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18 protocols using 1100 lc msd

1

Synthesis of Azido-Amino PEG Intermediate

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The reagents and solvents were obtained from Sigma-Aldrich and were used as received. Olanzapine (OZ, MW 312.43 g/mol) was purchased from Merck KGaA (Darmstadt, Germany). Ethanol, Dulbecco’s phosphate-buffered saline (DPBS), anhydrous dimethyl sulfoxide (DMSO), sodium chloride, and sodium hydroxide were obtained from Merck KGaA (Darmstadt, Germany). The water used was produced with Milli-Q ® (Millipore Corporation, Billerica, MA, USA). Merck silica gel 60 (230–400 mesh) was employed for column chromatography, and Merck thin layer chromatography (TLC) aluminum sheets (silica gel 60 F254) were employed for TLC. NMR spectra were obtained with a Bruker DRX-400 AVANCE or a Bruker Avance III 500 spectrometer in the indicated solvents. The chemical shifts are referenced to the solvent signal (CDCl3: δ(1H) = 7.26 ppm, δ(13C) = 77.0 ppm) or to the signal of a trace acetone for solutions in D2O (δ(1H) = 2.22 ppm, δ(13C)CH3 = 30.9 ppm). Chemical shifts (δ) are reported in ppm, and the H–H coupling constants (J) are reported in Hz. An Agilent 1100 LC/MSD running with an electrospray source was used in mass spectrometry measurements. The intermediate α-azido-ω-amino hexa(ethylene glycol) 3 was synthesized as previously reported in Reference [27 (link)].
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2

LC-MS Analysis of RNA Samples

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Samples of GMP, GDP, and GTP were analysed by LC-MS using an Agilent 1100 LC-MSD. Analysis was carried out using a Zorbax Eclipse XDB-C8 Rapid Resolution HT 3.0 × 50 mm 1.8 micron column. Buffer A is 1% acetonitrile and 0.08% trifluoroacetic acid in milliQ water, and Buffer B is 90% acetonitrile and 0.08% trifluoroacetic acid in milliQ water. Flow rate was 0.425 mls/min, and the gradient was 0% – 40% Buffer B over 8 min. The MS was conducted with positive polarity, fragmentor voltage was 170, drying gas flow 12 L/min, drying gas temperature 350°C, and nebuliser pressure 40 psig. Mass spectra were registered in full-scan mode (m/z 200 to 3000 step size 0.15). RNA samples were analysed by electrospray ionization (ESI) -LC-MS performed by Axolabs GmbH (Kulmbach, Germany) using a Dionex Ultimate3000 RS system coupled to a Bruker maXis Q-ToF mass spectrometer. The samples were analysed with an improved version of the protocol established for ribonucleotide digestion analysis34 (link). Analysis of 4 pmol and 50 pmol of an equimolar solution of chemically synthesised pp-RNA24nts and ppp-RNA24nts treated with RNase T2 served as control. Characterisation of reovirus genome RNA was performed with 50 μl (13 μg) of the RNase T2 digest.
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3

Synthesis and Characterization of Novel Compounds

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Synthesis. All chemicals used were of reagent grade. Yields refer to purified products and are not optimized. Merck silica gel 60 (230−400 mesh) was used for column chromatography. Merck TLC plates and silica gel 60 F254 were used for TLC. NMR spectra were obtained with a Bruker 400 AVANCE spectrometer in the indicated solvents. Melting points were determined in open capillaries in a Gallenkamp apparatus and were uncorrected. The chemical shifts are referenced to the residual not deuterated solvent signal (CHD2OD: δ (1H) = 3.31 ppm, δ (13C) = 49.86 ppm). The values of the chemical shifts are expressed in ppm, and the coupling constants (J) in Hz. An Agilent 1100 LC/MSD operating with an electrospray source was used in mass spectrometry experiments. The purity of compounds 1bh was assessed by RP-HPLC (Agilent 1100 series) and was found to be higher than 95% [40 (link)]. A Zorbax Eclipse XDB-C8 column (4.6 × 150 mm, 5 μm) was used in the HPLC analysis with methanol-H2O (0.1% formic acid) (80:20) as the mobile phase at a flow rate of 0.5 mL/min. UV detection was achieved at 280 nm. The absorption spectra were recorded with a PerkinElmer Lambda 900 in the indicated solvent. UV-B irradiations were conducted using a Multyrays chamber equipped with 2 GT15T8 Hg UV-B tubes (2 × 15 Watt) in continuous rotation.
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4

