Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• brightly fluorescent. Diffusion of H+ down the gradient at the edges allows protons to outrun the lumbering 8 and create a thin region of protonated 7 which escapes the quenching. The thinness of this bright region is determined by the diffusion coefficient of H+ in the matrix. We dry the paper carefully

• so that the diffusion coefficient of H+ is about an order of magnitude lower than that found in bulk water [85]. This procedure results in edges of 1–2 mm thickness during an experiment runtime of about 30 minutes (Figure 6). Too much or too little drying destroys the edge detection capability quite

• slightly and then erase the original photograph to leave behind the thin expansion region as the outline. This behaviour can be modelled semi-quantitatively using well-known equations of acid-base equilibria and diffusion [85]. A bit of arts The arts offer an excellent balancing influence for scientists

Synthesis of cyclic N¹-pentylinosine phosphate, a new structurally reduced cADPR analogue with calcium-mobilizing activity on PC12 cells

• Ahmed Mahal,
• Stefano D’Errico,
• Nicola Borbone,
• Brunella Pinto,
• Agnese Secondo,
• Valeria Costantino,
• Valentina Tedeschi,
• Giorgia Oliviero,
• Vincenzo Piccialli and
• Gennaro Piccialli

Beilstein J. Org. Chem. 2015, 11, 2689–2695, doi:10.3762/bjoc.11.289

• results indicate that 3 and 4 possess almost the same activity, thus indicating that the role of the pyrophosphate bridge is not stringent and that the introduction of an alkyl chain in the N1 position of the purine base improves the permeation of the cell membrane by passive diffusion or through an

Biocatalysis for the application of CO₂ as a chemical feedstock

• Apostolos Alissandratos and
• Christopher J. Easton

Beilstein J. Org. Chem. 2015, 11, 2370–2387, doi:10.3762/bjoc.11.259

• , the archetypal super-enzyme for which catalytic rates reach the limits of diffusion [30][31]. CO2 consumed by enzymes is therefore efficiently replenished through rapid HCO3− dehydration (Figure 2). Living organisms have developed various mechanisms to increase the effective concentration of CO2

• enzymes used. The application of enzymes within whole-cells allows their production and utilisation with minimal processing and circumvents biocatalyst purification, though in this case there are limitations related to substrate/product diffusion and background metabolic activity. The optimal approach in

• each case, as for any multi-enzymatic synthesis, will depend on a combination of factors such as the number of enzymes to be utilised, the ease of substrate and product diffusion through the cell membrane, and the presence of unwanted background reactions. Within a well-understood cellular chassis, the

Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

• Shintaro Kawano,
• Toshiyuki Kida,
• Mitsuru Akashi,
• Hirofumi Sato,
• Motohiro Shizuma and
• Daisuke Ono

Beilstein J. Org. Chem. 2015, 11, 2355–2364, doi:10.3762/bjoc.11.257

• Information File 1. Dynamic light scattering (DLS) The particle size distribution was measured at 25 °C using DLS6000HL (Otsuka Electronic Co.) equipped with a He-Ne laser (wavelength 632.8 nm). The mean particle diameter was calculated from the diffusion coefficients using the Stokes–Einstein equation. The

Half-sandwich nickel(II) complexes bearing 1,3-di(cycloalkyl)imidazol-2-ylidene ligands

• Johnathon Yau,
• Kaarel E. Hunt,
• Laura McDougall,
• Alan R. Kennedy and
• David J. Nelson

Beilstein J. Org. Chem. 2015, 11, 2171–2178, doi:10.3762/bjoc.11.235

• , elemental analysis and X-ray crystallography (Figure 1). Selected crystallographic data can be found in Table 1, and some key bond lengths in Table 2. X-ray quality crystals were obtained by slow diffusion of pentane into a DCM solution of each complex. The 1H NMR spectra show the expected features; a sharp

Ru complexes of Hoveyda–Grubbs type immobilized on lamellar zeolites: activity in olefin metathesis reactions

