Showing papers in "Organic and Biomolecular Chemistry in 2005"

Recognition and activation by ureas and thioureas: stereoselective reactions using ureas and thioureas as hydrogen-bonding donors.

Abstract: Hydrogen-bonding interaction plays a crucial role in the molecular recognition and activation processes of various biologically important reactions that are mediated by enzymes and antibodies in living organisms. Recently, it has been shown that a hydrogen-bonding donor can be used as a general acid catalyst for various types of reactions in organic chemistry. In this article, we describe enantioselective reactions catalyzed by urea and thiourea derivatives as general acid catalysts as well as diastereoselective reactions. This perspective provides an overview of this rapidly growing field.

The golden gate to catalysis

Abstract: The use of gold in homogeneous catalysis is a relatively new field of transition metal catalysis, but has already witnessed spectacular achievements. By virtue of their unique ability to activate carbon–carbon double and triple bonds as soft, carbophilic Lewis acids, gold salts are highly efficient catalysts for the formation of C–C, C–O, C–N, and C–S bonds. Moreover, they are capable of activating C–H bonds of aromatic and other substrates, opening unprecedented pathways for their functionalisation. By using chiral allenes as substrates, gold catalysts can even be applied in stereoselective target-oriented synthesis.

Organocatalysis with proline derivatives: improved catalysts for the asymmetric Mannich, nitro-Michael and aldol reactions

Abstract: Tetrazole and acylsulfonamide organocatalysts derived from proline have been synthesised and applied to the asymmetric Mannich, nitro-Michael and aldol reactions to give results that are superior to the proline-catalysed counterpart.

Lectins: tools for the molecular understanding of the glycocode

Abstract: Recent progress in glycobiology has revealed that cell surface oligosaccharides play an essential role in recognition events. More precisely, these saccharides may be complexed by lectins, carbohydrate-binding proteins other than enzymes and antibodies, able to recognise sugars in a highly specific manner. The ubiquity of lectin–carbohydrate interactions opens enormous potential for their exploitation in medicine. Therefore, extraordinary effort is made into the identification of new lectins as well as into the achievement of a deep understanding of their functions and of the precise mechanism of their association with specific ligands. In this review, a summary of the main features of lectins, particularly those found in legumes, will be presented with a focus on the mechanism of carbohydrate-binding. An overview of lectin–carbohydrate interactions will also be given, together with an insight into their energetics. In addition, therapeutic applications of lectins will be discussed.

Urea vs. thiourea in anion recognition

Abstract: Neutral anion receptors (LH) form stable 1 : 1 H-bond [LH⋯X]− complexes with carboxylates, halides and phosphate (X−). Some of the [LH⋯X]− complexes, in presence of an excess of X−, release an HX fragment, with formation of [HX2]− and the deprotonated receptor L−. The tendency towards deprotonation increases with the acidity of the receptor and with the stability of the [HX2]− self-complex. Thus, the more acidic thiourea containing receptor deprotonates in the presence all the investigated anions except chloride, whereas the less acidic urea containing receptor undergoes deprotonation only in the presence of fluoride, due to the high stability of [HF2]−.

Asymmetric hydrogenation of aromatic compounds

Abstract: The asymmetric hydrogenation of aromatic and heteroaromatic compounds arguably presents one of the most attractive methods for the synthesis of six-membered cyclic compounds. In recent years, a number of promising stereoselective methods for the asymmetric hydrogenation of pyridines and related heterocycles have been reported.

Novel molecular drug carrier: encapsulation of oxaliplatin in cucurbit[7]uril and its effects on stability and reactivity of the drug

Abstract: Oxaliplatin forms a stable 1 : 1 inclusion complex with cucurbit[7]uril as indicated by NMR, mass spectrometry, isothermal titration calorimetry and X-ray crystallography. The encapsulation of the drug results in a large enhancement in stability, a moderate decrease in reactivity toward guanosine but a much larger decrease in reactivity toward L-methionine, which suggests the encapsulation not only increases the stability of the drug but also may reduce unwanted side effects caused by protein binding of the platinum drug. A preliminary in vitro assay using various tumor cell lines reveals that the encapsulation results in a decrease in the antitumor activity of oxaliplatin.