Comprehensive Analytical Characterization of Synthesized Compounds

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Liquid chromatography-mass spectrometry (LC/MS), NMR spectroscopy, and elemental analysis methods were applied to confirm the structure and purity of all synthesised compounds.
LC/MS analysis was performed on an 1100 LC (Agilent Technologies) with ELSD, UV (DAD 200–400 nm), and mass detection (1100 LCMSD, Agilent Technologies, APCI, and ES positive ionization). The most used column was the Onix C18 50 × 4.6 mm; eluent 1–0.1% TFA in water; eluent 2–0.1% TFA in acetonitrile, gradient—eluent 1–2.9 min, eluent 2–0.2 min, eluent 1—rinsing, flow rate—3.75 mL/min.
The structures of key target final compounds were unambiguously confirmed by 1H, 13C{1H},13C apt, COSY, HSQC, and NOESY NMR spectroscopy. For structure confirmation of intermediates, 1H NMR spectroscopy was applied, and in some cases, if it was necessary, 13C{1H} NMR spectra were also registered. NMR spectra were registered on spectrometers Bruker DRX 400 (400.13 MHz for protons, 100.61 MHz for carbons, 376.50 MHz for fluorine), Bruker Avance II+ 600 (600.11 MHz for protons, 150.93 MHz for carbons), Avance IIIHD 500 (500.13 MHz for protons, 125.78Mhz for carbons), and spectrometer Bruker Avance III 400 UltraShield Plus (400 MHz). CDCl3 and DMSO-d6 were used as solvents.
Elemental analysis was performed on Vario MICRO cube CHNS analyser (Elementar Analysensysteme GmbH, Hanau, Germany).
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5

Synthesis and Polymerization of Benzofulvenes

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The details of the preparation of benzofulvene derivatives and their spontaneous polymerization are described in (ESI). NMR spectra were recorded with either a Bruker DRX-400 AVANCE or Bruker DRX-500 AVANCE spectrometer in the indicated solvents (TMS as internal standard): the values of the chemical shifts are expressed in ppm and the coupling constants (J) in Hz. An Agilent 1100 LC/MSD operating with an electrospray source was used in mass spectrometry experiments.
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6

Analytical Techniques for Chemical Characterization

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UV spectra were acquired with a Cary 300 spectrometer. IR spectra were obtained using a Nicolet 5700FTIR microscope spectrometer. Analytical HPLC was conducted on an Agilent system with a 1260 Quat-Pump and DAD detector. For semi-preparative HPLC, a reverse-phase C18 column (Spursil 5μm C18 column: 250 × 10.0 mm) was used with MeCN-H2O as a solvent system. LC-MS was performed on a 1100–6410 Triple Quad from Agilent or an Agilent 1100 LC/MSD with a G1946D single quadrupole mass spectrometer. High-resolution mass spectrometry was carried out on a XEVO G2-XS QTof from Waters. NMR data were collected using a Bruker-600 or an ADVANCE HD 800 MHz and a Bruker Avance Ⅲ HD 700 MHz spectrometer, where chemical shifts (δ) were reported in ppm and referenced to DMSO-d6 solvent signal (δH 2.49 and δC 39.5), CDCl3 solvent signal (δH 7.26 and δC 77.0) and acetone-d6 solvent signal (δH 2.04 and δC 206.0). 3T3-L1 fibroblast cell (pre-adipocyte) line was purchased from the Cell Center of the Institute of Basic Medicine, Chinese Academy of Medical Sciences.
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7

