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27 protocols using aviii400

1

Synthesis and Characterization of 5-Iodo-dUTP

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Reagents and solvents were purchased from commercial suppliers and used without further purification, unless otherwise stated. 5′-O-(4,4′-dimethoxytrityl)-5-iodo-2′-deoxyuridine 2 was synthesised following an established procedure.20 (link) Column chromatography was carried out using open columns packed with Merck grade 60 silica gel topped with 0.5 cm of sand. TLC analysis was performed on Merck silica gel 60 silica sheets. 1H, 13C, and 31P NMR spectra were obtained on Bruker AVIII300 or AVIII400 spectrometers. Chemical shifts (δ) are given in ppm and are relative to the residual solvent peak. Electrospray mass (ESI-MS) spectra were measured by either Waters micromass LCT electrospray time-of-flight (ES-TOF), Waters Xevo G2-XS, or Synapt G2S mass spectrometers. Milli-Q water purified with a Millipore Elix-Gradient A10 system (resistivity > 18 μΩ cm, TOC ≤ 5 ppb, Millipore, France) was used for DNA sample preparation.
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2

Characterization of Polymer Membranes

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The Fourier transform infrared (FTIR, Bruker TENSOR27, Billerica, MA, USA) spectra of the polymers and membranes were determined in the peak range of 4000 to 700 cm−1. The 1H NMR (Bruker AV III 400) spectra wEre measured using deuterated dimethyl sulfoxide (D6-DMSO) as the solvent and tetramethylsilane (TMS) as an internal standard. The thermal gravimetric analysis (TGA, TA Q50, TA Instruments, New Castle, DE, USA) of membranes was performed in the temperature range of 80 to 750 °C under a nitrogen atmosphere. The mechanical properties of the membranes were tested using 11-3 5KN apparatus (L&W, Stockholm, Swedish).
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3

Synthesis and Characterization of Sialic Acid Derivatives

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Reagents were purchased from Sigma-Aldrich,
Acros Organics, and Alfa Aesar. N-Acetylneuraminc
acid and 2-O-methyl-α-d-N-acetylneuraminic acid were purchased from Carbosynth Limited. All
of the reagents were used without further purification. 1H NMR and 13C NMR spectra were recorded at room temperature
(RT) using the following spectrometers: Bruker AVIII400 at 400 and
101 MHz, respectively, and Bruker Ascend 400 at 400 and 101 MHz, respectively.
Thin-layer chromatography (TLC) was performed using commercially available
Macherey-Nagel aluminum backed plates coated with a 0.20 mm layer
of 60 Å silica gel with a fluorescence indicator UV254. TLC plates
were visualized using ultraviolet light of 254 nm wavelength. Silica
gel column chromatography was carried out using Sigma-Aldrich 60 Å
silica gel (35–70 μm). Mass spectra were recorded with
a Bruker Daltonics MicrOTOF-Q II spectrometer.
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4

Characterization of Organic Compounds

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The reagents and chemicals for the targeted scheme were obtained from Merck (Burlington, MA, USA), Fischer (Waltham, MA, USA) and Acros Organics (Guglielmo Marconi, Verona, Veneto, Italy) and were used as supplied. All solvents were of analytical grade and were purified by distillation before use in the experimental protocols. FT-IR (Fourier transform infrared spectra) were estimated on the Bruker OPUS FT-IR spectrometer by attenuated total reflection (Diamond ATR) on solid films. Meanwhile, 1H NMR and 13C NMR were recorded via the Bruker DPX-400 and at 500 MHz, AV400, or AV(III)400 (Bruker, Zurich, Switzerland) machines using deuterated chloroform (CDCl3) and were employed to report chemical shifts in ppm. The ESI-HRMS data were recorded using the Bruker Micro TOF-ESI (Bruker Daltonics, Germany) positive targeted mode. The elemental analysis (CHN) was performed on the CE-440 Elemental Analyzer (Exeter Analytical (Coventry, UK) Ltd.). Melting points were estimated on the Gallenkamp instrument (Fisons, Uckfield, UK).
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5