DNA-programmed assembly of nanostructures

Abstract: DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.

Rational Design and Synthesis of New Quorum-Sensing Inhibitors Derived From Acylated Homoserine Lactones and Natural Products From Garlic

Abstract: Parallel solution-phase synthesis of sulfide AHL analogues (10a-s) by one-pot or a sequential approach is reported. The corresponding sulfoxides 13a-e and sulfones 14a-e were prepared to expand the diversity of the 19-member array of sulfides . Likewise, dithianes 12a-c were prepared with similarity both to sulfides 10a-s and to bioactive structures from garlic. Design and biological screening of all compounds presented in this work targeted inhibition of quorum-sensing comprising competitive inhibition of transcriptional regulators LuxR and LasR. The design was based on critical interactions within the binding-site and structural motifs in molecular components isolated from garlic, 7 and 8, shown to be quorum-sensing inhibitors but not antibiotics. A potent quorum-sensing inhibitor N-(heptylsulfanylacetyl)-l-homoserine lactone (10c) was identified. Together with data collected for the other analogues, the resulting structure-activity relationship led to a hypothesis in which competitive binding was assumed.

Boron dipyrromethene fluorophore based fluorescence sensor for the selective imaging of Zn(II) in living cells

Abstract: A simple PET fluorescence sensor (BDA) for Zn2+ that utilizes 1,3,5,7-tetramethyl-boron dipyrromethene as a reporting group and di(2-picolyl)amine as a chelator for Zn2+ has been synthesized and characterized. BDA has an excitation (491 nm) and emission wavelength (509 nm) in the visible range. The fluorescence quantum yields of the zinc-free and zinc-bound states of BDA are 0.077 and 0.857, respectively. With a low pKa of 2.1 ± 0.1, BDA has the advantage of less sensitivity to pH than fluorescein-based Zn2+ sensors, and the fluorescence emission of zinc-binding is pH-independent in the range of pH 3–10. Under physiological conditions, metal ions such as Na+, K+, Ca2+, Mg2+, Mn2+ and Fe2+ have little interference. The apparent dissociation constant (Kd) is 1.0 ± 0.1 nM. Using fluorescence microscopy, the sensor is shown to be capable of imaging intracellular Zn2+ changes.

Chemical studies on antioxidant mechanisms and free radical scavenging properties of lignans

Abstract: The antioxidant activity, in terms of radical scavenging capacity, of altogether 15 different lignans was measured by monitoring the scavenging of the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The effect of differences in skeletal arrangement or the degree of oxidation of the lignans was investigated in a structure–activity relationship study. A large variety in the radical scavenging capacities of the different lignans was observed and related to some structural features. Lignans with catechol (3,4-dihydroxyphenyl) moieties exhibited the highest radical scavenging capacity, while the corresponding guaiacyl (3-methoxy-4-hydroxyphenyl) lignans showed a slightly weaker scavenging capacity. In addition, the butanediol structure was found to enhance the activity, whereas a higher degree of oxidation at the benzylic positions decreased the activity. Additionally, the readily available lignans (−)-secoisolariciresinol, a mixture of hydroxymatairesinol epimers and (−)-matairesinol were studied in more detail, including kinetic measurements and identification of oxidation products in the reactions with DPPH and ABAP (2,2-azobis(2-methylpropionamidine) dihydrochloride. The identification of reaction products, by GC–MS, HPLC–MS and NMR spectroscopy, showed that dimerisation of the two aromatic moieties was the major radical termination reaction. Also, the formation of adducts was a predominant reaction in the experiments with ABAP. The kinetic data obtained from the reactions between the lignans and DPPH indicated a complex reaction mechanism.

