A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

• DNA polymerases in primer extension experiments and PCR [4][16]. To develop fluorescently labelled oligonucleotides that undergo energy transfer reactions [17] we recently applied 2’-propargyl-modified uridine 1 as DNA building block (Scheme 1) [15][18][19]. A simple look on the three-dimensional

• is 54%. Automated DNA synthesis with 7 as building block required a slightly extended coupling time of 10 min. The phosphoramidite for the “clickable” nucleoside 1 is commercially available. After preparation, the detritylated oligonucleotides DNA1a (“a” = arabino) and DNA1r (“r” = ribo) were cleaved

• CPG (1 µmol) were purchased from Proligo. The commercially available ribo-configured 2’-O-propargyluridine was purchased from ChemGenes. For the arabino-configured building block 7 a slightly extended coupling time of 10 minutes was used. After preparation, the trityl-off oligonucleotides were cleaved

Solution-phase automated synthesis of an α-amino aldehyde as a versatile intermediate

• Hisashi Masui,
• Sae Yosugi,
• Shinichiro Fuse and
• Takashi Takahashi

Beilstein J. Org. Chem. 2017, 13, 106–110, doi:10.3762/bjoc.13.13

• chiral building block [13][14][15][16][17][18]. It is sufficiently stable and its configurational rigidity allows stereoselective addition of nucleophiles to the aldehyde [19]. The most conventional synthesis of 4a involves the protection of the amine, the carboxylic acid, and the alcohol moiety of

A versatile route to polythiophenes with functional pendant groups using alkyne chemistry

• Xiao Huang,
• Li Yang,
• Rikard Emanuelsson,
• Jonas Bergquist,
• Maria Strømme,
• Martin Sjödin and
• Adolf Gogoll

Beilstein J. Org. Chem. 2016, 12, 2682–2688, doi:10.3762/bjoc.12.265

• , Sweden 10.3762/bjoc.12.265 Abstract A new versatile polythiophene building block, 3-(3,4-ethylenedioxythiophene)prop-1-yne (pyEDOT) (3), is prepared from glycidol in four steps in 28% overall yield. pyEDOT features an ethynyl group on its ethylenedioxy bridge, allowing further functionalization by

• ][4][5][6][7][8][9], as well as ion sensing devices [10], biosensors [11], and thermoelectric polymers [12]. Therefore, the chemistry of its building block 3,4-ethylenedioxythiophene (EDOT) and the functionalization of the basic structure have been attracting interest as well [13]. The vast amount of

• research on functionalized polypyrroles [14] and polythiophenes [15] demonstrates that the attachment of functionalized pendant groups to the conjugated polymer backbone provides access to novel properties and applications. An EDOT building block to which highly functionalized pendants can easily be

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

• Elisabeth Mairhofer,
• Elisabeth Fuchs and
• Ronald Micura

Beilstein J. Org. Chem. 2016, 12, 2556–2562, doi:10.3762/bjoc.12.250

• ], started from inosine leading to c3A after 8 steps via a 5-amino-4-imidazolecarboxamide (AICA) riboside derivative with 8% overall yield. Another 4 steps followed to achieve a properly protected building block for RNA solid-phase synthesis [16]. With a total of 12 steps, the approach is not very attractive

• . Because of this frustrating situation, we set out to develop an efficient and easy-to-handle synthesis of a 3-deazaadenosine phosphoramidite building block. Results and Discussion Previously described synthetic routes to c3A via nucleosidation In 1966, Rousseau, Townsend, and Robins reported the

• nucleoside 7 in 28% yield after chromatographic separation from the corresponding 3’-regioisomer. Finally, the 5’-O-DMTr-2’-O-TIPS protected 3-deazaadenosine derivative 7 was converted into the phosphoramidite building block 8 with 2-cyanoethyl diisopropylchlorophosphoramidite in the presence of N

Synthesis, dynamic NMR characterization and XRD studies of novel N,N’-substituted piperazines for bioorthogonal labeling

