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14 protocols using trimethylsilyl chloride

1

Willow Bark Extraction and Compound Purification

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Fifteen willow hybrids (Tables S1 and S2) were harvested and supplied
from Carbons Finland Oy, VTT Technical Research Center of Finland
Ltd., and Lantmännen Lantbruk. The bark was manually peeled
and cut into 2 cm pieces and stored at −20 °C for further
use. The barks were ground into 1 mm particle size and dried at 40
°C in an oven. Acetone, arabinose, N,O-bistrifluoroacetamide (BSTFA), (+)-catechin, DMSO-d6, fructose, galactose, glucose, heneicosylic
acid (C21 acid), mannose, picein, pyridine-d5, raffinose,
rhamnose, salicin, trimethylsilyl chloride (TMCS), xylitol, and xylose
were supplied from Sigma-Aldrich, Finland. Betulinol (99.5% purity)
was supplied by Åbo Akademi University. Triandrin was purified
by chromatography (Figure S1) based on
its size and hydrophobicity differences among all bioactive molecules
from willow hybrid Karin bark extract.15 (link) The purity (ca. 90%) of triandrin was assessed from its nuclear
magnetic resonance (NMR) spectra (Figures S2–S4).16 (link) The exact match between the willow
hybrid and their associated experiment is summarized in Table S1.
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2

Synthesis of Polyamide Monomers

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Anhydrous dimethyl acetamide (DMAc, 99%), anhydrous pyridine (Py), dimethyl amino pyridine (DMAp), trimethylsilylchloride (TMSC, >98%), N, N dimethyl formamide (DMF), 3-methoxycarbonyl-phenylboronic acid and tetrahydrofuran (THF, 99%) were purchased from Sigma Aldrich (Sigma Aldrich, St. Louis, MO, USA) and used as received. NaOH (sodium hydroxide), sulfuric acid (H2SO4), Tetrakis(triphenylphosphine) palladium (0) (Pd(PPh3)4), potassium carbonate (K2CO3), hydrochloric acid and thionyl chloride (SOCl2) were obtained from Scharlau (Scharlab, Barcelona, Spain). The diacid 5′-tert-butyl-m-terphenyl-3,3″-dicarboxylic acid (tBTmDA) was synthesized following the procedure previously reported [27 (link)].
o-Hydroxydiamine 2,2-bis(3-amino-4-hydroxy phenyl)-hexafluoropropane (APAF) was purchased from Apollo Scientific (Apollo Scientific, Stockport, Cheshire, UK) and purified through sublimation at 220–225 °C before use. 4,4′-(hexafluoroisopropylidene) dianiline (6FpDA, Apollo Scientific, Stockport, Cheshire, UK) purified through sublimation at 220 °C and 5′-terbutil-m-terphenyl-3,3″-dichloride (tBTmCl) were employed as monomers to create the polyamide without o-hydroxy groups (PA). The synthesis of the corresponding HPA was carried out as described elsewhere [28 (link)].
The dichloride monomer (tBTmCl) was prepared from the corresponding diacid, as described below.
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3

Antioxidant Biochemical Assay Protocol

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Dithiothreitol (DTT), nitroblue tetrazolium (NBT), H2O2, titanium dioxide, dichloromethane, pyridine, N,O-bis(trimethylsilyl) trifluoroacetamide, trimethylsilyl chloride, sodium azide, thiobarbituric acid (TBA), methionine, catalase, peroxidase, cholesterol, maltose, octadecane, phenol, palmitic acid, sorbitol, ammonia and potassium phosphate buffer were purchased from Sigma-Aldrich (Saint Louis, MO, USA). Tetracosane and 4-aminoantipyrine were purchased from Fluka (Bucharest, Romania). Sulfuric acid was purchased from Fisher Chemical (New Hampshire, EUA). TrichloroAcetic acid (TCA) was purchased from BIOCHEM Chemopharma (Cosne-Cours-sur-Loire, France). Guaiacol and polyvinylpyrrolidone (PVP) were purchased from Acrós Organics. Triton-X and ascorbic acid were purchased from Panreac. Acetic acid, ethylenediaminetetraAcetic acid (EDTA) and phenylmethylsulfonyl fluoride (PMSF) were purchased from VWR (Pennsylvania, EUA). Riboflavin, n-hexane p.a., methanol p.a., sodium carbonate (Na2CO3), dimethyl sulfoxide (DMSO), potassium sulfate and quercetin were purchased from Merck (Darmstadt, Germany). Luteolin and oleuropein were purchased from Extrasynthese (Genay, France).
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4