Catalytic asymmetric hydroamination of non-activated olefins

Abstract: Hydroamination is a highly atom-economical process in which an amine N–H functionality is added to an unsaturated carbon–carbon linkage. This potentially highly useful process gives access to various nitrogen-containing basic and fine chemicals as well as naturally occurring alkaloid skeletons. Asymmetric hydroamination reactions promoted by chiral catalysts are particularly attractive. This review highlights recent progress in the development of early transition metal catalysts for the asymmetric hydroamination of non-activated alkenes.

Synthesis and photophysical evaluation of charge neutral thiourea or urea based fluorescent PET sensors for bis-carboxylates and pyrophosphate.

Abstract: The synthesis of the fluorescent photoinduced electron transfer (PET) chemosensors 1–3 for bis-anions such as bis-carboxylates and pyrophosphate in organic solvents is described herein. These sensors are based on the receptor–spacer–fluorophore–spacer–receptor motif where the receptors are charge neutral aromatic thiourea or urea receptors and the fluorophore is anthracene. The anion recognition was evaluated using 1H NMR as well as absorption and fluorescence spectroscopy in DMSO. For simple anions such as acetate or fluoride, the recognition was shown to be through hydrogen bonding of the corresponding anion to the receptors. This gave rise to only minor changes in the absorption spectra, but significant changes in the fluorescence emission spectra, which was substantially (70–95%) quenched. Analysis of these recognition events implied a 1 : 2 (sensor : anion) binding and ideal PET behaviour for ions such as AcO− and H2PO4−. For F−, the luminescent quenching indicated a 1 : 1 binding, but we deduced that this was due more to complete quenching of the excited state after the addition of one equivalent of the anion. For all of the anions, the quenching contributed to enhanced efficiency of PET from the receptors to the excited state of the fluorophore. In the case of the bis-anions (ambient), such as di-carboxylates, similar fluorescence quenching was observed. However, here either a 1 : 1 or a 1 : 2 binding was observed depending on the length of the spacer separating the two carboxylate moieties and the nature of the receptor. Whereas both pyrophosphate and malonate gave rise to a 1 : 1 binding, glutarate gave rise to ∼1 : 2 binding for the thiourea sensors 1 and 2. However, for the urea based sensor 3, the binding was found to be 1 : 1 for all the bis-anions. For such a 1 : 1 binding we propose that the anion most likely bridges the fluorophore moiety. This was also evident from the 1H NMR (DMSO-d6) spectrum where the anthracene resonances were significantly affected. By simply modifying the electronic structure of the receptor, the sensitivity of the recognition process could also be modified; e.g. compound 1, bearing the trifluoromethyl substituent, showed stronger binding to the bis-anions than 2, which possessed a simple phenyl moiety.

Oligo- and poly-nucleotides: 50 years of chemical synthesis

Abstract: It is fifty years since the first chemical synthesis of a dinucleoside phosphate and a dinucleotide with natural 3′→5′-internucleotide linkages was reported The main developments in the methodology of oligo- and poly-nucleotide synthesis that have taken place since are described

Biotransformation of the sesquiterpene (+)-valencene by cytochrome P450cam and P450BM-3

Abstract: The sesquiterpenoids are a large class of naturally occurring compounds with biological functions and desirable properties. Oxidation of the sesquiterpene (+)-valencene by wild type and mutants of P450cam from Pseudomonas putida, and of P450BM-3 from Bacillus megaterium, have been investigated as a potential route to (+)-nootkatone, a fine fragrance. Wild type P450cam did not oxidise (+)-valencene but the mutants showed activities up to 9.8 nmol (nmol P450)−1 min−1, with (+)-trans-nootkatol and (+)-nootkatone constituting >85% of the products. Wild type P450BM-3 and mutants had higher activities (up to 43 min−1) than P450cam but were much less selective. Of the many products, cis- and trans-(+)-nootkatol, (+)-nootkatone, cis-(+)-valencene-1,10-epoxide, trans-(+)-nootkaton-9-ol, and (+)-nootkatone-13S,14-epoxide were isolated from whole-cell reactions and characterised. The selectivity patterns suggest that (+)-valencene has one binding orientation in P450cam but multiple orientations in P450BM-3.

