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Beilstein Journal of Organic Chemistry (BJOC)

Abstract
The article describes the immobilization of different probe oligonucleotides (4, 7, 10) carrying each a racemic mixture of 2,3-bis(hexadecyloxy)propan-1-ol (1a) at the 5’-terminus on a stable artificial lipid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The bilayer separates two compartments (cis/trans channel) of an optical transparent microfluidic sample carrier with perfusion capabilities. Injection of unlabeled target DNA sequences (6, 8, or 9), differing in sequence and length, leads in the case of complementarity to the formation of stable DNA duplexes at the bilayer surface. This could be verified by Sybr Green I double strand staining, followed by incubation periods and thorough perfusions, and was visualized by single molecule fluorescence spectroscopy and microscopy. The different bilayer-immobilized complexes consisting of various DNA duplexes and the fluorescent dye were studied with respect to the kinetics of their formation as well as to their stability against perfusion.

Beilstein J. Org. Chem. 2014, 10, 2307–2321. doi:10.3762/bjoc.10.240

http://www.beilstein-journals.org/bjoc/content/10/1/240 2014/10/03 - 06:42

Abstract
Covalently interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function. The ideal DNA cross-link to study protein–DNA interactions should be specific and easy to synthesize, be stable during protein binding experiments, have a short covalent linker to avoid steric hindrance of protein binding, and should be available as a mimic for both A/T and G/C base pairs to cover all possible binding specificities. Several covalent interstrand cross-links have been described in the literature, but most of them fall short of at least one of the above criteria. We developed an efficient method to site-specifically and reversibly cross-link thionucleoside base pairs in synthetic duplex oligodeoxynucleotides by bisalkylation with 1,2-diiodoethane resulting in an ethylene-bridged base pair. Both linked A/T and G/C base pair analogs can conveniently be prepared which allows studying any base pair-opening enzyme regardless of its sequence specificity. The cross-link is stable in the absence of reducing agents but the linker can be quickly and tracelessly removed by the addition of thiol reagents like dithiothreitol. This property makes the cross-linking reaction fully reversible and allows for a switching of the linked base pair from locked to unlocked during biochemical experiments. Using the DNA methyltransferase from Thermus aquaticus (M.TaqI) as example, we demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI.

Beilstein J. Org. Chem. 2014, 10, 2293–2306. doi:10.3762/bjoc.10.239

http://www.beilstein-journals.org/bjoc/content/10/1/239 2014/10/03 - 06:42

Abstract
An efficient one-pot tandem cyclization/[3 + 2] cycloaddition reaction of N’-(2-alkynylbenzylidene)hydrazides with ethyl 4,4,4-trifluorobut-2-ynoate under silver triflate-catalyzed or electrophile-mediated conditions is described. Various trifluoromethylated pyrazolo[5,1-a]isoquinolines were afforded in moderate to excellent yield by this developed method.

Beilstein J. Org. Chem. 2014, 10, 2286–2292. doi:10.3762/bjoc.10.238

http://www.beilstein-journals.org/bjoc/content/10/1/238 2014/10/01 - 02:31

Abstract
An effective method for the synthesis of short oligoribonucleotides in solution has been elaborated. Novel 2'-O-(2-cyanoethyl)-5'-O-(1-methoxy-1-methylethyl) protected ribonucleoside 3'-phosphoramidites have been prepared and their usefulness as building blocks in RNA synthesis on a soluble support has been demonstrated. As a proof of concept, a pentameric oligoribonucleotide, 3'-UUGCA-5', has been prepared on a precipitative tetrapodal tetrakis(4-azidomethylphenyl)pentaerythritol support. The 3'-terminal nucleoside was coupled to the support as a 3'-O-(4-pentynoyl) derivative by Cu(I) promoted 1,3-dipolar cycloaddition. Couplings were carried out with 1.5 equiv of the building block. In each coupling cycle, the small molecular reagents and byproducts were removed by two quantitative precipitations from MeOH, one after oxidation and the second after the 5'-deprotection. After completion of the chain assembly, treatment with triethylamine, ammonia and TBAF released the pentamer in high yields.

Beilstein J. Org. Chem. 2014, 10, 2279–2285. doi:10.3762/bjoc.10.237

http://www.beilstein-journals.org/bjoc/content/10/1/237 2014/10/01 - 02:31

Abstract
A very simple and convenient reaction for 1,3-diketone preparation from carboxylic acids and aromatic ketones in TFAA/TfOH system is described. When the β-phenylpropionic acids were used as starting materials, they initially gave 1-indanones and then underwent further acylation with the formation of 2-(β-phenylpropionyl)-1-indanones as the main reaction products. In addition, the application of the proposed protocol allowed for the synthesis of selected polysubstituted pyrazoles in a one-pot procedure directly from acids and ketones.