• Hynek Balcar,
• Naděžda Žilková,
• Martin Kubů,
• Michal Mazur,
• Zdeněk Bastl and
• Jiří Čejka

Beilstein J. Org. Chem. 2015, 11, 2087–2096, doi:10.3762/bjoc.11.225

• ), with large BET areas and pore volumes, proved to be very suitable supports, due to easy attachment of bulky organometallic complexes onto silica surface ensuring rapid diffusion of reactants to the active catalytic sites [5][6][7][8][9][10][11][12]. Several strategies of immobilization have been

• -metathesis, in accord with the characters of both reactants (classes of reactants in CM according to Grubbs [35]). The data presented indicated that the depressed activity of HGIIN+Cl−/MCM-22 in the self-metathesis of methyl oleate was not connected with a slow diffusion of the reactant to the active centers

The marine sponge Agelas citrina as a source of the new pyrrole–imidazole alkaloids citrinamines A–D and N-methylagelongine

• Christine Cychon,
• Ellen Lichte and
• Matthias Köck

Beilstein J. Org. Chem. 2015, 11, 2029–2037, doi:10.3762/bjoc.11.220

• cytotoxic activity. Classical agar diffusion assays were performed using the fungus Aspergillus niger, the yeast Saccharomyces cerevisiae as well as the Gram-negative bacterium Escherichia coli, and the Gram-positive bacterium Micrococcus luteus and Mycobacterium phlei as test organisms. In agar diffusion

• . Antimicrobial assay As already described in [18] the antimicrobial activities were determined by agar diffusion tests using paper disks of 6 mm diameter soaked with 20 µL of the test compound in MeOH (1 mg/mL). The microorganisms were obtained from the HZI collection, grown on standard media, and cultured in

Investigation of the role of stereoelectronic effects in the conformation of piperidones by NMR spectroscopy and X-ray diffraction

• Cesar Garcias-Morales,
• David Ortegón-Reyna and
• Armando Ariza-Castolo

Beilstein J. Org. Chem. 2015, 11, 1973–1984, doi:10.3762/bjoc.11.213

• the 6-311++G(d,p) basis set. This basis set includes diffusion and polarization functions, and performs better for the description of molecular orbitals from geometry optimization and NBO analysis. General procedure for the synthesis of 2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-ones The compounds 1–2

Hexacoordinate Ru-based olefin metathesis catalysts with pH-responsive N-heterocyclic carbene (NHC) and N-donor ligands for ROMP reactions in non-aqueous, aqueous and emulsion conditions

• Shawna L. Balof,
• K. Owen Nix,
• Matthew S. Olliff,
• Sarah E. Roessler,
• Arpita Saha,
• Kevin B. Müller,
• Ulrich Behrens,
• Edward J. Valente and
• Hans-Jörg Schanz

Beilstein J. Org. Chem. 2015, 11, 1960–1972, doi:10.3762/bjoc.11.212

• complex 12 suitable for X-ray diffraction were obtained via layer diffusion of heptane into a concentrated THF solution (Figure 2). Hexacoordinated complex 12 adopts the expected distorted octahedral coordination sphere around the Ru center with trans chloride and cis DMAP ligands. In comparison to

• ; N, 12.41; found: C, 58.26; H, 6.49, N, 11.74. Crystal structure determination of complex 12. Crystals suitable for X-ray diffraction were obtained by layer diffusion of heptane into a THF solution of complex 12 at ambient temperatures over a period of 3 d to yield dark brown prisms. The crystals do

Effective ascorbate-free and photolatent click reactions in water using a photoreducible copper(II)-ethylenediamine precatalyst

• Redouane Beniazza,
• Natalia Bayo,
• Florian Molton,
• Carole Duboc,
• Stéphane Massip,
• Nathan McClenaghan,
• Dominique Lastécouères and
• Jean-Marc Vincent

