Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

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

• temperature overnight. After the reaction was completed, the labeled acpcPNA was cleaved from the solid support with trifluoroacetic acid (500 µL × 30 min × 3). After drying and washing with diethyl ether, the residue was purified by reversed-phase HPLC and characterized by MALDI–TOF mass spectrometry

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

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

• protecting groups (acetate, isobutyrate, diphenylcarbamoyl groups), the N6-Boc protecting group on adenine was impervious. We tried different acidic conditions (trifluoroacetic acid, acetic acid with heat, AlCl3 [23][24][25]), but all of these conditions started to degrade the oligomer without completely

• reflux with 1 M TBAF for 4 days. Finally, we decided to remove the Boc groups on adenine with trifluoroacetic acid (TFA), even though we also expected the loss of the DMTr group on 29. When 29 was treated with 20% of TFA in CH2Cl2, a mixture of 32 and 33 formed after 4 h. The TBDPS moiety was found to be

Expeditive synthesis of trithiotriazine-cored glycoclusters and inhibition of Pseudomonas aeruginosa biofilm formation

• Meriem Smadhi,
• Sophie de Bentzmann,
• Anne Imberty,
• Marc Gingras,
• Raoudha Abderrahim and
• Peter G. Goekjian

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

• 87% yield. The benzyl protected D-glucose glycocluster 12 was similarly prepared from tri-O-benzyl-β-D-glucopyranosyl azide 6 [39] in 92% yield. The removal of the silyl groups with TBAF led to complete degradation of the scaffold. Ammonium fluoride in THF or trifluoroacetic acid also led to the

Syntheses of ¹⁵N-labeled pre-queuosine nucleobase derivatives

• Jasmin Levic and
• Ronald Micura

Beilstein J. Org. Chem. 2014, 10, 1914–1918, doi:10.3762/bjoc.10.199

• therefore decided to directly purify the crude product by reversed-phase column chromatography (HPLC) and obtained compound 1 in excellent yield and purity. We mention that compound 1 was isolated as salt of trifluoroacetic acid (TFA) using 1% TFA in the eluent and it was assumed to exist in 1:1

• µL, 2.2 mmol) and ethanol (3 mL). The mixture was refluxed overnight and evaporated to dryness. The residue was purified by reversed-phase (C18) column chromatograpy (eluent A: 1% trifluoroacetic acid in H2O; eluent B: acetonitrile; 0–20% B in 50 min, 4 mL/min) to yield 49 mg of compound 1 (75

• , RP C18 chromatography, 35%. b) NaOAc·3H2O (2 equiv), acetonitrile/water, 40 °C, 4 h, 63%. c) H2N-NH2·H2O (10 equiv), ethanol, reflux, 14 h, RP C18 chromatography, 75%. Compound 1 was isolated as salt of trifluoroacetic acid (TFA). Synthesis of [15N9]-preQ1 base (2). a) [15N]-KCN (1 equiv), Na2CO3

Application of cyclic phosphonamide reagents in the total synthesis of natural products and biologically active molecules

• Thilo Focken and
• Stephen Hanessian

Beilstein J. Org. Chem. 2014, 10, 1848–1877, doi:10.3762/bjoc.10.195

• , however, the diastereomeric products were not separable by chromatographic means. Cleavage of the ephedrine auxiliary was accomplished by a three-step protocol. Treatment of 137a,b and 138a,b with trifluoroacetic acid in methanol followed by reaction with TMSBr and subsequent hydrolysis of the TMS ester

Synthesis of rigid p-terphenyl-linked carbohydrate mimetics

• Maja Kandziora and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2014, 10, 1749–1758, doi:10.3762/bjoc.10.182

• )benzene by column chromatography or distillation. Besides, Brønsted acids like trifluoroacetic acid, p-toluenesulfonic acid, that are usually used to generate ketals, or weaker acids like pyridine/hydrogen fluoride led to a side product [35]. The Lewis acid-promoted rearrangement of 1,3-dioxolanyl

Orthogonal dual thiol–chloroacetyl and thiol–ene couplings for the sequential one-pot assembly of heteroglycoclusters