Beilstein J. Org. Chem. 2014, 10, 2270–2278. doi:10.3762/bjoc.10.236

http://www.beilstein-journals.org/bjoc/content/10/1/236 2014/09/26 - 09:45

Abstract
The synthesis of a new phenolphthalein azide derivative, which can be easily utilized in polymer analogous reactions, is presented. The subsequent cycloaddition reaction with propargyl-functionalized methoxypoly(ethylene glycol) yielded polymers bearing phenolphthalein as the covalently attached end group. In presence of per-β-cyclodextrin-dipentaerythritol, the formation of stable inclusion complexes was observed, representing an interesting approach towards the formation of star shaped polymers. The decolorization of a basic polymer solution caused by the complexation was of great advantage since this behavior enabled following the complex formation by UV–vis spectroscopy and even the naked eye.

Beilstein J. Org. Chem. 2014, 10, 2263–2269. doi:10.3762/bjoc.10.235

http://www.beilstein-journals.org/bjoc/content/10/1/235 2014/09/26 - 09:45

Abstract
1,2,3-Triaminoguanidinium chloride was combined with benzaldehyde and hydratropic aldehyde to furnish the corresponding tris(imines), which were converted into 1,2,3-tris(benzylamino)guanidinium salts by catalytic hydrogenation in the former, and by borane reduction in the latter case. The resulting alkyl-substituted triaminoguanidinium salts underwent a threefold carbamoylation with aryl isocyanates to furnish 1,2,3-tris(ureido)guanidinium salts, while p-toluenesulfonyl isocyanate led only to a mono-ureido guanidinium salt. With aryl isothiocyanates, 3-hydrazino-1H-1,2,4-triazole-5(4H)-thione derivatives were obtained. Compounds 7a and 8 show interesting solid-state structures with intra- and intermolecular hydrogen bonds.

Beilstein J. Org. Chem. 2014, 10, 2255–2262. doi:10.3762/bjoc.10.234

http://www.beilstein-journals.org/bjoc/content/10/1/234 2014/09/24 - 19:58

Abstract
A combination of cyclic voltammetry and in situ scanning tunneling microscopy was employed to examine the adsorption and phase transition of 1,1’-dibenzyl-4,4’-bipyridinium molecules (abbreviated as DBV2+) on a chloride-modified Cu(111) electrode surface. The cyclic voltammogram (CV) of the Cu(111) electrode exposed to a mixture of 10 mM HCl and 0.1 mM DBVCl2 shows three distinguishable pairs of current waves P1/P’1, P2/P’2, and P3/P’3 which are assigned to two reversible electron transfer steps, representing the reduction of the dicationic DBV2+ to the corresponding radical monocationic DBV+• (P1/P’1) and then to the uncharged DBV0 (P3/P’3) species, respectively, as well as the chloride desorption/readsorption processes (P2/P’2). At positive potentials (i.e., above P1) the DBV2+ molecules spontaneously adsorb and form a highly ordered phase on the c(p × √3)-precovered Cl/Cu(111) electrode surface. A key element of this DBV2+ adlayer is an assembly of two individual DBV2+ species which, lined up, forms a so-called “herring-bone” structure. Upon lowering the electrode potential the first electron transfer step (at P1) causes a phase transition from the DBV2+-related herring-bone phase to the so-called "alternating stripe" pattern built up by the DBV+• species following a nucleation and growth mechanism. Comparison of both observed structures with those found earlier at different electrode potentials on a c(2 × 2)Cl-precovered Cu(100) electrode surface enables a clear assessment of the relative importance of adsorbate–substrate and adsorbate–adsorbate interactions, i.e., template vs self-assembly effects, in the structure formation process of DBV cations on these modified Cu electrode surfaces.

