Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• at a concentration of about 0.001 M. The prepared solution should be clear and homogeneous with no visible precipitation or opalescence. If the ligand is poorly soluble in water, other solvents can be used, but some of them may interfere by absorbing light and raising the wavelength cut-off, as well

• increase in the cuvette, usually best seen in the long-wavelength range of the spectrum, is a clear evidence of precipitation or colloid/aggregate formation in the cuvette, which completely hampers further experiments. The characterization of the thermal stability of the ligand solution by collecting it’s

Recent applications of click chemistry for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles

• Vivek Poonthiyil,
• Thisbe K. Lindhorst,
• Vladimir B. Golovko and
• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 11–24, doi:10.3762/bjoc.14.2

• File 1, Figure S5). Furthermore TEM revealed partial aggregation of the particles (Supporting Information File 1, Figure S6). However, despite this partial aggregation the ATT-AuNP solution was stable without any precipitation at least for three months when stored at 4 °C. Similar observations have

• obtained. In further experiments the CuAAC was attempted using a solution of purified GlcNAc azide 34. Water and THF were used as the solvent in a 1:1 ratio to be in line with the conditions reported by Boisselier et al. [62]. However, even with these conditions precipitation of the particles could not be

• , it may be that although the conditions reported by Boisselier et al. work well for smaller sized particles, however, may not be enough to overcome the precipitation of the larger sized AuNPs (>10 nm) caused by Cu as observed by some groups. Unfortunately our attempts to synthesize smaller sized (≈2

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• is concerned, analysis of the composition of the aggregates, as accounted for by nr values, enabled us to evidence i) the effect of inorganic electrolytes, which ensure charge counterbalance, resulting in low ζ-potential and precipitation and ii) the effect of the structure of the polyamine branches

A novel synthetic approach to hydroimidazo[1,5-b]pyridazines by the recyclization of itaconimides and HPLC–HRMS monitoring of the reaction pathway

• Dmitry Yu. Vandyshev,
• Khidmet S. Shikhaliev,
• Andrey Yu. Potapov,
• Michael Yu. Krysin,
• Fedor I. Zubkov and
• Lyudmila V. Sapronova

Beilstein J. Org. Chem. 2017, 13, 2561–2568, doi:10.3762/bjoc.13.252

• probable routes of the cascade recyclization process, because ions of the protonable substances are only fixed in the given ESI–MS conditions, and precipitation of the product is observed as the reaction proceeds. The latter causes a decreased content of the imidazopyridazine 9d in the liquid phase is

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• quite soluble in water, turbidity becomes noticeable after a longer time, and in the case of 100 mM specimens, even precipitation of a solid was observed. The turbidity caused the worse quality of 1H NMR spectra; however, chemical shifts and changes in the shape of the peaks are clearly visible. For the

• ) Interactions between naphthyl groups (stacking) leading to micellization or aggregation. (c) Inclusion complexation of naphthyl into the CD cavity leading to supramolecular polymerization. (d) Free 2c. (e) Interaction between CD moieties leading to aggregation or precipitation. Preparation of 2I-O-, 3I-O- and

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• , such as precipitation (e.g., the conversion of I-Me to II-Me in Scheme 1), or kinetic barriers (inertness of RfOxCH2I in Scheme 3 or the precursor to V in Scheme 1). With the fluorous iodides, the extent of chlorination generally provides a measure of the degree to which the electron-withdrawing

Is the tungsten(IV) complex (NEt₄)₂[WO(mnt)₂] a functional analogue of acetylene hydratase?

• Matthias Schreyer and
• Lukas Hintermann

Beilstein J. Org. Chem. 2017, 13, 2332–2339, doi:10.3762/bjoc.13.230

• -Markovnikov hydration [18][24][25][26][27][28]. Results and Discussion Tungsten complex (NEt4)2[WO(mnt)2] (1) was prepared according to the literature procedure from Na2WO4, Na2mnt and buffered aqueous dithionite, followed by precipitation with Et4NBr (Scheme 3a) [29]. The compound was characterized by 1H and

Phosphonic acid: preparation and applications

• Charlotte M. Sevrain,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2017, 13, 2186–2213, doi:10.3762/bjoc.13.219

• ). As exemplified in Figure 9, the use of TFA induces the formation of the phosphonic acid 29 concomitantly with the formation of carboxylic acid from the tert-butyl ester. The final compounds were purified by removing the excess of TFA (72.4 °C at 1 bar) [138], using HPLC [137] or by precipitation in

• opening of the benzoxazole fragment (after 3 days in contact with water), were produced [200]. This side reaction is likely explained by the sensitivity of the product to acidic condition coming from the acidity of the phosphonic acid function. During the hydrolysis the precipitation of the phosphonic