Fullerene Derivatives Synthesis and Characterization

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C60 (99.5%) and C70 (95%) were purchased from SES Research and MER corporation respectively. CH2Cl2 was freshly distilled over CaH2 before use. All other reagents and solvents were purchased from Aldrich and used without further purification. Compounds 13 and 710 were synthesised according to previously reported procedure [20 (link)]. Infra-red spectra were measured as KBr discs using a Nicolet Avatar 380 FTIR spectrometer over the range 400–4000 cm−1. 1H and 13C NMR spectra were obtained using Bruker DPX 300, Bruker DPX 400, Bruker AV(III) 400 or Bruker AV(III) 500 spectrometers. Mass spectrometry was carried out using a Bruker microTOF spectrometer and a Bruker ultraFlexIII MALDI–TOF spectrometer using trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile (DCTB) as supporting matrix. UV–vis spectra were measured using a Lambda 25 Perkin Elmer Spectrometer. EPR spectra were obtained on a Bruker EMX EPR spectrometer.
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6

NMR Spectroscopy and Chromatographic Techniques

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One- and two-dimensional
NMR spectra were recorded in CDCl3 on a Bruker AVIII400
or a Bruker AVII600 instrument (Bruker, Rheinstetten,
Germany). Tetramethylsilane (TMS) (Sigma-Aldrich, St. Louis, MO, USA)
was used as a reference. Flash chromatography was performed on a Biotage
Select Flash instrument equipped with Biotage Sfär silica (Si)
gel columns (Biotage, Uppsala, Sweden) or on a VersaFlash system (Supelco,
Bellefonte, PA, USA) with Versapak normal phase Si gel columns. Open
column chromatography was performed on Sephadex LH20 (Pharmacia, Uppsala,
Sweden) or MCI gel CHP20P (Supelco). Fractions were combined as indicated
by their UV absorbance or by analytical TLC.
Analytical TLC
was carried out on normal phase silica gel 60F254, 0.2
mm thick layers (Merck, Darmstadt, Germany). Spots were visualized
by irradiation with short-wave (254 nm) and long-wave (366 nm) UV
rays (UVGL-58 instrument, Ultra-Violet Products, Upland, CA, USA)
and spraying the TLC-plates with a 1% solution of Ce(SO4)2 in 10% aqueous H2SO4, followed
by heating (105 °C, 5 min). Preparative TLC was done on Si gel
60F254 plates, 0.5 mm thickness (Merck), with visualization
by UV irradiation. Some fractions were purified by centrifugally accelerated
TLC (CA-TLC) on a Chromatotron model 7924T (Harrison Research, Palo
Alto, CA, USA) on gypsum-containing Si gel (Merck).71 All chemicals and solvents were of the highest quality
grade.
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7

NMR Spectroscopy and HPLC Analysis

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1H and 13C NMR spectra were recorded on a Bruker AV-III-400 or 500 MHz NMR spectrometer. Chemical shifts are reported in δ values in ppm downfield from TMS as the internal standard. 1H NMR data are reported as follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, b = broad, m = multiplet), coupling constant (Hz), integration. 13C chemical shifts are reported in δ values in ppm downfield from TMS as the internal standard. Low resolution mass spectra were obtained on Waters Acquity Ultra Performance LC with electrospray ionization and SQ detector by injecting sample in a steady flow of 1 mM ammonium acetate in 20% water-acetonitrile at the rate of 0.2 mL/min. The purity of compounds were determined by analytical HPLC, performed on a Shimadzu Prominence-HPLC with ELSD PDA multi, and a Gemini NX C-18 column (250 × 4.6 mm, 5μ) with mobile phase (A) 0.1% Formic Acid in water and mobile phase (B) 0.1% Formic Acid in Acetonitrile using following gradient of B/A (0 min, 10%), (5 min, 90%), (6 min, 95%), (10 min, 95%), (10 min, 10%) and (14 min, 10%) at 1.0 mL/min flow rate. Analytical thin layer chromatography was performed on 250 μm silica gel F254 plates. Preparative thin layer chromatography was performed on 1000 μm silica gel F254 plates. Flash column chromatography was performed employing 230–400 mesh silica gel.
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8