Beilstein J. Org. Chem. 2015, 11, 1950–1959, doi:10.3762/bjoc.11.211

• sodium salt of the 4-benzoylbenzoic acid with Cu(OTf)2 in water, the precipitate which formed being recrystallized by slow diffusion of Et2O in a THF solution (Scheme 2). Then, 4 equivalents of EDA were reacted with 4 in THF, the solution immediately turned deep blue. Slow diffusion of diethyl ether

Synthesis, antimicrobial and cytotoxicity evaluation of new cholesterol congeners

• Mohamed Ramadan El Sayed Aly,
• Hosam Ali Saad and
• Shams Hashim Abdel-Hafez

Beilstein J. Org. Chem. 2015, 11, 1922–1932, doi:10.3762/bjoc.11.208

• to the Kirby–Bauer disc diffusion method (Figure 2) [47]. The results shown in Figure 2 revealed that the chalcone modified cholesterol derivatives 6a,c and 7b were the most potent derivatives against E. coli. They were as active as ampicillin and insignificantly varied with each other. Thus, the

• according to the Kirby–Bauer disc diffusion method (Figure 2). Although, the series was inactive against A. flavus, they showed some promising antifungal results against C. albicans. As shown in Figure 2, only chalcone 6c was as active as the control (amphotericin B). Cholesterols 6a,b, 7a,b, 11b, 13 and 20

Cross-metathesis of polynorbornene with polyoctenamer: a kinetic study

• Yulia I. Denisova,
• Maria L. Gringolts,
• Alexander S. Peregudov,
• Liya B. Krentsel,
• Ekaterina A. Litmanovich,
• Arkadiy D. Litmanovich,
• Eugene Sh. Finkelshtein and
• Yaroslav V. Kudryavtsev

Beilstein J. Org. Chem. 2015, 11, 1796–1808, doi:10.3762/bjoc.11.195

• and their self-diffusion is replaced with a faster cooperative diffusion. In that case slowly decreases with c corresponding to a distance at which hydrodynamic interactions are screened out. For the PCOE solution Figure 1b displays a quite different concentration dependence of . In the dilute regime

Synthesis and structures of ruthenium–NHC complexes and their catalysis in hydrogen transfer reaction

• Chao Chen,
• Chunxin Lu,
• Qing Zheng,
• Shengliang Ni,
• Min Zhang and
• Wanzhi Chen

Beilstein J. Org. Chem. 2015, 11, 1786–1795, doi:10.3762/bjoc.11.194

• and 2 are stable in air and under light irradiation. Single crystals suitable for X-ray diffraction could be obtained by slow diffusion of Et2O into CH3CN solutions and the detailed structure of 1 is depicted in Figure 1. In complex 1, the central ruthenium ion is hexacoordinated by two bidentate NHC

• -phenanthroline in heat acetonitrile solution afforded 4 and 5, respectively. Even excess triphenylphosphine and 1,10-phenanthroline were used, only one and two coordinated acetonitrile ligands were substituted in complexes 4 and 5. Crystallization by slow diffusion of diethyl ether into their acetonitrile

• crystallization by slow diffusion of Et2O into the CH3CN solution gave 4 as yellow solid. Yield: 75 mg, 40%. Anal. calcd for C32H32F12N7P3Ru: C, 41.04; H, 3.44; N, 10.47; found: C, 41.10; H, 3.40; N, 10.58; 1H NMR (DMSO-d6) δ 8.99 (s, 1H), 8.46 (s, 1H), 8.38 (s, 1H), 7.87 (s, 1H), 7.57(s, 13H), 7.42 (s, 2H), 7.25

Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly

• Masahiko Iyoda and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2015, 11, 1596–1613, doi:10.3762/bjoc.11.175

• the slow scanning rate of 3 mV s−1 owing to the intermolecular mixed-valence interaction between the TTF•+ and TTF moieties under diffusion-controlled conditions. In the case of 31, the first oxidation potential (E1/2 = 0.14 V vs Fc/Fc+) is lower than that of 32 with alkyl groups (E1/2 = 0.20 V