Synthesis and Characterization of Naproxen Derivatives

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All reagents were commercially available materials and were used without further purification. (+)-(S)-2-(6-Methoxynaphthalen-2-yl)propanoic acid (≥98%) was provided from AmBeed (Arlington Heights, IL, USA). L-proline (≥98.5%) was obtained from Carl Roth (Karlsruhe, Germany). Trimethylsilyl chloride (≥99%) (TMSCl) was purchased from Sigma-Aldrich (Steinheim am Albuch, Germany). Ammonium hydroxide solution 25% (NH3∙H2O) was of analytical grade obtained from StanLab (Lublin, Poland). Methanol (MeOH), ethanol (EtOH), propan-2-ol (i-PrOH), propan-1-ol (PrOH), butan-1-ol (BuOH), dimethyl sulfoxide, chloroform, ethyl acetate, diethyl ether, toluene, and n-hexane of high purity were purchased from Chempur (Gliwice, Poland). Deuterated chloroform (CDCl3) (99.8%) (+0.03% TMSCl) was provided by Eurisotop (Cheshire, England). Acetonitrile was provided by J.T. Baker (Radnor, Pennsylvania, USA). PBS (pH 7.4), potassium dihydrogen phosphate (p.a.) was purchased from Merck (Darmstadt, Germany). For cell culture studies, murine fibroblast cell line, L929, and all cell culture reagents were purchased from Sigma Aldrich (Poznań, Poland), while all sterile, single-use cell culture plasticware was purchased from VWR (Gdańsk, Poland).
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5

Isolation and Characterization of Sponge Chitin

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Air-dried specimens of the marine sponge A. fistularis (Figure 1) have been delivered by INTIB GmbH (Freiberg, Germany). The chemical reagents used for isolation of sponge chitinous skeleton—sodium hydroxide and acetic acid—were supplied by Chempur (Poland). Silica in form of nanopowder (>99.8%, BET: 225 m2/g), horseradish peroxidase (EC 1.11.1.7, activity ~150 U/mg), 50 mM phosphate buffer (pH 7–9), 100 mM acetate buffer (pH 3–6), bis–trimethylsilyltrifluoroacetamide (BSTFA) + 1% trimethylsilyl chloride (TMCS), 17α-ethinylestradiol (≥99%) (EE2), and Bradford reagent were purchased from Sigma Aldrich (Saint Louis, MO, USA).
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6

Lipid Vesicle Preparation and Characterization

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Polyethylene glycol (PEG; Mw = 6000 g mol−1), polyvinyl alcohol (PVA; Mw = 13,000 to 23,000 g mol−1, 87 to 88% hydrolyzed), calcein, trimethylsilyl chloride, 2-[methoxy (polyethyleneoxy) propyl] trimethoxy silane, and melittin were purchased from Sigma-Aldrich. DMPC, DOPC, egg PC, and Rhod-labeled lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (ammonium salt) (Rhod PE) were purchased from Avanti Polar Lipids. TA and sodium acetate were purchased from Macklin. Iron acetylacetonate [Fe(acac)3] and Mops were purchased from Adamas-beta. Terbium acetylacetonate [Tb(acac)3] was purchased from Bide Pharmatech. Chloroform, hexane, and sucrose were purchased from General-reagent. Pluronic F-68 was purchased from Thermo Fisher Scientific. HRP was purchased from Crgent Biotech. Amplex Red was purchased from Energy Chemical.
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7