Beilstein J. Org. Chem. 2014, 10, 2243–2254. doi:10.3762/bjoc.10.233

http://www.beilstein-journals.org/bjoc/content/10/1/233 2014/09/24 - 19:58

Abstract
Monitoring glycoconjugates has been tremendously facilitated by the development of metabolic oligosaccharide engineering. Recently, the inverse-electron-demand Diels–Alder reaction between methylcyclopropene tags and tetrazines has become a popular ligation reaction due to the small size and high reactivity of cyclopropene tags. Attaching the cyclopropene tag to mannosamine via a carbamate linkage has made the reaction even more efficient. Here, we expand the application of cyclopropene tags to N-acylgalactosamine and N-acylglucosamine derivatives enabling the visualization of mucin-type O-glycoproteins and O-GlcNAcylated proteins through Diels–Alder chemistry. Whereas the previously reported cyclopropene-labeled N-acylmannosamine derivative leads to significantly higher fluorescence staining of cell-surface glycoconjugates, the glucosamine derivative gave higher labeling efficiency with protein preparations containing also intracellular proteins.

Beilstein J. Org. Chem. 2014, 10, 2235–2242. doi:10.3762/bjoc.10.232

http://www.beilstein-journals.org/bjoc/content/10/1/232 2014/09/24 - 19:58

Abstract
Higher aminosugars are interesting targets in carbohydrate synthesis since these compounds play important roles in biological systems. However, their availability from natural sources is limited. Thus, in order to investigate their biological function, the development of facile and adaptable routes to this class of compounds is of fundamental importance. Our synthetic route towards these target molecules makes use of readily accessible pentoses and hexoses, which are subjected to indium-mediated two-carbon chain elongation. Subsequent ozonolysis and treatment with base yields α,β-unsaturated aldehydes, which are stereoselectively epoxidized using Jørgenson’s protocol. After Wittig chain elongation the obtained allylic epoxides were regio- and stereoselectively opened with trimethylsilyl azide under palladium catalysis. Finally, a suitable deprotection protocol, starting with acidic acetate cleavage and ozonolysis was established. Peracetylation of the products simplifies purification and subsequent azide reduction followed by final deacetylation using methanolic sodium methoxide furnishes the title compounds.

Beilstein J. Org. Chem. 2014, 10, 2230–2234. doi:10.3762/bjoc.10.231

http://www.beilstein-journals.org/bjoc/content/10/1/231 2014/09/19 - 18:34

Abstract
Novel cis/trans-4- and cis/trans-5-(2-vinylstyryl)oxazoles have been synthesized by Wittig reactions from the diphosphonium salt of α,α’-o-xylene dibromide, formaldehyde and 4- and 5-oxazolecarbaldehydes, respectively. In contrast, trans-5-(2-vinylstyryl)oxazole has been synthesized by the van Leusen reaction from trans-3-(2-vinylphenyl)acrylaldehyde which is prepared from o-vinylbenzaldehyde and (formylmethylene)triphenylphosphorane. The 4- and 5-(2-vinylstyryl)oxazoles afford, by photochemical intramolecular cycloaddition, diverse fused oxazoline-benzobicyclo[3.2.1]octadienes, which are identified and characterized by spectroscopic methods. The photoproducts formed are relatively unstable and spontaneously or on silica gel undergo oxazoline ring opening followed by formation of formiato- or formamido-benzobicyclo[3.2.1]octenone derivatives. On irradiation of 4-(2-vinylstyryl)oxazole small quantities of electrocyclization product, 4-(1,2-dihydronaphthalen-2-yl)oxazole, are isolated and spectroscopically characterized.

Beilstein J. Org. Chem. 2014, 10, 2222–2229. doi:10.3762/bjoc.10.230

http://www.beilstein-journals.org/bjoc/content/10/1/230 2014/09/19 - 18:34

Abstract
Natural product-like macrocycles were designed as potential antibacterial compounds. The macrocycles featured a D-glucose unit fused into a 12- or 13-member macrolactone. The rings are connected via the C6’ and anomeric (C1’) positions of the monosaccharide. The new macrocycles/macrolides were characterized by X-ray crystallography. Their structures showed that, in addition to the ester and alkene units, the dihedral angle about the glycosidic linkage (exo-anomeric effect) influenced the overall shape of the molecules. Glycosylation of an available hydroxy group on the macrocycle gave a hybrid macrolide with features common to erythromycin and sophorlipid macrolactone. Weak antibiotic activity (MICs <100 μg/mL) was observed for several of the compounds.

Beilstein J. Org. Chem. 2014, 10, 2215–2221. doi:10.3762/bjoc.10.229

http://www.beilstein-journals.org/bjoc/content/10/1/229 2014/09/19 - 18:34

Abstract
A novel approach for the catalyzed formation of bisindolylmethane derivatives (BIMs) is described. This methodology is the unique example where AgOTf has been successfully used for the activation of aldehydes, giving easy access to a broad range of bisindolyl derivatives with excellent results. Moreover, the simplicity and easy operational methodology using a small amount of commercially available AgOTf (1–3 mol %), one of the lowest catalytic charge used in this process to date, makes this procedure an alternative approach for this interesting and appealing reaction.