Intermolecular addition reactions of N-alkyl-N-chlorosulfonamides to unsaturated compounds

• Gerold Heuger and
• Richard Göttlich

Beilstein J. Org. Chem. 2015, 11, 1226–1234, doi:10.3762/bjoc.11.136

• using copper(I) chloride as the catalyst, which (after oxidation to copper(II) chloride) captures carbon radicals at a diffusion controlled rate [38]. Indeed using copper(I) chloride as the catalyst we obtained a yield of 60% of the addition product with sulfonamide 1a being the remaining side product

New palladium–oxazoline complexes: Synthesis and evaluation of the optical properties and the catalytic power during the oxidation of textile dyes

• Rym Hassani,
• Mahjoub Jabli,
• Yakdhane Kacem,
• Jérôme Marrot,
• Damien Prim and
• Béchir Ben Hassine

Beilstein J. Org. Chem. 2015, 11, 1175–1186, doi:10.3762/bjoc.11.132

• nitrogen atoms to form a planar palladium ring system (Scheme 2). Crystallization by slow diffusion of pentane into a solution of 8 in dichloromethane gave suitable crystals for an X-ray diffraction study. The molecular structure is presented in Figure 2 (see Supporting Information File 1 for the cif of

Cathodic hydrodimerization of nitroolefins

• Michael Weßling and
• Hans J. Schäfer

Beilstein J. Org. Chem. 2015, 11, 1163–1174, doi:10.3762/bjoc.11.131

• accelerated at higher temperatures compared to the radical dimerization. It should be mentioned that at the cathode deep red species are formed that become colorless upon addition of acetic acid. In an undivided cell and an unstirred electrolyte, which allows diffusion between the electrodes, a red colour

Quarternization of 3-azido-1-propyne oligomers obtained by copper(I)-catalyzed azide–alkyne cycloaddition polymerization

• Shun Nakano,
• Akihito Hashidzume and
• Takahiro Sato

Beilstein J. Org. Chem. 2015, 11, 1037–1042, doi:10.3762/bjoc.11.116

• intensities of echo signals at ca. 8.9 ppm were evaluated as a function of the intensity of the pulse-filed-gradient for dilute DMSO-d6 solutions of the oligoAPMe of three different concentrations, as can be seen in Figure 2a. Using the Sterjkal equation, the self-diffusion coefficients (D) were determined

• from the slopes of the straight lines in Figure 2a, and extrapolated to the zero concentration to obtain the limiting diffusion coefficient (D0) (Figure 2b). It should be noted here that the extrapolation to the zero concentration is rather normal, indicating that the iodide counterions of oligoAPMe

• gyromagnetic ratio, and τ the 90°–180° pulse distance (a), and the concentration dependency of apparent self-diffusion coefficient D for the oligoAPMe in DMSO-d6 at 30 °C (b). A typical example of the three-dimensional structure of oligoAPMe of n = 11 built with ChemBio3D software (version 13.0) (a), a rodlike

Glycoluril–tetrathiafulvalene molecular clips: on the influence of electronic and spatial properties for binding neutral accepting guests

• Yoann Cotelle,
• Marie Hardouin-Lerouge,
• Stéphanie Legoupy,
• Olivier Alévêque,
• Eric Levillain and
• Piétrick Hudhomme

Beilstein J. Org. Chem. 2015, 11, 1023–1036, doi:10.3762/bjoc.11.115

• isolated in around 20% yield. Whereas all attempts at growing crystals of molecular clips 1 and 4 of sufficient quality for X-ray analysis have been unsuccessful so far, suitable single crystals were obtained by slow diffusion from a solution of clips 2 and 3 in a CH2Cl2/hexane mixture. Considering the

Properties of PTFE tape as a semipermeable membrane in fluorous reactions

• Brendon A. Parsons,
• Olivia Lin Smith,
• Myeong Chae and
• Veljko Dragojlovic

Beilstein J. Org. Chem. 2015, 11, 980–993, doi:10.3762/bjoc.11.110

• to some compounds, such as dimethyl phthalate, solvent adsorption to the tape altered its permeability and allowed diffusion through channels of solvent within the PTFE tape. In this case, the solvent-filled pores of the PTFE tape are chemically more akin to the adsorbed solvent rather than to the