• Michele Fiore,
• Gour Chand Daskhan,
• Baptiste Thomas and
• Olivier Renaudet

Beilstein J. Org. Chem. 2014, 10, 1557–1563, doi:10.3762/bjoc.10.160

• . General procedure for Boc deprotection. All cyclic peptides were dissolved in CH2Cl2 and then a solution at 40% of trifluoroacetic acid in CH2Cl2 with 2.5% of water as scavenger was added. The reaction was run until disappearance of stating material (1 h). Evaporation of the solvent and precipitation in

A promising cellulose-based polyzwitterion with pH-sensitive charges

• Thomas Elschner and
• Thomas Heinze

Beilstein J. Org. Chem. 2014, 10, 1549–1556, doi:10.3762/bjoc.10.159

• solvents, like dioxane and CH2Cl2, is decreased and the deprotection has to be carried out in trifluoroacetic acid (TFA), followed by a subsequent anion exchange by dialysis of the polymer solution against aqueous sodium chloride and water. 7b was prepared from the polycation 6 by alkaline treatment, but

Asymmetric Ugi 3CR on isatin-derived ketimine: synthesis of chiral 3,3-disubstituted 3-aminooxindole derivatives

• Giordano Lesma,
• Fiorella Meneghetti,
• Alessandro Sacchetti,
• Mattia Stucchi and
• Alessandra Silvani

Beilstein J. Org. Chem. 2014, 10, 1383–1389, doi:10.3762/bjoc.10.141

• trifluoroacetic acid (TFA, 3a) under various reaction conditions. Compound 1 was easily prepared by treatment of isatin with (S)-phenyl ethylamine in the presence of MgSO4 [16]. The results of this initial study are reported in Table 1. Running the reaction in 2,2,2-trifluoroethanol for 4 days produced only a

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• with methanol (yields 60–90%). In the case of an oil-like substance (Х = ОEG, n = 2) chromatography on silica gel was performed. The quantitative removal of Boc groups was achieved by the treatment of the obtained peptides with trifluoroacetic acid. Salt forms (trifluoroacetates or hydrochlorides) of

• was suspended in methanol, filtered, dissolved in water, sedimentated with methanol, and dried in vacuo. Protocol 2: Preparation of oligoglycines (HCl·GlynNH-X-NHGlyn·HCl; n = 1–7, X = С2, С10 and OEG). The Boc-derivative (0.5 mmol) was dissolved in trifluoroacetic acid (5 mL), the reaction mixture

Magnesium bis(monoperoxyphthalate) hexahydrate as mild and efficient oxidant for the synthesis of selenones

• Andrea Temperini,
• Massimo Curini,
• Ornelio Rosati and
• Lucio Minuti

Beilstein J. Org. Chem. 2014, 10, 1267–1271, doi:10.3762/bjoc.10.127

• efficient and mild methods for their synthesis is of considerable interest. A few previous papers report the synthesis of selenones 2 by oxidation of the corresponding selenides 1 with potassium permanganate [4], trifluoroacetic acid [4] and hydrogen peroxide in trifluoroethanol with stoichiometric amounts

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• protecting group for the amino function and Bn (benzyl) or related protecting groups for the side chains of trifunctional amino acids. Usually, Boc can be removed by treatment with TFA (trifluoroacetic acid), whereas Bn deprotection requires strong acids such as HF [32]. Hence, this Boc/Bn protecting-group

Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

• Tatyana V. Abramova,
• Sergey S. Belov,
• Yulia V. Tarasenko and
• Vladimir N. Silnikov

Beilstein J. Org. Chem. 2014, 10, 1151–1158, doi:10.3762/bjoc.10.115

• fact helped us to estimate the comparative length and purity of homooligomers. The yield in each cycle was 96–98%. After completion of the pentamer synthesis and cleavage of the oligomer from the support, the Boc protective group was removed by trifluoroacetic acid (TFA). Target homopentamers 7a,d,e

• -protected 2-aminomethylmorpholino nucleosides: i) di-tert-butyl dicarbonate ((Boc)2O), triethylamine (TEA), pyridine (Py); ii) AcOH/H2O. Loading of the Boc-Gly-PAM resin with the morpholino nucleosides 5a,d,e: i) Dimethyl oxalate, TEA, MeOH; ii) 4, TEA, Py; iii) trifluoroacetic acid (TFA)/CH2Cl2/PhSH; iv