GC-MS Metabolite Profiling of Derivatized Samples

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The dried extract was mixed with 50 μl methoxyamine hydrochloride (15 mg/ml in pyridine, Sigma Aldrich) and incubated at 30 °C for 90 min. After adding 100 μl N,O-Bis(trimethylsilyl)trifluoroacetamide containing 1% trimethylsilyl chloride (Sigma Aldrich), the mixture was further incubated at 60 °C for 1 h. The derivatized sample was analysed using a GC (Agilent 7890A), coupled with a triple quadrupole mass analyser (Agilent 7000B). The ion source temperature, transfer line temperature and injector temperature were set at 230 °C, 290 °C and 250 °C, respectively. The oven temperature ramp was set as follows: initially at 60 °C for 2 min, increased to 300 °C at a rate of 7.5 °C/min and held for 6 min. The carrier gas was helium at a flow rate of 1.0 ml/min. Derivatized samples of 1 μl were injected via splitless mode, and analyzed under full scan mode. Metabolites were separated on a DB-5MS capillary column (30 m X 0.25 mm i.d., 0.25 μm film thickness) consisting of a stationary phase of 5% phenyl 95% methylpolysiloxane, and detected in electron impact ionization mode at 70 eV. Acquired mass range was 50 – 650 Da. Samples were randomized and analysed within 24 h after derivatization.
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8

Silica-Supported Copper-Based Catalyst

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Copper(II) chloride dihydrate, sodium hydroxide, urea, ammonium hydroxide solution (25% NH3 in H2O) and ethylene glycol (EG) were used as received (Sigma-Aldrich, St. Louis, MO, USA). The silica support material, Aerosil-200 was provided by Evonik free of charge. The silica was modified prior to use by treating with trimethyl silyl chloride (Sigma-Aldrich, St. Louis, MO, USA).
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9

Solvent Characterization for Ibuprofen Extraction

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All reagents were commercially available materials and were used without further purification. (RS)-Ibuprofen (99%) was obtained from Acros Organics (Geel, Belgium). l-Valine (≥99%) was purchased from Carl Roth (Karlsruhe, Germany). Trimethylsilyl chloride (≥99%) (TMSCl) was provided by Sigma-Aldrich (Steinheim am Albuch, Germany). Methanol (MeOH), ethanol (EtOH), propan-2-ol (iPrOH), propan-1-ol (PrOH), butan-1-ol (BuOH), pentan-1-ol (AmOH), hexan-1-ol (HexOH), heptan-1-ol (HeptOH), acetic acid, potassium chloride, sodium chloride, orthophosphoric acid (98%), diethyl ether was high purity obtained from Chempur (Gliwice, Poland). Ammonium hydroxide solution 25% (NH3·H2O) was of analytical grade purchased from StanLab (Lublin, Poland). Acetonitrile (≥99.9%) for HPLC gradient grade and n-octanol (≥99%) were provided by Sigma-Aldrich (Steinheim am Albuch, Germany). Disodium hydrogen phosphate dihydrate (≥99%) (Na2HPO4·2H2O), disodium hydrogen phosphate dodecahydrate (99%) (Na2HPO4·12H2O) were provided by Fisher Bioreagents (Pittsburgh, Pennsylvania, USA) and sodium dihydrogen phosphate anhydrous (98%) (NaH2PO4) was obtained from Acros Organics (Geel, Belgium). Potassium dihydrogen phosphate anhydrous (99%) was obtained from Merck (Darmstadt, Germany). Deuterated chloroform (CDCl3) (99.8%) (+0.03% TMSCl) was purchased from Eurisotop (Cheshire, England).
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10

Quartz Surface Preparation and Bacterial Growth Assay

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Quartz (SiO2) was purchased from
Ted Pella, Inc. (Redding, CA, USA). Tetrafluoromethane (CF4) and oxygen (O2) gas was obtained from Brazos Valley
Welding Supply, Inc. and used directly as purchased (Bryan, College
Station, TX, USA). Potassium hydroxide (98%, reagent grade) was purchased
from Ward’s Science (Rochester, NY, USA). Trimethylsilyl chloride
(TMCS, ≥ 95.0%) was obtained from Sigma-Aldrich Co. (St. Louis,
MO, USA) and used with the hexane (≥95.0%) purchased from Avantor
Performance Materials, Inc. (CenterValley, PA, USA). The 200-proof
pure ethanol (HPLC grade) utilized was ordered from Koptec (King of
Prussia, PA, USA). For bacterial experiments, tryptic soy agar (TSA),
tryptic soy broth (TSB), and TSB containing 0.6% yeast extract (TSB-YE)
were procured from Becton, Dickinson and Co. (Sparks, MD, USA).
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