• Constantin Mamat,
• Marc Pretze,
• Matthew Gott and
• Martin Köckerling

Beilstein J. Org. Chem. 2016, 12, 2478–2489, doi:10.3762/bjoc.12.242

• biologically and pharmacologically activity and was modified with an azide moiety at the C-terminus to yield SNEWILPRLPQH-Azp 6 (the synthesis is reported elsewhere) [29]. The structure of 6 and the click reaction is shown in Scheme 2. For labeling purposes, building block 4b (10-fold excess) was added to

• conditions using a small inhibitory molecule for the EphB4 receptor. For this purpose, the azide-containing building block 5b was reacted with 8 [30] to give 9. The resulting reference compound 9 was obtained after 3 h reaction time in a high yield of 76%. The reaction is shown in Scheme 3. Preparation of

• ], FBAM (log P = 2.7) [41], 4-fluorobenzaldehyde (log P = 1.9) [42] or the click labeling building block p-[18F]F-SA (log P = 1.7) [43], the lipophilicity of our 18F-building blocks is reduced. The hydrophilic character of the building blocks enables a radiolabeling in aqueous solutions and the influence

Enduracididine, a rare amino acid component of peptide antibiotics: Natural products and synthesis

• Darcy J. Atkinson,
• Briar J. Naysmith,
• Daniel P. Furkert and
• Margaret A. Brimble

Beilstein J. Org. Chem. 2016, 12, 2325–2342, doi:10.3762/bjoc.12.226

• protected L-allo-enduracididine residue 102 (Scheme 22). The synthesis of this building block was achieved using a combination of reported procedures beginning with protected aspartic acid 103. Using a protocol reported by Rudolph et al. [65] nitro alcohol 61 was accessed in two steps. Following procedures

Elongated and substituted triazine-based tricarboxylic acid linkers for MOFs

• Arne Klinkebiel,
• Ole Beyer,
• Barbara Malawko and
• Ulrich Lüning

Beilstein J. Org. Chem. 2016, 12, 2267–2273, doi:10.3762/bjoc.12.219

• the methoxy group gave the respective amino and hydroxy-substituted triazine linkers. Keywords: isoreticular; linker; MOF; Suzuki coupling; triazine; Introduction A typical building block for many metal–organic frameworks (MOFs) [1][2][3][4] carries two functional groups such as carboxylic acids or

• -benzenetricarboxylic acid (BTC, forming HKUST-1 [6] in the presence of copper ions), an obvious elongated building block is BTB (1,3,5-benzenetribenzoate, Figure 1, left) forming for instance MOF-14 [7]. But this type of elongation has a drawback: the direct vicinity of the aryl groups does not allow planarity due to

Silica-supported sulfonic acids as recyclable catalyst for esterification of levulinic acid with stoichiometric amounts of alcohols

• Raimondo Maggi,
• N. Raveendran Shiju,
• Veronica Santacroce,
• Giovanni Maestri,
• Franca Bigi and
• Gadi Rothenberg

Beilstein J. Org. Chem. 2016, 12, 2173–2180, doi:10.3762/bjoc.12.207

• , respectively. All of these polymers are the subject of many studies [5][6][7][8][9][10][11]. Levulinic acid (LA) is one of the most important platform chemicals as it is a versatile building block for a variety of value-added agrochemicals, fine chemicals and pharmaceutical intermediates [12][13] (Scheme 1

DNA functionalization by dynamic chemistry

• Zeynep Kanlidere,
• Oleg Jochim,
• Marta Cal and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203

• obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose

• was performed. The base-labile cyanoethyl group [51][52] is known to be resistant under synthesis conditions for the preparation of the phosphoramidite building block and for solid-phase oligonucleotide synthesis [49][53]. Building blocks compatibility with solid-phase synthesis of DNA single strands