New directions in supramolecular transition metal catalysis

Abstract: Supramolecular chemistry has grown into a major scientific field over the last thirty years and has fueled numerous developments at the interfaces with biology and physics, clearly demonstrating its potential at a multidisciplinary level. Simultaneously, organometallic chemistry and transition metal catalysis have matured in an incredible manner, broadening the pallet of tools available for chemical conversions. The interface between supramolecular chemistry and transition metal catalysis has received surprisingly little attention. It provides, however, novel and elegant strategies that could lead to new tools in the search for effective catalysts, as well as the possiblity of novel conversions induced by metal centres that are in unusual environments. This perspective describes new approaches to transition metal catalyst development that evolve from a combination of supramolecular strategies and rational ligand design, which may offer transition metal catalysts for future applications.

Chemistry and biology of wortmannin.

Abstract: Recent synthetic and biological studies of the viridin class of steroidal furans have revealed multiple opportunities for fundamental discoveries as well as advanced drug design. Wortmannin is a potent enzyme inhibitor that binds to the ATP site of important regulatory kinases such as PI-3 kinase and Polo-like kinase. The natural product shares a unique mechanism-based biological activation pathway with other viridins. Furthermore, while there have been several encouraging approaches toward the total synthesis of these compounds, there is still ample room for improvements in synthetic strategies and tactics, and the development of structurally simplified analogs that exert more specific biological effects and are devoid of toxicity issues that have thwarted the clinical development of the parent compounds.

One-pot multi-step synthesis: a challenge spawning innovation.

Abstract: Creating one-pot synthetic routes is a challenge that is already spawning new chemistry, enzymes, materials, and mechanistic insight. Through one-pot reactions, the chemical products that add value to our lives can be produced with less waste and greater economic benefits. Within this Emerging Area, we describe models for designing one-pot reactions as well as advanced catalysts created to facilitate their realization.

Enantioselective Friedel–Crafts type addition of indoles to nitro-olefins using a chiral hydrogen-bonding catalyst – synthesis of optically active tetrahydro-β-carbolines

Abstract: The enantioselective Friedel–Crafts addition of indoles to nitro-olefins using chiral hydrogen-bonding bis-sulfonamides as the catalysts has been developed. The reactions, in the presence of only 2 mol% catalyst, generally proceed in high yields and with enantioselectivities up to 64% ee, and the enantiomeric excess can be improved to >98% ee by recrystallization. Various synthetic transformations of the Friedel–Crafts adducts are demonstrated: the nitro group can easily be reduced to the corresponding amine and the product obtained can undergo a stereocontrolled Pictet–Spengler cyclization to give, for example, enantiopure tetrahydro-β-carbolines. The X-ray structure of the chiral bis-sulfonamides has been determined and based on these structures the mechanism for the stereoselectivity in the reaction is discussed.

Synthesis and characterisation of highly emissive and kinetically stable lanthanide complexes suitable for usage 'in cellulo'.

Abstract: The synthesis and photophysical characterisation are reported of a series of cationic, neutral and anionic europium and terbium complexes based on structurally related, nonadentate ligands based on the cyclen macrocycle. Each complex incorporates a tetraazatriphenylene moiety and overall absolute emission quantum yields are in the range 15–40% in aerated aqueous media. Dynamic quenching of the lanthanide excited state occurs with electron-rich donors, e.g. iodide, ascorbate and urate, and a mechanistic interpretation is put forward involving an electron transfer process. The cationic lanthanide complexes are taken up by NlH/3T3 cells and tend to localise inside the cell nucleus.