• . An important requirement of PV reactions is that, in order to ensure an effective reaction, the rate of passive diffusion of the reagent through the fluorous phase to the substrate layer must be significantly greater than the diffusion of the substrate to the reagent layer [9]. Ryu and Curran’s work

• reported a variation of the PV method that allows the use of lighter reagents without the need for a U-tube by dissolving one of the reagents in a heavy solvent [18]. Curran and Werner established that such a reaction operates by an extractive mechanism, rather than the passive diffusion-controlled reagent

Tuning the size of a redox-active tetrathiafulvalene-based self-assembled ring

• Sébastien Bivaud,
• Sébastien Goeb,
• Vincent Croué,
• Magali Allain,
• Flavia Pop and
• Marc Sallé

Beilstein J. Org. Chem. 2015, 11, 966–971, doi:10.3762/bjoc.11.108

• +, [M6L3-8TfO−]4+, [M6L3-7TfO−]5+ species and matching perfectly with theoretical ones (Supporting Information File 1, Figure S8). Single crystals of assembly M6L3 were grown by slow diffusion of ethyl acetate in DMSO and allowed for determining unambiguously the solid-state structure by a synchrotron X

Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2015, 11, 913–929, doi:10.3762/bjoc.11.103

• lipophilicity but mainly the chemical structure and topology of the head group is of decisive importance for the optimal interaction of a lipo-oligonucleotide with an artificial lipid bilayer. Moreover, fluorescence half-live and diffusion time values were measured to determine the diffusion coefficients of the

• low rate but proved highly stable against perfusion. Diffusion time measurements of LON 10 inserted within the lipid bilayer Additionally, the diffusion times of LON 10 at positions 1, 2, and 3 (Figure 13A–C, Table 1) were measured in order to characterize its binding at and within the bilayer. Right

• above the bilayer (position 2), the diffusion of the oligomer is significantly reduced as compared to that in free solution (position 1). From the fitted and normalized fluorescence correlation curves (Figure 13C), the corresponding diffusion times could be deduced as summarized in Table 1. The

Copper ion salts of arylthiotetrathiafulvalenes: synthesis, structure diversity and magnetic properties

• Longfei Ma,
• Jibin Sun,
• Xiaofeng Lu,
• Shangxi Zhang,
• Hui Qi,
• Lei Liu,
• Yongliang Shao and
• Xiangfeng Shao

Beilstein J. Org. Chem. 2015, 11, 850–859, doi:10.3762/bjoc.11.95

• the reaction system was increased to higher than 10−3 mol L−1, TTFs 1–7 afforded the ionic salts showing the same phase as those of the corresponding single crystalline ones. The single crystalline salts were obtained by a conventional two-phase diffusion method. In a typical procedure, the CuBr2

Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

• Christian Benkhäuser and
• Arne Lützen

Beilstein J. Org. Chem. 2015, 11, 693–700, doi:10.3762/bjoc.11.79

• signals (e.g., around 9.8, 7.5, and 5.3 ppm) which might indicate that some minor amounts of oligomers/polymers are still existing. However, the intensity of these signals was so low, that we could not assign a diffusion coefficient to them in a 2D-DOSY experiment to corroborate this assumption

Trifluoromethyl-substituted tetrathiafulvalenes

• Olivier Jeannin,
• Frédéric Barrière and
• Marc Fourmigué

Beilstein J. Org. Chem. 2015, 11, 647–658, doi:10.3762/bjoc.11.73

• cooling, the solution is poured in 100 mL of iced water and filtered. The dried precipitate is purified twice by column chromatography on silica gel with dichloromethane elution. Crystals were obtained by diffusion of pentane into a concentrated dichloromethane solution (0.17 g, 0.044 mmol). Yield: 60