• Supporting Information File 1). Synthesis of the phosphoramidite building block 4 [23]. DMTr: dimethoxytrityl group, Fmoc: 9-fluorenylmethylcarbonyl, DMAP: 4-dimethylaminopyridine, DIEA: N,N-diisopropylethylamine. Synthesis of the phosphoramidite building block 11. Sequences of modified oligonucleotide and

The direct oxidative diene cyclization and related reactions in natural product synthesis

• Juliane Adrian,
• Leona J. Gross and
• Christian B. W. Stark

Beilstein J. Org. Chem. 2016, 12, 2104–2123, doi:10.3762/bjoc.12.200

• precursor in this total synthesis. The subsequent cobalt-catalyzed cyclization reaction proceeded chemoselectively in the presence of the alkyne moiety and provided the trans-disubstituted THF 22 in high yield [69][70][71]. Finally, building block 23, one important fragment in the total synthesis of

• diastereomer using a highly efficient and stereocontrolled synthetic strategy to construct the desired bis-THF ring building block 73 in two steps (Scheme 15) [120][121]. Thus, starting from commercially available trans-1,5,9-decatriene (71) a stereo- and positionselective Sharpless AD reaction [86][87][88

Economical and scalable synthesis of 6-amino-2-cyanobenzothiazole

• Jacob R. Hauser,
• Hester A. Beard,
• Mary E. Bayana,
• Katherine E. Jolley,
• Stuart L. Warriner and
• Robin S. Bon

Beilstein J. Org. Chem. 2016, 12, 2019–2025, doi:10.3762/bjoc.12.189

• nanostructures in cellulo [12][13]. The precursor of D-aminoluciferin, 6-amino-2-cyanobenzothiazole (ACBT, 8), is an attractive building block for BLI probes and for handles for CBT ligations, because of the ease of derivatisation of its amino group. Like other functionalised CBTs, ACBT is available from

• commercial suppliers, but expensive. Thus, the development of an economical and scalable synthesis of ACBT would enable studies that require larger amounts of this building block. The traditional synthesis of ACBT 8 involves the cyanation of 6-amino-2-chlorobenzothiazole (7) with an excess of potassium

Synthesis and NMR studies of malonyl-linked glycoconjugates of N-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries

• Markus Nörrlinger,
• Sven Hafner and
• Thomas Ziegler

Beilstein J. Org. Chem. 2016, 12, 1939–1948, doi:10.3762/bjoc.12.183

• , the tert-butyl ester groups of building blocks 1a–d were removed under acid conditions with a 2:1 mixture of formic acid and dichloromethane at room temperature to give the corresponding free acids 2a–d in 97–98% yield (Scheme 1, Table 2). Partially deprotected building block 3 was prepared from 1a as

• follows. First, removal of the Fmoc group in 1a under basic conditions with triethylamine in DMF gave the crude amino derivate which was acetylated with Ac2O to give building block 7 in 60% yield. Removal of the acetyl groups of the sugar moiety in 7 to afford compound 3 could be achieved in a virtually

• to generate glycopeptide libraries of more complex nature by automated SPOT synthesis. cis- and trans rotamer of protected PNA building blocks 1a–d and 2a–d. cis- and trans rotamer of unprotected PNA-building block 3. Rotameric structures of dimeric PNA glycoconjugate 4. 1H NMR (400 MHz) of building

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• remarkable optical and redox properties, azulene proved to be an excellent building block for developing a large variety of materials ranging from NLO chromophores [13] to molecular switches [14][15] and liquid crystals [16] or high-conductance materials [17]. In contrast to most aromatic compounds which

A flow reactor setup for photochemistry of biphasic gas/liquid reactions

• Josef Schachtner,
• Patrick Bayer and
• Axel Jacobi von Wangelin

Beilstein J. Org. Chem. 2016, 12, 1798–1811, doi:10.3762/bjoc.12.170

• . Following an optimized Schenck ene reaction procedure, N-methyl-1,2,3,6-tetrahydrophthalimide (1a) was reacted with molecular oxygen in the presence of methylene blue as sensitizer (Scheme 6). The resultant hydroperoxide motif (2a) constitutes a valuable carbocyclic building block. For reasons of