Two-stage enzyme mediated drug release from LMWG hydrogels

Abstract: An enzymatically cleavable low molecular weight gelator-(model) drug conjugate system can be employed to effect a two-step enzyme mediated drug release, demonstrating the potential of LMWG systems for the development of drug delivery devices.

A chiral molecular recognition approach to the formation of optically active quaternary centres in aza-Henry reactions

Abstract: An approach to asymmetric catalysis based on chiral molecular recognition by the combination of chiral Lewis acids and chiral organocatalysis for the formation of optically active quarternary centers in the aza-Henry reaction is presented; this procedure leads to products with up to 98% ee and a diastereomeric ratio of 14 : 1 in excellent yields with catalyst loadings of 5 mol%.

Antioxidant activity of olive phenols: mechanistic investigation and characterization of oxidation products by mass spectrometry

Abstract: In this work, the antioxidant activity of olive phenols is first characterized by their stoichiometries ntot (number of radicals trapped per antioxidant molecule) and their rate constants for the first H-atom abstraction k1 by the stable radical DPPH. It appears that oleuropein, hydroxytyrosol and caffeic acid have the largest k1 values, whereas dihydrocaffeic acid, an intestinal metabolite of caffeic acid, is the best antioxidant in terms of ntot. For phenols with a catechol moiety ntot is higher than two, implying an antioxidant effect of their primarily formed oxidation products. A HPLC–MS analysis of the main products formed in the AAPH-induced oxidation of olive phenols reveals the presence of dimers and trimers. With hydroxytyrosol and dihydrocaffeic acid, oligomerization can take place with the addition of water molecules. The antioxidant activity of olive phenols is then evaluated by their ability to inhibit the AAPH-induced peroxidation of linoleic acid in SDS micelles. It is shown that olive phenols and quercetin act as retardants rather than chain breakers like α-tocopherol. From a detailed mechanistic investigation, it appears that the inhibition of lipid peroxidation by olive phenols can be satisfactorily interpreted by assuming that they essentially reduce the AAPH-derived initiating radicals. Overall, olive phenols prove to be efficient scavengers of hydrophilic peroxyl radicals with a long lasting antioxidant effect owing to the residual activity of some of their oxidation products.

Arginine magic with new counterions up the sleeve

Abstract: The elusive questions how arginine-rich sequences allow peptides and proteins to penetrate cells or to form voltage-gated ion channels are controversial topics of current scientific concern. The possible contributions of exchangeable counterions to these puzzling processes remain underexplored. The objective of this report is to clarify scope and limitations of certain counteranions to modulate cellular uptake and anion carrier activity of oligo/polyarginines. The key finding is that the efficiency of counteranion activators depends significantly on many parameters such as activator–membrane and activator–carrier interactions. This finding is important because it suggests that counteranions can be used to modulate not only efficiency but also selectivity. Specifically, activator efficiencies are found to increase with increasing aromatic surface of the activator, decreasing size of the transported anion, increasing carrier concentration as well as increasing membrane fluidity. Efficiency sequences depend on membrane composition with coronene > pyrene ≫ fullerene > calix[4]arene carboxylates in fluid and crystalline DPPC contrasting to fullerene > calix[4]arene ≈ coronene > pyrene carboxylates in EYPC with or without cholesterol or ergosterol. In HeLa cells, the efficiency of planar activators (pyrene) exceeds that of spherical activators (fullerenes, calixarenes). Polyarginine complexes with pyrene and coronene activators exhibit exceptional excimer emission. Decreasing excimer emission with increasing ionic strength reveals dominant hydrophobic interactions with the most efficient carboxylate activators. Dominance of ion pairing with the inefficient high-affinity sulfate activators is corroborated by the reversed dependence on ionic strength. These findings on activator–carrier and activator–membrane interactions are discussed as supportive of arene-templated guanidinium–carboxylate pairing and interface-directed translocation as possible origins of the superb performance of higher arene carboxylates as activators.