Beilstein J. Org. Chem. 2014, 10, 2206–2214. doi:10.3762/bjoc.10.228

http://www.beilstein-journals.org/bjoc/content/10/1/228 2014/09/19 - 18:34

Abstract
Transition metal-mediated N–O bond cleavage reactions of heterobicycloalkene-fused 3-methyl-2-isoxazolines were investigated. Optimal cleavage conditions were found with Raney nickel/AlCl3 mediation in aqueous methanol. The reaction provided a diverse collection of novel heterobicycle-fused β-hydroxyketones with good to excellent yields (66–95%) and without the need for chromatographic purification.

Beilstein J. Org. Chem. 2014, 10, 2200–2205. doi:10.3762/bjoc.10.227

http://www.beilstein-journals.org/bjoc/content/10/1/227 2014/09/19 - 18:34

Abstract
The synthesis of 1,2,3-trisubstituted indoles was investigated. More specifically, straightforward synthetic routes towards 1-(1,2-diarylindol-3-yl)-N-PG-THIQs (PG = protecting group, THIQ = tetrahydroisoquinoline) employing transition metal-catalyzed C–H and N–H-bond functionalization were explored. It was found that the synthesis of the target compounds is strongly dependent on the order of events. Hence, depending on the requirements of a synthetic problem the most suitable and promising pathway can be chosen. Additionally, a new synthetic approach towards 1,2-diarylindoles starting from 1-arylindole could be established in the course of our investigation by using a palladium-catalyzed protocol. Such 1,2-diarylindoles were successfully reacted with N-Boc-THIQ to furnish 1,2,3-trisubstituted indoles as target compounds. Furthermore, regioselective N-arylation of protected and unprotected 1-(indol-3-yl)-THIQs was successfully conducted using either simple iron or copper salts as catalysts.

Beilstein J. Org. Chem. 2014, 10, 2186–2199. doi:10.3762/bjoc.10.226

http://www.beilstein-journals.org/bjoc/content/10/1/226 2014/09/19 - 18:34

Abstract
An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA.

Beilstein J. Org. Chem. 2014, 10, 2175–2185. doi:10.3762/bjoc.10.225

http://www.beilstein-journals.org/bjoc/content/10/1/225 2014/09/12 - 16:39

Abstract
DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.

Beilstein J. Org. Chem. 2014, 10, 2166–2174. doi:10.3762/bjoc.10.224

http://www.beilstein-journals.org/bjoc/content/10/1/224 2014/09/12 - 16:39

Abstract
Carbon–oxygen single bonds are ubiquitous in natural products whereas efficient methods for their reductive defunctionalization are rare. In this work an environmentally benign protocol for the activation of carbon–oxygen single bonds of alcohols towards a reductive bond cleavage under visible light photocatalysis was developed. Alcohols were activated as 3,5-bis(trifluoromethyl)-substituted benzoates and irradiation with blue light in the presence of [Ir(ppy)2(dtb-bpy)](PF6) as visible light photocatalyst and Hünig’s base as sacrificial electron donor in an acetonitrile/water mixture generally gave good to excellent yields of the desired defunctionalized compounds. Functional group tolerance is high but the protocol developed is limited to benzylic, α-carbonyl, and α-cyanoalcohols; with other alcohols a slow partial C–F bond reduction in the 3,5-bis(trifluoromethyl)benzoate moiety occurs.

