) under the catalysis of Pd2(dba)3/ferrocene-type diphosphine ligand.

Disila-analogues of the synthetic retinoids EC23 and TTNN: synthesis, structure and biological evaluation by Josef B. G. Gluyas; Christian Burschka; Steffen Dörrich; Judith Vallet; Hinrich Gronemeyer; Reinhold Tacke (6914-6929).
Silicon chemistry offers the potential to tune the effects of biologically active organic molecules. Subtle changes in the molecular backbone caused by the exchange of a carbon atom for a silicon atom (sila-substitution) can significantly alter the biological properties. In this study, the biological effects of a two-fold sila-substitution in the synthetic retinoids EC23 (4-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-ylethynyl)benzoic acid (4a)) and TTNN (6-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)-2-naphthoic acid (7a)) as well as their corresponding analogues with an indane instead of a 1,2,3,4-tetrahydronaphthalene skeleton (compounds 5a and 8a) were investigated. Two-fold C/Si exchange in 4a, 5a, 7a and 8a leads to the silicon-analogues disila-EC23 (4b), 5b, disila-TTNN (7b) and 8b, which contain a 1,2,3,4-tetrahydro-1,4-disilanaphthalene (4b, 7b) or 1,3-disilaindane skeleton (5b, 8b). Exchange of the SiCH2Si moiety of 5b for an SiOSi fragment leads to the disiloxane 6 (2-oxa-1,3-disilaindane skeleton). The EC23 derivative 5a, the TTNN derivative 8a and the silicon-containing analogues 4b, 5b, 6, 7b and 8b were synthesised, and the biological properties of the C/Si pairs 4a/4b, 5a/5b, 7a/7b and 8a/8b and compound 6 were evaluated in vivo using RAR isotype-selective reporter cells. EC23 (4a) and its derivatives disila-EC23 (4b), 5a, 5b and 6 are very potent RAR agonists, which are even more potent than the powerful reference compound TTNPB. Disila-substitution of EC23 (4a) and 5a leads to a moderate decrease in RARα activation, whereas the RARβ,γ activation is almost not affected. In contrast, two-fold C/Si exchange in the weak retinoid agonist TTNN (7a) and 8a resulted in considerably different effects: a significant increase (7a→7b) and almost no change (8a→8b) in transcription activation potential for all three RAR isotypes. Disila-TTNN (7b) can be regarded as a powerful RARβ,γ-selective retinoid.

Amphiphilic 2,6-pyridylene ethynylene “meta-ethynylpyridine” polymers having chiral oligo(oxyethylene) side chains were developed as hosts for saccharide recognition. The polymers were prepared via a Sonogashira reaction and fractionated by gel permeation chromatography (GPC). They showed circular dichroism (CD) activity due to their higher-order chiral helical structures, and their CD and UV-vis spectra changed depending on not only saccharide recognition but also molecular size, temperature, and metal cation recognition.

Double diastereoselection in anti aldol reactions mediated by dicyclohexylchloroborane between an l-erythrulose derivative and chiral aldehydes by Santiago Díaz-Oltra; Purificación Ruiz; Eva Falomir; Juan Murga; Miguel Carda; J. Alberto Marco (6937-6944).
Anti aldol reactions of an l-erythrulose derivative with several α-chiral aldehydes mediated by dicyclohexylboron chloride are examined. Good yields and stereoselectivities are observed. The results are best explained when the reactions are assumed to occur via boat-like transition states with minimization of 1,3-allylic strain and avoidance of syn pentane interactions.

First total synthesis of dioxepine bastadin 3 by Santiago Pérez-Rodríguez; Raquel Pereira-Cameselle; Ángel R. de Lera (6945-6950).
The synthesis of dioxepine bastadin 3, a tyrosine–tyramine derivative with a dibenzo-1,3-dioxepine scaffold that is rarely present among natural products, is described. The dibenzo-1,3-dioxepine ring was formed early in the sequence and the (E)-2-(hydroxyimino)-N-alkylamide was generated in the last step by oxidation of the 2-amino-N-alkylamide precursor. The presumably biogenetic late-stage ring formation starting from congener bastadin 3 failed. A new synthesis of this alkaloid was also developed. This new route requires a minimal use of protecting groups and the order of the two key steps was reversed relative to the route to dioxepine bastadin 3.

Anion binding in aqueous media by a tetra-triazolium macrocycle by Nicholas G. White; Sílvia Carvalho; Vítor Félix; Paul D. Beer (6951-6959).
Three tetra-triazole macrocycles were synthesized in good yields by the copper(i)-catalysed cycloaddition of bis-triazole azides and bis-alkynes. One of these was alkylated to give a cyclic tetra-triazolium receptor, which complexes anions strongly in competitive DMSO–water mixtures. In 1 : 1 DMSO–water, the tetracationic receptor exhibits a preference for the larger halides, bromide and iodide, with all halides associating more strongly than the oxoanion, acetate. The sulfate dianion is complexed far more strongly than any of the monobasic anions (Ka > 104 M−1). Quantum mechanics/molecular mechanics simulations corroborate the experimentally determined anion binding selectivity trends.