Dye-functionalized head-to-tail coupled oligo(3-hexylthiophenes) - perylene-oligothiophene dyads for photovoltaic applications

Abstract: A series of novel donor–acceptor systems, consisting of head-to-tail coupled oligo(3-hexylthiophene)s covalently linked to perylenemonoimide, is described. These hybrid molecules, which differ by the length of the oligothiophene units from a monothiophene up to an octathiophene, were created via effective palladium-catalyzed Negishi and Suzuki cross-coupling reactions in good to excellent yields. The optical and electrochemical properties of these compounds were determined and based on this series structure–property relationships have been established which give vital information for the fabrication of photovoltaic devices. Because the synthesized perylenyl–oligothiophenes distinguish themselves by a high absorption between 300 and 550 nm and an almost complete fluorescence quenching of the perylene acceptor, they meet the requirements for organic solar cells.

Persistent pi radical cations: self-association and its steric control in the condensed phase.

Abstract: π Radical cations, which are highly reactive in general, can be made persistently stable by appropriate structural modification with heteroatoms, π-conjugated systems, and alkyl substituents. Many of these π radical cations undergo self-association in the condensed phase. The steric control of such self-association of stabilized π radical cations is the subject of the present article. Such an association can result in the formation of π- and/or σ-dimers. The π-dimerization in particular is now considered as an important intermolecular interaction for model studies of a charge-transport phenomenon in positively doped conducting polymers. On the other hand, the intermolecular interactions can be suppressed when the π-system is modified with sterically demanding structural units, for example, by annelation with bicycloalkene frameworks. This structural modification not only brings about unusual stabilization of the radical cations but provides valuable information on the electronic structure/properties of the positively charged π-systems in a segregated state.

Prebiotic carbohydrate synthesis: zinc–proline catalyzes direct aqueous aldol reactions of α-hydroxy aldehydes and ketones

Abstract: Zn–proline catalyzed aldolisation of glycoladehyde gave mainly tetroses whereas in the cross-aldolisation of glycoladehyde and rac-glyceraldehyde, pentoses accounted for 60% of the sugars formed with 20% of ribose.

[3 + 3] Cycloadditions and related strategies in alkaloid natural product synthesis.

Abstract: In this article we describe a strategically unusual approach to piperidines via formal [3 + 3] cycloaddition reactions. The scope and limitations of these processes are outlined and their employment in the synthesis of alkaloid natural products is delineated.

Electron-transfer mechanism in radical-scavenging reactions by a vitamin E model in a protic medium

Abstract: The scavenging reaction of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH˙) or galvinoxyl radical (GO˙) by a vitamin E model, 2,2,5,7,8-pentamethylchroman-6-ol (1H), was significantly accelerated by the presence of Mg(ClO4)2 in de-aerated methanol (MeOH). Such an acceleration indicates that the radical-scavenging reaction of 1H in MeOH proceeds via an electron transfer from 1H to the radical, followed by a proton transfer, rather than the one-step hydrogen atom transfer which has been observed in acetonitrile (MeCN). A significant negative shift of the one-electron oxidation potential of 1H in MeOH (0.63 V vs. SCE), due to strong solvation as compared to that in MeCN (0.97 V vs. SCE), may result in change of the radical-scavenging mechanisms between protic and aprotic media.

Tetrakis(imidazolium) macrocyclic receptors for anion binding.

Abstract: New (tetrakis)imidazolium macrocyclic receptor systems of variable cavity size have been synthesised by stepwise alkylation reactions of bis(imidazolium) precursor compounds. Proton NMR titration studies reveal the macrocycles to strongly bind halide and benzoate anions, with two receptor systems displaying notable selectivity for fluoride in competitive acetonitrile–water (9 : 1) solvent media.