Effect of the π-conjugation length on the properties and photovoltaic performance of A–π–D–π–A type oligothiophenes with a 4,8-bis(thienyl)benzo[1,2-b:4,5-b′]dithiophene core

• Ni Yin,
• Lilei Wang,
• Yi Lin,
• Jinduo Yi,
• Lingpeng Yan,
• Junyan Dou,
• Hai-Bo Yang,
• Xin Zhao and
• Chang-Qi Ma

Beilstein J. Org. Chem. 2016, 12, 1788–1797, doi:10.3762/bjoc.12.169

• . China Department of Chemistry, Xi’an Jiaotong Liverpool University, 111 Ren Ai Road, Dushu Lake Higher Education Town, Suzhou, Jiangsu, 215123, P. R. China 10.3762/bjoc.12.169 Abstract Benzo[1,2-b:4,5-b′]dithiophene (BDT) is an excellent building block for constructing π-conjugated molecules for the

• variation, and good reproducibility in photovoltaic performance [5][6][7]. To date, PCEs of more than 9% for small molecule OSCs (SMOSCs) have been reported [8][9][10][11][12]. Among various electron-donating moieties, benzo[1,2-b:4,5-b′]dithiophene (BDT) has been widely used as the central building block

• ), TBDT = 4,8-bis(5-alkyl-2-thienyl)benzo[1,2-b:4,5-b′]dithiophene) is shown in Scheme 1. The bithiophene building block, 3,4'-dihexyl-5'-iodo-2,2'-bithiophene-5-carbaldehyde (11) was synthesized by an ipso-substitution of 10, which was synthesized by a Suzuki coupling of 9 with 6, with ICl. The

Rearrangements of organic peroxides and related processes

• Ivan A. Yaremenko,
• Vera A. Vil’,
• Dmitry V. Demchuk and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2016, 12, 1647–1748, doi:10.3762/bjoc.12.162

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• building block [34][35][36]. 1.1.3 Epoxide opening: The nucleophilic opening of epoxides is probably the most abundant type of reaction leading to furans and pyrans. It, for example, plays an important role in the biosynthesis of ionophoric terrestrial and marine polyethers (see chapter 1.3). In this

Star-shaped and linear π-conjugated oligomers consisting of a tetrathienoanthracene core and multiple diketopyrrolopyrrole arms for organic solar cells

• Hideaki Komiyama,
• Chihaya Adachi and
• Takuma Yasuda

Beilstein J. Org. Chem. 2016, 12, 1459–1466, doi:10.3762/bjoc.12.142

• -accepting diketopyrrolopyrrole (DPP) arms, and its linear analogue, TTA-DPP4 and TTA-DPP2 (Figure 1). TTA can be regarded as a promising central core unit for star-shaped π-conjugated oligomers, and has previously been utilized as a building block of semiconducting polymers for OSCs [24] and organic field

Automated glycan assembly of a S. pneumoniae serotype 3 CPS antigen

• Markus W. Weishaupt,
• Stefan Matthies,
• Mattan Hurevich,
• Claney L. Pereira,
• Heung Sik Hahm and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2016, 12, 1440–1446, doi:10.3762/bjoc.12.139

• variability. Herein, we report the first iterative automated glycan assembly (AGA) of a conjugation-ready S. pneumoniae serotype 3 CPS trisaccharide. This oligosaccharide was assembled using a novel glucuronic acid building block to circumvent the need for a late-stage oxidation. The introduction of a washing

• block 1 was designed (Figure 2). A levulinoyl (Lev) ester was chosen as temporary protecting group (TPG) since the Fmoc (fluorenylmethoxycarbonyl) group led to a loss of stereocontrol during glycosylations with this glucuronic acid (GlcA) building block (data not shown). Glucose building blocks 2 and 3