Olefin cross metathesis based de novo synthesis of a partially protected L-amicetose and a fully protected L-cinerulose derivative

• Bernd Schmidt and
• Sylvia Hauke

Beilstein J. Org. Chem. 2014, 10, 1023–1031, doi:10.3762/bjoc.10.102

• (Scheme 2). The benzoate scrambling was completely suppressed by avoiding highly nucleophilic alkoxide intermediates, which was achieved with acidic deprotection conditions. Thus, treating the mixture of 11 and 12 with trifluoroacetic acid in dichloromethane at ambient temperature resulted in desilylation

Allenylphosphine oxides as simple scaffolds for phosphinoylindoles and phosphinoylisocoumarins

• G. Gangadhararao,
• Ramesh Kotikalapudi,
• M. Nagarjuna Reddy and
• K. C. Kumara Swamy

Beilstein J. Org. Chem. 2014, 10, 996–1005, doi:10.3762/bjoc.10.99

• and a suitable P(III) precursor via a base-mediated reaction. The reaction proceeds via the intermediacy of allenylphosphine oxides. Similarly, phosphinoylisocoumarins were prepared from allenylphosphine oxides in a trifluoroacetic acid-mediated reaction; the latter also acts as a solvent

• . Interestingly, in the presence of wet trifluoroacetic acid, in addition to phosphinoylisocoumarins, phosphorus-free isocoumarins were also obtained. Key products were characterized by single crystal X-ray crystallography. Keywords: allenes; indoles; isocoumarins; organophosphorus; phosphinoyl-heterocycles

• . To achieve this, we treated the functionalized allene precursors 4a–j that are tethered with a methyl ester group, with an excess of trifluoroacetic acid at room temperature for 6 h. Gratifyingly, this readily leds to the phosphinoylisocoumarins 20–29 (Scheme 7) in good yields. In the case of

Molecular architecture with carbohydrate functionalized β-peptides adopting 3₁₄-helical conformation

• Nitin J. Pawar,
• Navdeep S. Sidhu,
• George M. Sheldrick,
• Dilip D. Dhavale and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2014, 10, 948–955, doi:10.3762/bjoc.10.93

• resin. Simultaneous tert-butyloxycarbonyl (Boc)-deprotection and cleavage of the β-glycopeptides from solid support using 5% trifluoroacetic acid (TFA) in dry dichloromethane provided β-glycopeptides D-glucose(Bn) 1 and 7, D-galactose(acetonide) 3, and D-xylose(Bn, acetonide) 5 with all sugar hydroxy

Primary-tertiary diamine-catalyzed Michael addition of ketones to isatylidenemalononitrile derivatives

• Akshay Kumar and
• Swapandeep Singh Chimni

Beilstein J. Org. Chem. 2014, 10, 929–935, doi:10.3762/bjoc.10.91

• and 60% ee, respectively (Table 3, entries 1 and 2). The reaction carried out with strong acids such as trifluoromethanesulfonic acid (TsOH) and trifluoroacetic acid (TFA) gave 4a in good yields of 86% and 89% and high enantioselectivities of 97% ee and 96% ee (Table 3, entries 3 and 4). The

A new manganese-mediated, cobalt-catalyzed three-component synthesis of (diarylmethyl)sulfonamides

• Antoine Pignon,
• Erwan Le Gall and
• Thierry Martens

Beilstein J. Org. Chem. 2014, 10, 425–431, doi:10.3762/bjoc.10.39

• efficiency. Experimental General procedure: A dried 50 mL round bottomed flask equipped with a reflux condenser was flushed with argon and charged with acetonitrile (5 mL). Manganese dust (1.4 g, 25 mmol), trifluoroacetic acid (0.1 mL, 1.3 mmol) and 1,2-dibromoethane (0.1 mL, 1.15 mmol) were added under

Synthesis of new enantiopure poly(hydroxy)aminooxepanes as building blocks for multivalent carbohydrate mimetics

• Léa Bouché,
• Maja Kandziora and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2014, 10, 213–223, doi:10.3762/bjoc.10.17

• h; b) TBSCl, imidazole, DMAP, CH2Cl2, 3 d, rt; c) 1. DIBAL-H, CH2Cl2, −78 °C, 3.5 h; 2. N-benzylhydroxylamine, MgSO4, CH2Cl2, rt, 16 h. [TFA = trifluoroacetic acid, DMAP = 4-(N,N-dimethylamino)pyridine, DIBAL-H = diisobutylaluminium hydride] Synthesis of 1,2-oxazines syn-7, syn-9 and syn-10