Beilstein J. Org. Chem. 2014, 10, 2157–2165. doi:10.3762/bjoc.10.223

http://www.beilstein-journals.org/bjoc/content/10/1/223 2014/09/10 - 22:40

Abstract
We report on the synthesis as well as the optical, electrochemical and morphological properties of two polyrotaxanes (4a and 4b), which consist of electron-accepting 9,9-dicyanomethylenefluorene 1 as an inclusion complex in persilylated β- or γ-cyclodextrin (TMS-β-CD, TMS-γ-CD) (1a, 1b) and methyltriphenylamine as an electron-donating molecule. They are statistically distributed into the conjugated chains of 9,9-dioctylfluorene 3 and compared with those of the corresponding non-rotaxane 4 counterpart. Rotaxane formation results in improvements of the solubility, the thermal stability, and the photophysical properties. Polyrotaxanes 4a and 4b exhibited slightly red-shifted absorption bands with respect to the non-rotaxane 4 counterpart. The fluorescence lifetimes of polyrotaxanes follow a mono-exponential decay with a value of τ = 1.14 ns compared with the non-rotaxane, where a bi-exponential decay composed of a main component with a relative short time of τ1 = 0.88 (57.08%) and a minor component with a longer lifetime of τ2 = 1.56 ns (42.92%) were determined. The optical and electrochemical band gaps (ΔEg) as well as the ionization potential and electronic affinity characterized by smaller values compared to the values of any of the constituents. AFM reveals that the film surface of 4a and 4b displays a granular morphology with a lower dispersity supported by a smaller roughness exponent compared with the non-rotaxane counterpart.

Beilstein J. Org. Chem. 2014, 10, 2145–2156. doi:10.3762/bjoc.10.222

http://www.beilstein-journals.org/bjoc/content/10/1/222 2014/09/10 - 22:40

Abstract
The imidazole–Ag(I)–imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I) leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.

Beilstein J. Org. Chem. 2014, 10, 2139–2144. doi:10.3762/bjoc.10.221

http://www.beilstein-journals.org/bjoc/content/10/1/221 2014/09/10 - 22:40

Abstract
IsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability.

Beilstein J. Org. Chem. 2014, 10, 2131–2138. doi:10.3762/bjoc.10.220

http://www.beilstein-journals.org/bjoc/content/10/1/220 2014/09/08 - 20:06

Abstract
We report a new synthetic route to 5,11-disubstituted indeno[1,2-b]fluorene-6,12-diones that is amenable to larger scale reactions, allowing for the preparation of gram amounts of material. With this new methodology, we explored the effects on crystal packing morphology for the indeno[1,2-b]fluorene-6,12-diones by varying the substituents on the silylethynyl groups.

Beilstein J. Org. Chem. 2014, 10, 2122–2130. doi:10.3762/bjoc.10.219

http://www.beilstein-journals.org/bjoc/content/10/1/219 2014/09/06 - 00:13

Abstract
This review discusses the tertiary phosphines possessing various chiral skeletons that have been used in asymmetric nucleophilic organocatalytic reactions, including annulations of allenes, alkynes, and Morita–Baylis–Hillman (MBH) acetates, carbonates, and ketenes with activated alkenes and imines, allylic substitutions of MBH acetates and carbonates, Michael additions, γ-umpolung additions, and acylations of alcohols.

Beilstein J. Org. Chem. 2014, 10, 2089–2121. doi:10.3762/bjoc.10.218

http://www.beilstein-journals.org/bjoc/content/10/1/218 2014/09/06 - 00:13

Beilstein J. Org. Chem. 2014, 10, 2087–2088. doi:10.3762/bjoc.10.217

http://www.beilstein-journals.org/bjoc/content/10/1/217 2014/09/06 - 00:13

Abstract
The study of Pd-catalysed cyclisation reactions of alkenols using different catalytic systems is reported. These transformations affect the stereoselective construction of mono- and/or bicyclic oxaheterocyclic derivatives depending on a starting alkenol. The substrate scope and proposed mechanism of Pd-catalysed cyclisation reactions are also discussed. Moreover, the diastereoselective Pd-catalysed cyclisation of appropriate alkenols to tetrahydrofurans and subsequent cyclisation provided properly substituted 2,5-dioxabicyclo[2.2.1]heptane and 2,6-dioxabicyclo[3.2.1]octane, respectively. Such bicyclic ring subunits are found in many natural products including ocellenynes and aurovertines.

Beilstein J. Org. Chem. 2014, 10, 2077–2086. doi:10.3762/bjoc.10.216

http://www.beilstein-journals.org/bjoc/content/10/1/216 2014/09/03 - 13:19

Abstract
Chiral phosphorus ligands have been widely used in transition metal-catalyzed asymmetric reactions. Herein, we report a new synthesis approach of chiral biaryls containing a phosphorus moiety using P(O)R2-directed Pd-catalyzed C–H activation; the functionalized products are produced with good enantioselectivity.

Beilstein J. Org. Chem. 2014, 10, 2071–2076. doi:10.3762/bjoc.10.215

http://www.beilstein-journals.org/bjoc/content/10/1/215 2014/09/03 - 13:19

Abstract
A facile and efficient synthetic protocol for the synthesis of α-amino amidines has been developed using a molecular iodine-catalyzed three-component coupling reaction of isocyanides, amines, and aldehydes. The presented strategy offers the advantages of mild reaction conditions, low environmental impact, clean and simple methodology, high atom economy, wide substrate scope and high yields.