• product since crystallization, precipitation and dialysis constitute the possible methods of purification. The purification by chromatography requires, due to the high polarity of phosphonic acids, reversed-phase chromatography and is therefore limited to preparative RP-HPLC [218]. Despites these

An efficient Pd–NHC catalyst system in situ generated from Na₂PdCl₄ and PEG-functionalized imidazolium salts for Mizoroki–Heck reactions in water

• Nan Sun,
• Meng Chen,
• Liqun Jin,
• Wei Zhao,
• Baoxiang Hu,
• Zhenlu Shen and
• Xinquan Hu

Beilstein J. Org. Chem. 2017, 13, 1735–1744, doi:10.3762/bjoc.13.168

• 40 °C for 1 h to ensure the completion of H2 releasing. After that, MeO-PEG1900-OMs (19.7 g, 10 mmol) was added and the mixture was refluxed for 24 h. Then, the resulting suspension was filtered off and the filtrate was concentrated under vacuum. Precipitation with MTBE afforded 18.2 g (93%) of MeO

• ), 58.2, 46.3. Synthesis of imidazolium salts L1, L2 and L3 A mixture of MeO-PEG1900-Im (3.9 g, 2 mmol) and the corresponding organic bromide (2.4 mmol) was heated in a sealed tube at 100 oC for 24 h. The resulting imidazolium salts was isolated by precipitation with MTBE. Imidazolium salt L1. Yield: 3.9

An effective Pd nanocatalyst in aqueous media: stilbene synthesis by Mizoroki–Heck coupling reaction under microwave irradiation

• Carolina S. García,
• Paula M. Uberman and
• Sandra E. Martín

Beilstein J. Org. Chem. 2017, 13, 1717–1727, doi:10.3762/bjoc.13.166

• , precipitation or organic extraction eventually lead to a dramatic drop of the catalytic activity. As a result of this, and in order to perform the reuse experiment, repeated runs on the same batch were performed; reusing the reaction mixture with the PVP-Pd nanocatalyst. By this procedure in both, Suzuki

Block copolymers from ionic liquids for the preparation of thin carbonaceous shells

• Sadaf Hanif,
• Bernd Oschmann,
• Dmitri Spetter,
• Muhammad Nawaz Tahir,
• Wolfgang Tremel and
• Rudolf Zentel

Beilstein J. Org. Chem. 2017, 13, 1693–1701, doi:10.3762/bjoc.13.163

• cycles. The reaction mixture was stirred for 20 h at 70 °C. Afterwards the mixture was purified by precipitation in acetone. 1H NMR (400 MHz, DMSO-d6) δ (ppm) 9.85 (m, C-2 of imidazolium ring), 8.01 (m, C-4 and C-5 of imidazolium ring), 5.63 (s, CH2CN), 4.62 (br, polymer backbone), 2.91 (m, polymer

• ) PIL was dissolved in DMSO. After three freeze-pump-thaw cycles the mixture was stirred at 40 °C for 20 h. Afterwards the polymer was worked up by precipitation in acetone. 1H NMR (400 MHz, DMSO-d6) δ (ppm) 9.85 (m, C-2 of imidazolium ring), 7.85 (m, C-4 and C-5 of imidazolium ring), 5.64 (s, CH2CN

Oxidative dehydrogenation of C–C and C–N bonds: A convenient approach to access diverse (dihydro)heteroaromatic compounds

• Santanu Hati,
• Ulrike Holzgrabe and
• Subhabrata Sen

Beilstein J. Org. Chem. 2017, 13, 1670–1692, doi:10.3762/bjoc.13.162

• including aliphatic, aromatic and heteroaromatic aldehydes. Neither the steric nor the electronic properties of the substituents on the aldehydes affect the yield of the reaction. In general, the crude products were isolated by simple extraction or precipitation from the reaction mixture in moderate to

Encaging palladium(0) in layered double hydroxide: A sustainable catalyst for solvent-free and ligand-free Heck reaction in a ball mill

• Wei Shi,
• Jingbo Yu,
• Zhijiang Jiang,
• Qiaoling Shao and
• Weike Su

Beilstein J. Org. Chem. 2017, 13, 1661–1668, doi:10.3762/bjoc.13.160

• , Zhejiang, China 10.3762/bjoc.13.160 Abstract In this paper, the synthesis of a cheap, reusable and ligand-free Pd catalyst supported on MgAl layered double hydroxides (Pd/MgAl-LDHs) by co-precipitation and reduction methods is described. The catalyst was used in Heck reactions under high-speed ball