• ]. The building blocks were synthesized in high yields using standard protecting group chemistry (see Supporting Information File 1). Solid support 4 was prepared according to an established procedure [28]. The automated glycosylation protocol employed three times three equivalents of building block to

The EIMS fragmentation mechanisms of the sesquiterpenes corvol ethers A and B, epi-cubebol and isodauc-8-en-11-ol

• Patrick Rabe and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 1380–1394, doi:10.3762/bjoc.12.132

• requires a de novo synthesis for each isotopomer, or at least a partial degradation of a terpene and reconstruction with a 13C-labelled building block. Alternatively, a 13C-labelled terpene may be obtained by feeding of labelled precursors to the producing organism, but this strategy will require high

Biradical vs singlet oxygen photogeneration in suprofen–cholesterol systems

• Fabrizio Palumbo,
• Francisco Bosca,
• Isabel M. Morera,
• Inmaculada Andreu and
• Miguel A. Miranda

Beilstein J. Org. Chem. 2016, 12, 1196–1202, doi:10.3762/bjoc.12.115

• i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain 10.3762/bjoc.12.115 Abstract Cholesterol (Ch) is an important lipidic building block and a target for oxidative degradation, which can be induced via free radicals or singlet oxygen (1O2). Suprofen (SP) is a

• membranes, cholesterol (Ch) is the most important lipidic building block. It is required for permeability, fluidity, and integrity of all animal cell membranes. However, as an unsaturated lipid, Ch is susceptible to oxidative degradation, which can result in potentially pathologic consequences encompassing

NeoPHOX – a structurally tunable ligand system for asymmetric catalysis

• Jaroslav Padevět,
• Marcus G. Schrems,
• Robin Scheil and
• Andreas Pfaltz

Beilstein J. Org. Chem. 2016, 12, 1185–1195, doi:10.3762/bjoc.12.114

• respect. Threonine as a chiral building block is available in both enantiomeric forms at a moderate price. The most effective ligand in this series, bearing a bulky CMe2OSiMe2t-Bu group at the stereogenic center, induced excellent enantioselectivities in the Ir-catalyzed asymmetric hydrogenation of

Efficient syntheses of climate relevant isoprene nitrates and (1R,5S)-(−)-myrtenol nitrate

• Sean P. Bew,
• Glyn D. Hiatt-Gipson,
• Graham P. Mills and
• Claire E. Reeves

Beilstein J. Org. Chem. 2016, 12, 1081–1095, doi:10.3762/bjoc.12.103

• associated with the synthesis of (E)-2-methyl-4-bromobut-2-en-1-ol validated the importance of this seemingly valuable starting material and useful building block. Indeed it is not commercially available and has been reported in the patent literature only once. Following the procedure of Gurumurthy et al

One-pot synthesis of enantiomerically pure N-protected allylic amines from N-protected α-amino esters

• Gastón Silveira-Dorta,
• Sergio J. Álvarez-Méndez,
• Víctor S. Martín and
• José M. Padrón

Beilstein J. Org. Chem. 2016, 12, 957–962, doi:10.3762/bjoc.12.94

• addition, allylic amines serve as versatile structural building block units for the synthesis of various functionalized organic compounds, playing an important role as intermediates in asymmetric synthesis [2]. Furthermore, asymmetric allylic amines can be obtained in enantiomerically pure form from

A robust synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin

• Matthias Bender,
• Henrik Mouritsen and
• Jens Christoffers

Beilstein J. Org. Chem. 2016, 12, 912–917, doi:10.3762/bjoc.12.89

• 3 as C-ring synthon. The first report by Ashton et al. [14][15] used N-(D-ribityl)-3-hydroxyaniline (2) as A-ring fragment. The second report by Yoneda et al. [16][17][18] employed 4-benzyloxy-2-chlorobenzaldehyde (4) as building block for the A-ring. Both syntheses suffer from several drawbacks