Beilstein J. Org. Chem. 2014, 10, 2065–2070. doi:10.3762/bjoc.10.214

http://www.beilstein-journals.org/bjoc/content/10/1/214 2014/09/03 - 13:19

Abstract
We have investigated the adsorption of perylene-3,4,9,10-tetracarboxylic acid dianhydride (PTCDA) on the clean and on the oxygen pre-covered Cu(100) surface [referred to as (√2 × 2√2)R45° – 2O/Cu(100)] by scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Our results confirm the (4√2 × 5√2)R45° superstructure of PTCDA/Cu(100) reported by A. Schmidt et al. [J. Phys. Chem. 1995, 99,11770–11779]. However, contrary to Schmidt et al., we have no indication for a dissociation of the PTCDA upon adsorption, and we propose a detailed structure model with two intact PTCDA molecules within the unit cell. Domains of high lateral order are obtained, if the deposition is performed at 400 K. For deposition at room temperature, a significant density of nucleation defects is found pointing to a strong interaction of PTCDA with Cu(100). Quite differently, after preadsorption of oxygen and formation of the (√2 × 2√2)R45° – 2O/Cu(100) superstructure on Cu(100), PTCDA forms an incommensurate monolayer with a structure that corresponds well to that of PTCDA bulk lattice planes.

Beilstein J. Org. Chem. 2014, 10, 2055–2064. doi:10.3762/bjoc.10.213

http://www.beilstein-journals.org/bjoc/content/10/1/213 2014/09/03 - 13:19

Abstract
We have developed a new photoremovable protecting group for caging phosphates in the near UV. Diethyl 2-(4-hydroxy-1-naphthyl)-2-oxoethyl phosphate (14a) quantitatively releases diethyl phosphate upon irradiation in aq MeOH or aq MeCN at 350 nm, with quantum efficiencies ranging from 0.021 to 0.067 depending on the solvent composition. The deprotection reactions originate from the triplet excited state, are robust under ambient conditions and can be carried on to 100% conversion. Similar results were found with diethyl 2-(4-methoxy-1-naphthyl)-2-oxoethyl phosphate (14b), although it was significantly less efficient compared with 14a. A key step in the deprotection reaction in aq MeOH is considered to be a Favorskii rearrangement of the naphthyl ketone motif of 14a,b to naphthylacetate esters 25 and 26. Disruption of the ketone-naphthyl ring conjugation significantly shifts the photoproduct absorption away from the effective incident wavelength for decaging of 14, driving the reaction to completion. The Favorskii rearrangement does not occur in aqueous acetonitrile although diethyl phosphate is released. Other substitution patterns on the naphthyl or quinolin-5-yl core, such as the 2,6-naphthyl 10 or 8-benzyloxyquinolin-5-yl 24 platforms, also do not rearrange by aryl migration upon photolysis and, therefore, do not proceed to completion. The 2,6-naphthyl ketone platform instead remains intact whereas the quinolin-5-yl ketone fragments to a much more complex, highly absorbing reaction mixture that competes for the incident light.

Beilstein J. Org. Chem. 2014, 10, 2038–2054. doi:10.3762/bjoc.10.212

http://www.beilstein-journals.org/bjoc/content/10/1/212 2014/08/30 - 16:30

Abstract
A new 4-hydroxy-L-proline derivative with a charged 1-ethylpyridinium-4-phenoxy substituent has been synthesized with the aim of facilitating mechanistic studies of proline-catalyzed reactions by ESI mass spectrometry. The charged residue ensures a strongly enhanced ESI response compared to neutral unmodified proline. The connection by a rigid linker fixes the position of the charge tag far away from the catalytic center in order to avoid unwanted interactions. The use of a charged catalyst leads to significantly enhanced ESI signal abundances for every catalyst-derived species which are the ones of highest interest present in a reacting solution. The new charged proline catalyst has been tested in the direct asymmetric inverse aldol reaction between aldehydes and diethyl ketomalonate. Two intermediates in accordance with the List–Houk mechanism for enamine catalysis have been detected and characterized by gas-phase fragmentation. In addition, their temporal evolution has been followed using a microreactor continuous-flow technique.