Spectroscopic Characterization of Organic Compounds

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All compounds were fully characterized by spectroscopic data. The NMR spectra were recorded on Bruker AVIII-400 (1H: 400 MHz, 13C: 100 MHz) or Bruker AVIII-500 (1H: 500 MHz, 13C: 125 MHz) and chemical shifts (δ) are expressed in ppm, and J values are given in Hz, CDCl3 was used as solvent. IR spectra were recorded on a FT-IR Thermo Nicolet Avatar 360 using a KBr pellet. The reactions were monitored by thin-layer chromatography (TLC) using silica gel GF254. The melting points were determined on XT-4A melting point apparatus and are uncorrected. HRMS were performed on a Agilent LC/Msd TOF and monoisotopic mass instrument.
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9

Characterization of Organic Compounds

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All glassware was dried before use. All solvents were used in p.a. quality. All reagents were used as received from commercial suppliers unless otherwise stated. Reaction progress was monitored using TLC on aluminum sheets coated with silica gel 60 with 0.2 mm thickness (Pre-coated TLC-sheets ALUGRAM® Xtra SIL G/UV254). Visualization was achieved by UV light (254 nm and 363 nm) and/or by treatment with potassium manganite(VII) and heat. CC was performed using silica gel 60 (230–400 Mesh, MERCK AND CO.). All 1H NMR and 13C NMR spectra were recorded on BRUKER AVIII-400 in CDCl3. Chemical shifts (δ) were given in “parts per million” (ppm), referenced to the peak of TMS (δ = 0.00 ppm), using the solvent as internal standard (1H: δ(CDCl3) = 7.26 ppm; 13C: δ(CDCl3) = 77.16 ppm [26 (link)]). Coupling constants (J) were given in Hz. Spectroscopy splitting patterns were designated as singlet (s), doublet (d), triplet (t), quartet (q), pentet (p), multiplet (m), or combinations of that. MS were obtained using a BRUKER maXis spectrometer with ESI and the main signals were given in m/z units. IR were recorded on a BRUKER VERTEX FT-IR spectrometer. The following computer programs were used: MestReNova from Mestrelab Research and ChemDraw from PerkinElmer.
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10

Characterization of Bacterial Metabolites by NMR and GC-MS

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Nuclear magnetic resonance (NMR) data were collected at 9.4 or 14.1 T by a Bruker AVIII 400 or 600 MHz spectrometer, respectively. The AVIII 400 data were collected using a 5-mm BBFO+ probe. The AVIII 600 was equipped with a 1H/31P/13C/15N/D 5 mm QCI-P cryoprobe. Gas chromatography–mass spectrometry (GC–MS) in electron ionization mode (70 eV) was performed on dichloromethane solutions of BMNs on an Agilent Technologies 6890 GC interfaced to a 5973 mass selective detector from the same manufacturer (Cheshire, UK). The average linear retention index (LRI) was recorded (n=3) using the 25 m Agilent Technologies J&W DB-5 MS column (0.2 mm internal diameter, 0.33 μm film thickness) by reference to an alkane test mix (C7–C30) with the initial temperature set to 40°C (hold 5 min) and programmed to rise to 280°C at 10°C min−1 (hold 15 min). Helium carrier gas was used in constant flow mode (1 ml min−1). A 1-μl splitless injection was performed at 280°C. Mass-to-charge ratios (m/z) of the 10 most abundant ions (% abundance) are listed.
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