• catalytic activity in coupling reactions than that on acidic-supported materials. In the present work, co-precipitation was used for fabricating MgAl-LDHs with nitrate anions, followed by introducing disodium tetrachloropalladate (Na2PdCl4) into the LDH interlayer by the ion exchange method. The prepared

• /MgAl-LDHs) was designed and synthesized by co-precipitation and reduction methods. The catlyst was further applied to Heck reactions under HSBM conditions. The results indicate that the Pd is successfully dispersed on the surface of Pd/MgAl-LDHs, and a small quantity of Pd/MgAl-LDHs (2.5 mol % of Pd

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• can destroy the three dimensional structure and cause protein precipitation [19][20][21]. To avoid precipitation when using nonpolar substrates, the protein concentration usually is decreased leading to a loss in activity. As an example, the polymerization of phenylacetylene was achieved in water by

• the choice of the stabilization reagent. In case of PE–PEG, FhuA ΔCVFtev precipitation is observed. Filtering of the solution shows similar results as the reaction with the precipitate present, indicating a deactivation of the catalyst or restricted access of the substrate to the active site. The

• refolding reagent PE–PEG. The isolated yield increased from 5% to 52%. This is related to the increased FhuA ΔCVFtev stability in the presence of hydrophobic substrates. The hydrophobic phenylacetylene interacts with the micelles formed by the PE–PEG refolding reagent, causing the protein precipitation

A new member of the fusaricidin family – structure elucidation and synthesis of fusaricidin E

• Marcel Reimann,
• Louis P. Sandjo,
• Luis Antelo,
• Eckhard Thines,
• Isabella Siepe and
• Till Opatz

Beilstein J. Org. Chem. 2017, 13, 1430–1438, doi:10.3762/bjoc.13.140

• agitation for 2 h, 200 g/L sodium chloride was added to the mixture until phase separation of the organic and aqueous phase was visible. The isopropanol layer was concentrated in vacuo. The resulting extract was dissolved in methanol, centrifuged for better precipitation of salt residues, and the organic

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• byproducts after each coupling, oxidation and deprotection step. The techniques applied so far include precipitation, extraction, chromatography and nanofiltration. As regards coupling, all conventional chemistries, viz. phosphoramidite, H-phosphonate and phosphotriester strategies, have been attempted

• level that building blocks are required only in a moderate excess, 1.5–2.0 equiv [23]. The obvious challenge is the separation of the support-anchored ON chain from small molecular reagents after each coupling cycle, a step that on a solid-support can be carried out by simple washing. Precipitation

• was removed with 3% TCA in DCM and the derivatized support was isolated by precipitation with Et2O and recrystallization from a 1:9 (v/v) mixture of DCM and Et2O. 5´-O-DMTr-nucleosides (3.0 equiv of dT, dCBz, dGibu, dGDpa, dABz) were then coupled as 3´-(2-chlorophenylphosphate)s in a mixture of

An improved preparation of phorbol from croton oil

• Alberto Pagani,
• Simone Gaeta,
• Andrei I. Savchenko,
• Craig M. Williams and
• Giovanni Appendino

Beilstein J. Org. Chem. 2017, 13, 1361–1367, doi:10.3762/bjoc.13.133

• repeated extraction of croton oil with methanol to separate phorbol esters from triglycerides, and on the use of barium hydroxide as a base for the hydrolysis, using long (4–5 days) reaction times under mild basic conditions (pH ca. 8–9). After partition between ether and water, and precipitation of barium

Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• concentration of connector 9 necessary for the almost complete precipitation of the host polymer 8 can be explained by the high integrability of the host–guest system based on the shape-persistence of the polyconjugated polymer backbone of 8. Attachment of polymer 8 to silicon surfaces Planar silicon wafers, as

The effect of cyclodextrin complexation on the solubility and photostability of nerolidol as pure compound and as main constituent of cabreuva essential oil

• Joyce Azzi,
• Pierre-Edouard Danjou,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2017, 13, 835–844, doi:10.3762/bjoc.13.84

• slope was less than unity which indicates the formation of 1:1 inclusion complexes [18]. The Kf values (Table 1) were then calculated as indicated in Equation 1 (experimental part). For β-CD and γ-CD, precipitation occurred at concentrations above 1 mM. We can notice from Table 1, that the Kf values of

Cyclodextrins tethered with oligolactides – green synthesis and structural assessment

• Cristian Peptu,
• Mihaela Balan-Porcarasu,
• Alena Šišková,
• Ľudovít Škultéty and
• Jaroslav Mosnáček

Beilstein J. Org. Chem. 2017, 13, 779–792, doi:10.3762/bjoc.13.77

• previous papers [17] it was stated that CD-oligoester products may be separated from the reaction mixture by dissolution in DMF and precipitation into excess of dry THF in order to remove the unreacted CD. The procedure applied here resulted in two fractions for each sample, the THF insoluble (F1) and THF