Beilstein J. Org. Chem. 2014, 10, 2027–2037. doi:10.3762/bjoc.10.211

http://www.beilstein-journals.org/bjoc/content/10/1/211 2014/08/30 - 16:30

Abstract
Under basic conditions 4,5,12,13-tetraacetyl[2.2]paracyclophane (9) cyclizes by a double aldol condensation to provide the two aldols 12 and 15 in a 3:7 ratio. The structures of these compounds were obtained from X-ray structural analysis, spectroscopic data, and mechanistic considerations. On acid treatment 12 is dehydrated to a mixture of the condensed five-membered [2.2]paracyclophane derivatives 18–20, whereas 15 yields a mixture of the isomeric cyclopentadienones 21–23. The structures of these elimination products are also deduced from X-ray and spectroscopic data. The sequence presented here constitutes the simplest route so far to cyclophanes carrying an annelated five-membered ring.

Beilstein J. Org. Chem. 2014, 10, 2021–2026. doi:10.3762/bjoc.10.210

http://www.beilstein-journals.org/bjoc/content/10/1/210 2014/08/30 - 16:30

Abstract
Ethynyl[2.2]paracyclophanes are shown to be useful substrates for the preparation of complex, highly unsaturated carbon frameworks. Thus both the pseudo-geminal- 2 and the pseudo-ortho-diethynylcyclophane 4 can be dimerized by Glaser coupling to the respective dimers 9/10 and 11/12. Whereas the former isomer pair could not be separated so far, the latter provided the pure diastereomers after extensive column chromatography/recrystallization. Isomer 11 is chiral and could be separated on a column impregnated with cellulose tris(3,5-dimethylphenyl)carbamate. The bridge-extended cyclophane precursor 18 furnished the ring-enlarged cyclophanes 19 and 20 on Glaser–Hay coupling. Cross-coupling of 4 and the planar building block 1,2-diethynylbenzene (1) yielded the chiral hetero dimer 22 as the main product. An attempt to prepare the biphenylenophane 27 from the triacetylene 24 by CpCo(CO)2-catalyzed cycloisomerization resulted in the formation of the cyclobutadiene Co-complex 26. Besides by their usual spectroscopic and analytical data, the new cyclophanes 11, 12, 19, 20, 22, and 26 were characterized by X-ray structural analysis.

Beilstein J. Org. Chem. 2014, 10, 2013–2020. doi:10.3762/bjoc.10.209

http://www.beilstein-journals.org/bjoc/content/10/1/209 2014/08/28 - 05:52

Abstract
Riboflavin (RF), also known as vitamin B2, belongs to the class of water-soluble vitamins and is widely present in a variety of food products. It is sensitive to light and high temperature, and therefore, needs a consideration of these factors for its stability in food products and pharmaceutical preparations. A number of other factors have also been identified that affect the stability of RF. These factors include radiation source, its intensity and wavelength, pH, presence of oxygen, buffer concentration and ionic strength, solvent polarity and viscosity, and use of stabilizers and complexing agents. A detailed review of the literature in this field has been made and all those factors that affect the photo, thermal and chemical degradation of RF have been discussed. RF undergoes degradation through several mechanisms and an understanding of the mode of photo- and thermal degradation of RF may help in the stabilization of the vitamin. A general scheme for the photodegradation of RF is presented.

Beilstein J. Org. Chem. 2014, 10, 1999–2012. doi:10.3762/bjoc.10.208

http://www.beilstein-journals.org/bjoc/content/10/1/208 2014/08/28 - 05:52

Abstract
The reaction of 3-substituted indoles with dehydroalanine (Dha) derivatives under Lewis acid-mediated conditions has been investigated. The formation of 2-substituted tryptophans is proposed to occur through a selective alkylative dearomatization–cyclization followed by C3- to C2-alkyl migration and rearomatization.

Beilstein J. Org. Chem. 2014, 10, 1991–1998. doi:10.3762/bjoc.10.207

http://www.beilstein-journals.org/bjoc/content/10/1/207 2014/08/28 - 05:52

Abstract
Readily accessible, low-valency glycoclusters based on a triazine core bearing D-galactose and L-fucose epitopes are able to inhibit biofilm formation by Pseudomonas aeruginosa. These multivalent ligands are simple to synthesize, are highly soluble, and can be either homofunctional or heterofunctional. The galactose-decorated cluster shows good affinity for Pseudomonas aeruginosa lectin lecA. They are convenient biological probes for investigating the roles of lecA and lecB in biofilm formation.