Recent applications of the divinylcyclopropane–cycloheptadiene rearrangement in organic synthesis

• Sebastian Krüger and
• Tanja Gaich

Beilstein J. Org. Chem. 2014, 10, 163–193, doi:10.3762/bjoc.10.14

• alcohol led to a rearrangement cascade, which smoothly yielded hexacycle 157. This compound could be converted into isostemofoline (158), albeit in low yield. Isostemofoline could not be interconverted into stemofoline (159) using trifluoroacetic acid [136]. Danishefsky and coworkers [137][138][139

Recent advances in transition metal-catalyzed Csp²-monofluoro-, difluoro-, perfluoromethylation and trifluoromethylthiolation

• Grégory Landelle,
• Armen Panossian,
• Sergiy Pazenok,
• Jean-Pierre Vors and
• Frédéric R. Leroux

Beilstein J. Org. Chem. 2013, 9, 2476–2536, doi:10.3762/bjoc.9.287

• coworkers reported on the first Pd-catalyzed trifluoromethylation at C–H positions in aromatic compounds (Table 5) [67]. Pd(OAc)2 (10 mol %) was used as the catalyst, and Umemoto’s sulfonium tetrafluoroborate salt as the CF3 source rather than its triflate analogue. Trifluoroacetic acid and copper(II

• fluoral and morpholine, following the procedure described by B. R. Langlois et al. [77] Moderate to good yields were observed when the reaction was carried out in diglyme with cesium fluoride as a base (Table 14). More recently, compounds derived from trifluoroacetic acid appeared to be a cheap and

• trifluoroacetic acid as the source of CF3− [80]. Ag2O was chosen as an additive to promote the decarboxylation, and to accelerate the reductive elimination step by precipitation of AgI. To circumvent the use of moisture-sensitive sodium trifluoroacetate, M. Beller et al. employed a combination of methyl

A one-pot synthesis of 3-trifluoromethyl-2-isoxazolines from trifluoromethyl aldoxime

• Raoni S. B. Gonçalves,
• Michael Dos Santos,
• Guillaume Bernadat,
• Danièle Bonnet-Delpon and
• Benoit Crousse

Beilstein J. Org. Chem. 2013, 9, 2387–2394, doi:10.3762/bjoc.9.275

• . When the oxidation is carried out with DIB, weak acetic acid instead of strong trifluoroacetic acid is liberated, and the decomposition of the oxazolines is avoided. Faced with the moderate yield of 1a, we followed the reaction by using 19F NMR. The measurement of the crude mixture with 19F NMR

An overview of the synthetic routes to the best selling drugs containing 6-membered heterocycles

• Marcus Baumann and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2013, 9, 2265–2319, doi:10.3762/bjoc.9.265

Non-cross-linked polystyrene-supported 2-imidazolidinone chiral auxiliary: synthesis and application in asymmetric alkylation reactions

• Quynh Pham Bao Nguyen and
• Taek Hyeon Kim

Beilstein J. Org. Chem. 2013, 9, 2113–2119, doi:10.3762/bjoc.9.248

• necessary clarity to examine the alkylation process, another cleavable linker strategy was applied by treating the alkylated polymer 6a with trifluoroacetic acid (TFA) for 5 min at room temperature to produce compound 7a, which could be conveniently monitored by classical thin layer chromatography (TLC) [18

Post-Ugi gold-catalyzed diastereoselective domino cyclization for the synthesis of diversely substituted spiroindolines

• Amit Kumar,
• Dipak D. Vachhani,
• Sachin G. Modha,
• Sunil K. Sharma,
• Virinder S. Parmar and
• Erik V. Van der Eycken

Beilstein J. Org. Chem. 2013, 9, 2097–2102, doi:10.3762/bjoc.9.246

• ]. To our delight, when the above reaction was carried out with 1 equivalent of trifluoroacetic acid (TFA) the yield was improved to 81% (Table 1, entry 2). Apart from being a good proton source TFA might be working as a coligand. Experiments with PtCl2 as a catalyst did not show any conversion and the