• the γ-CD part, which is bigger than other CD homologues (8 glycoside units), to the lower solubility in THF resulting in precipitation of γ-CD-LA species with higher content of dilactate units. This fact is also reflected by the different weight percentage of F1 fractions. The α-CD-LA F1 was on 2%, β

• -CD-LA F1 was 5.5% and γ-CD-LA-F1 was 9% weight from total reaction mixture (Table 1). Thus, the proposed fractionation of the CD-oligoester samples did not provide proper purification and a significant part of the sample can be lost by precipitation. The purification procedure applied in the work of

Substitution of fluorine in M[C₆F₅BF₃] with organolithium compounds: distinctions between O- and N-nucleophiles

• Anton Yu. Shabalin,
• Nicolay Yu. Adonin and
• Vadim V. Bardin

Beilstein J. Org. Chem. 2017, 13, 703–713, doi:10.3762/bjoc.13.69

• ) in ether to a solution of K[C6F5BF3] (1-K) in DME causes precipitation of a white solid. Stirring of the suspension at 22 °C for 3 h with subsequent treatment with aqueous KF gave potassium 4-methyltetrafluorophenyltrifluoroborate, K[4-MeC6F4BF3] (2-K) and potassium 2

• unrecognized arylboron compounds. Reactions with BuLi In general, reactions of 1-K with BuLi proceed as reactions with MeLi although the precipitation was not observed. The reaction of BuLi (2 equiv) with 1-K in DME–hexanes at 22 °C for 2 h and the subsequent treatment of the reaction mixture with aqueous KF

• HRMS (Scheme 7). Discussion Above we mentioned that an addition of MeLi or PhLi in ether to a solution of 1-K in DME caused immediate precipitation. The combination of 1-K in DME with BuLi in hexanes or PhC≡CLi in ether does not lead to the formation of a solid phase. Because etherial solutions of MeLi

Conjecture and hypothesis: The importance of reality checks

• David Deamer

Beilstein J. Org. Chem. 2017, 13, 620–624, doi:10.3762/bjoc.13.60

• concentrated films. The products will accumulate in the pools when water returns either in the form of precipitation or as fluctuations in water levels related to hot springs or geyser activity. Conjecture: life originated in fresh water hydrothermal fields associated with volcanic land masses, then adapted to

• hypothesis: Life began in terrestrial fresh water Although most of the Earth's water today is salty seawater, a small fraction (~1%) is present in the form of fresh water distilled by evaporation from the ocean and falling on continental land masses as precipitation. The Hadean Earth did not have continents

• associated hydrothermal areas supplied by precipitation and dominated by hot springs and geyser activity. In contrast to the single rock-water interface of hydrothermal vents, hydrothermal fields have a more complex array of three interfaces in which minerals, water and atmosphere undergo continuous

Novel β-cyclodextrin–eosin conjugates

• Gábor Benkovics,
• Damien Afonso,
• András Darcsi,
• Szabolcs Béni,
• Sabrina Conoci,
• Éva Fenyvesi,
• Lajos Szente,
• Milo Malanga and
• Salvatore Sortino

Beilstein J. Org. Chem. 2017, 13, 543–551, doi:10.3762/bjoc.13.52

• 254 nm and 366 nm and they are carbonizable. Thus the products exhibit the expected characteristics of a fluorescent CD conjugate (Figure 3). Work-up of the reactions included the concentration of the reaction mixtures and selective precipitation of the CD-related compounds (conjugate and unreacted

Adsorption of RNA on mineral surfaces and mineral precipitates

• Elisa Biondi,
• Yoshihiro Furukawa,
• Jun Kawai and
• Steven A. Benner

Beilstein J. Org. Chem. 2017, 13, 393–404, doi:10.3762/bjoc.13.42

• carbonates and sulfates make conveniently simple systems where the natural-synthetic combination analysis can be easily applied. Other classes of minerals are more difficult to manage for two classes of reasons. First, the cation(s) in the mineral may be redox active. Here, in a precipitation to give a

• anions with different protonation states (for example, H2PO4−, HPO42−, and PO43−) are, de facto, the buffering species in the precipitation experiments. Nevertheless, we collected data for a variety of natural species, including several that are not conveniently made by double decomposition reactions

• system, we obtained natural specimens of the mineral aragonite and calcite. Experiments consistently showed that aragonite adsorbed more radiolabeled RNA than calcite. To obtain a synthetic mineral by precipitation, we reasoned that if RNA prefers to bind to aragonite over calcite, then perhaps RNA would