Beilstein J. Org. Chem. 2014, 10, 1981–1990. doi:10.3762/bjoc.10.206

http://www.beilstein-journals.org/bjoc/content/10/1/206 2014/08/28 - 05:52

Abstract
Conformational preferences of the pyrrolidine ring in nucleotide analogs 7–14 were investigated by means of NMR and molecular modeling. The effect of the relative configuration of hydroxy and nucleobase substituents as well as the effect of the alkylation or acylation of the pyrrolidine nitrogen atom on the conformation of the pyrrolidine ring were studied. The results of a conformational analysis show that the alkylation/acylation can be effectively used for tuning the pyrrolidine conformation over the whole pseudorotation cycle.

Beilstein J. Org. Chem. 2014, 10, 1967–1980. doi:10.3762/bjoc.10.205

http://www.beilstein-journals.org/bjoc/content/10/1/205 2014/08/24 - 01:06

Abstract
Highly efficient CO2 absorption was realized through formation of zwitterionic adducts, combining synthetic strategies to ionic liquids (ILs) and coordination. The essence of our strategy is to make use of multidentate cation coordination between Li+ and an organic base. Also PEG-functionalized organic bases were employed to enhance the CO2-philicity. The ILs were reacted with CO2 to form the zwitterionic adduct. Coordination effects between various lithium salts and neutral ligands, as well as the CO2 capacity of the chelated ILs obtained were investigated. For example, the CO2 capacity of PEG150MeBu2N increased steadily from 0.10 to 0.66 (mol CO2 absorbed per mol of base) through the formation of zwitterionic adducts being stabilized by Li+.

Beilstein J. Org. Chem. 2014, 10, 1959–1966. doi:10.3762/bjoc.10.204

http://www.beilstein-journals.org/bjoc/content/10/1/204 2014/08/22 - 07:59

Abstract
The monomer 2-methacrylamido-caprolactam (4) was synthesized from methacryloyl chloride (3) and racemic α-amino-ε-caprolactam (2). Copolymerization of 4 with N,N-dimethylacrylamide (5) was carried out by a free-radical mechanism using 2,2’-azobis(2-methylpropionitrile) (AIBN) as an initiator. The new copolymers show a lower critical solution temperature (LCST) in water and an upper critical solution temperature (UCST) in ethanol, 1-propanol, and 1-butanol. The solubility properties of the copolymers can be influenced significantly by the addition of randomly methylated β-cyclodextrin (CD). The complexation of the copolymers with CD, was confirmed by the use of ROESY-NMR-spectroscopy.

Beilstein J. Org. Chem. 2014, 10, 1951–1958. doi:10.3762/bjoc.10.203

http://www.beilstein-journals.org/bjoc/content/10/1/203 2014/08/22 - 07:59

Abstract
The Grignard reaction of 2,3-O-isopropylidene-α-D-lyxo-pentodialdo-1,4-furanoside and benzylmagnesium chloride (or bromide) afforded a non-separable mixture of diastereomeric benzyl carbinols and diastereomeric o-tolyl carbinols. The latter resulted from an unexpected benzyl to o-tolyl rearrangement. The proportion of benzyl versus o-tolyl derivatives depended on the reaction conditions. Benzylmagnesium chloride afforded predominantly o-tolyl carbinols while the application of benzylmagnesium bromide led preferably to the o-tolyl carbinols only when used in excess or at higher temperatures. The structures of the benzyl and o-tolyl derivatives were confirmed unambiguously by NMR spectral data and X-ray crystallographic analysis of their 5-ketone analogues obtained by oxidation of the corresponding mixture of diastereomeric carbinols. A possible mechanism for the Grignard reaction leading to the benzyl→o-tolyl rearrangement is also proposed.

Beilstein J. Org. Chem. 2014, 10, 1942–1950. doi:10.3762/bjoc.10.202

http://www.beilstein-journals.org/bjoc/content/10/1/202 2014/08/22 - 07:59

Abstract
Dimethyl (β-substituted) vinylphosphonates do not readily undergo cross metathesis reactions with Grubbs catalyst and terminal alkenes. However, the corresponding mono- or diallyl vinylphosphonate esters undergo facile cross metathesis reactions. The improved reactivity is attributed to a relay step in the cross metathesis reaction mechanism.

Beilstein J. Org. Chem. 2014, 10, 1933–1941. doi:10.3762/bjoc.10.201

http://www.beilstein-journals.org/bjoc/content/10/1/201 2014/08/22 - 07:59