Synthesis and Characterization of β-Diketoesters

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All chemicals were purchased from commercially available sources and used as received. Column chromatography was performed with silica gel (25–63 μm). High-resolution mass spectra were recorded on an Agilent 6520 Accurate Mass Q-TOF instrument. 1H nuclear magnetic resonance was recorded in CDCl3 or DMSO on a Bruker 500 MHz spectrometer. Reverse-phase liquid chromatography and mass spectrometry were performed on an Agilent 1100 LC/MSD instrument fitted with an Eclipse XBD-C18 (4.6 mm × 150 mm) column eluting at 1.0 mL min−1 employing an (acetonitrile/methanol)/water gradient (each containing 5 mM NH4OAc) from 70 to 100% acetonitrile/methanol over 15 min and holding at 100% acetonitrile/methanol for 2 min. Chemical shifts are reported in parts per million using either residual CHCl3 or DMSO as an internal reference. All compounds are >95% pure unless otherwise stated. Syntheses of 3-(hexyloxy)-aniline and 3-(hexyloxy)-4-methylaniline were performed using a protocol described by Marco and co-workers.56 (link)β-Diketoesters were synthesized with modification according to Milagre and co-workers.57 (link) Derivatives of 1 were synthesized by a modified procedure of Rose and co-workers.58 (link) Full compound characterization is provided in the Supporting Information.
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8

Melting Point and Spectroscopic Analysis

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Melting points were recorded on a Mel-Temp melting point apparatus and are uncorrected. Unless otherwise stated, all the materials were obtained from the commercial suppliers and are used without further purification. Chromatography was carried on silica gel (100–200 mesh). All the reactions were monitored by thin-layer chromatography and the spots were visualized under UV light. The 1H and 13C NMR spectra were recorded on Bruker FT-NMR spectrometer operating at 400 MHz for 1H and 100 MHz for 13C using TMS as an internal standard. Chemical shifts are expressed in δ (ppm) and coupling constants J in Hertz (Hz). Mass spectra were recorded on an Agilent 1100 LC/MSD.
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9

Synthesis and Polymerization of Compounds 3a-h

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The details of the synthesis and characterization of compounds 3a–h and their spontaneous polymerization are described in Supporting Information. The synthetic intermediates and the solvents were purchased from Sigma-Aldrich (Saint Louis, MO, USA) unless otherwise stated. NMR spectra were recorded with a Bruker (Karlsruhe, Germany) AC200, a Varian (Palo Alto, CA, USA) Mercury-300, a Bruker DRX-400 AVANCE, or a Bruker DRX-600 AVANCE spectrometer in the indicated solvents (TMS as internal standard). The values of the chemical shifts are expressed in ppm and the coupling constants (J) in Hz. An Agilent (Santa Clara, CA, USA) 1100 LC/MSD operating with an electrospray source was used in mass spectrometry experiments.
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10

Fmoc-Based Peptide Synthesis and Purification

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This peptide was synthesised manually by coupling resin 12 (0.14 mmol) scale with Fmoc-Ala-OH followed by Z-Val-OH using standard solid phase Fmoc procedures. Prior to each coupling the Fmoc was removed by treating the resin with (3 × 10 mL) of 20% piperidine in DMF for 10 min. HATU (4.5 equiv.) and DIPEA (10 equiv.) were used as the coupling reagents with 5-fold excess of each amino acid. Cleavage was performed by treatment of the peptide-resin with an ice-cold solution of (95% TFA, 2.5% H2O, 2.5% TIPS) for 30 min. Following filtration to remove the linker retaining resin, ether was added to the filtrate. The peptide was ether soluble so following evaporation of ether the peptide was solubilised in water and acetonitrile prior to lyophilisation. Aliquots of the peptide were solubilised in a (2 : 1 : 1) mixture of H2O–MeCN–MeOH (2 mL) and purified on a C8 reverse phase HPLC column (Agilent PrepHT Zorbax 300SB-C8, 21.2 × 250 mm, 7 m) using a linear solvent gradient of 15–60% (MeCN + 0.08% TFA) and (H2O + 0.08% TFA) over 40 min at a flow rate of 8 mL min−1. Fractions containing the product were combined and lyophilised to dryness to give peptide 13 (4.4 mg, 6.7%). The purified peptide was analysed by LCMS on an Agilent 1100 LC-MSD; estimated purity 65%; MS (ES+) m/z: 468.0 [M + H]+, 489.9 [M + Na]+; calcd for C22H30N3FO7: 467.2.
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