Interactions of 2-, 3- and 4-formyl phenylboronic acids (FPBAs) with sugars, amino sugars, aminoglycosides and various poly- and monoamines have been studied by UV-vis, 1H and 11B NMR titrations in water at variable pH. Behavior of 2-FPBA was anomalous in several aspects. Transformation of the acid into its conjugate base was slow in NMR time scale and was accompanied by intramolecular cyclization affording the respective benzoboroxole. The equilibrium constants for imine formation (Kimine) between 2-FPBA and simple monoamines including amino sugars were ca. 2 orders of magnitude larger than those with other isomers. Still one order of magnitude larger Kimine values were observed for 2-FPBA with aminoglycosides (kanamycin, amikacin, gentamicin, neomycin) and polyamines (spermine, spermidine). The examination of UV-vis and 11B NMR spectra of imines formed with 2-FPBA showed that formally neutral Schiff bases in fact were zwitterionic species containing a protonated imine group and an anionic B(OH)3 group. The enhanced stability of imines with monoamines can therefore be attributed to the electrostatic stabilization provided by the zwitterionic structure and further increased stability of imines with antibiotics and polyamines is explicable by additional stabilization of the borate anionic group by ion paring with ammonium groups not involved in Schiff base formation. Thanks to high molar absorptivity of protonated imines interaction of 2-FPBA with aminoglycosides allows detecting them spectrophotometrically in a μM concentration range in neutral aqueous solutions in the presence of sugars, amino sugars and amino acids.

A new and easy-to-prepare gelator based on cyano-substituted amide (BPNIA) was designed and synthesized. BPNIA could form thermoreversible gel in DMSO–H2O (v/v, 9 : 1) and ultrasound-stimulated gel in DMSO. FT-IR, UV–vis and XRD spectra indicated that the gelator molecules self-assemble into a fibrous network resulting from the cooperation of intermolecular hydrogen bonding, π–π stacking and cyano interactions. BPNIA can act as a highly selective colorimetric sensor for fluoride in DMSO, overcoming the interference of H2PO4, AcO and other halide anions. The deprotonation of the NH groups is responsible for the dramatic color change from colorless to yellow. Interestingly, the organogel of BPNIA could allow a two channel fluoride response by proton controlled reversible sol–gel transition and color changes.

Direct, nucleophilic radiosynthesis of [18F]trifluoroalkyl tosylates: improved labelling procedures by Patrick J. Riss; Valentina Ferrari; Laurent Brichard; Paul Burke; Robert Smith; Franklin I. Aigbirhio (6980-6986).
A rapid and efficient protocol to afford the title compound 2-[18F]-fluoro-2,2-difluoroethyl tosylate ([18F]7b) is described. Starting from [18F]fluoride ion, labelling reagent 7b was obtained in good yields and a high specific radioactivity. Compound ([18F]7b) was then used to synthesise a prospective radiotracer for PET-imaging in dementia.

An efficient high yielding improved method for the enantio- and diastereoselective cyclopropanation of chiral epoxides using triethylphosphonoacetate and base (Wadsworth–Emmons cyclopropanation) is reported. The utility of this protocol is illustrated by concise and practical synthesis of cascarillic acid, grenadamide and L-(−)-CCG-II, a cyclopropane containing natural products.

The tin(iv) bromide promoted reaction of 7-hydroxy-7-phenylhept-2-enyl(tributyl)stannane 11 with benzaldehyde gave a mixture of the epimeric 1,8-diphenyloct-3-ene-1,8-diols 12 and so indirect methods were developed for aliphatic 1,8-stereocontrol to complete diastereoselective syntheses of (±)-patulolide C 1 and (±)-epipatulolide C 40. (5Z)-3,7-syn-7-(2-Trimethylsilylethoxy)methoxyocta-1,5-dien-3-ol 17 was prepared from the tin(iv) chloride promoted reaction of 4-(2-trimethylsilylethoxy)methoxypent-2-enyl(tributyl)stannane 16 with acrolein (1,5-syn : 1,5-anti = 96 : 4). An Ireland–Claisen rearrangement of the corresponding benzoyloxyacetate 21 with in situ esterification of the resulting acid using trimethylsilyldiazomethane gave methyl (4E,7Z)-2,9-anti-2-benzyloxy-9-(2-trimethylsilylethoxy)methoxydeca-4,7-dienoate 22 together with 10–15% of its 2,9-syn-epimer 26, the 2,9-syn- : 2,9-anti-ratio depending on the conditions used. An 88 : 12 mixture of esters was taken through to the tert-butyldiphenylsilyl ether 38 of (±)-patulolide C 1 together with 6% of its epimer 39, by reduction, a Wittig homologation and deprotection/macrocyclisation. Following separation of the epimeric silyl ethers, deprotection of the major epimer 38 gave (±)-patulolide C 1. The success of 2,3-Wittig rearrangements of allyl ethers prepared from (5Z)-3,7-syn-7-(2-trimethylsilylethoxy)methoxyocta-1,5-dien-3-ol 17 was dependent on the substituents on the allyl ether. Best results were obtained using the pentadienyl ether 56 and the cinnamyl ether 49 that rearranged with >90 : 10 stereoselectivity in favour of (1E,5E,8Z)-3,10-syn-1-phenyl-10-(2-trimethylsilylethoxy)methoxyundeca-1,5,8-trien-3-ol 50. This product was taken through to the separable silyl ethers 38 and 39, ratio 7 : 93 by regioselective epoxidation and alkene reduction using diimide, followed by deoxygenation, ozonolysis, a Wittig homologation and selective deprotection/macrocyclisation. Deprotection of the major epimer 39 gave (±)-epipatulolide C 40.

Back cover (7015-7016).