The general procedure for the synthesis of benzylidene cyclopentanone derivatives was as follows: aromatic aldehyde (42.2 mmol) was added to a solution of 2.08 mmol cyclopentanone in ethanol (100 ml). The solution was stirred at room temperature for 10 min, and then NaOMe (54.8 mmol) solution was added dropwise. The mixture was stirred at a temperature of 25°C for 14 h. The mixture was poured into ice-water (150 ml) and filtered. The filtered cake was washed with water (20 ml × 2) and evaporated to dryness under reduced pressure. The solid part was purified by silica gel chromatography using CH2Cl2/CH3OH as an eluent. Thin-layer chromatography (TLC) was performed on Kieselgel 60 F254 plates. The melting point was measured on a Fisher-Johns melting apparatus and was uncorrected. 1H NMR spectrum was recorded on a Bruker 600 MHz instrument. The chemical shifts were presented in terms of parts per million using TMS as an internal reference. Electrospray ionization mass spectrometry (ESI-MS) data in positive mode was recorded on a Bruker Esquire 3000 spectrometer (Bruker, Billerica, MA). Column chromatography purification was performed on silica gel 60 (Merck, Kenilworth, NJ).
Esquire 3000 spectrometer
Manufactured by Bruker
Sourced in United States
The Esquire 3000 spectrometer is a mass spectrometer designed for high-performance ion trap mass analysis. It provides accurate mass measurements and reliable data for a wide range of applications.
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Lab products found in correlation
Silica gel 60, by Merck Group (3 mentions)
600 mhz instrument, by Bruker (2 mentions)
Avance ultrashield nmr spectrometer, by Bruker (2 mentions)
Unity inova spectrometer, by Agilent Technologies (1 mentions)
Acquity uplc ms system, by Waters Corporation (1 mentions)
Sq detector 2, by Waters Corporation (1 mentions)
Iraffinity 1, by Shimadzu (1 mentions)
Nexion 350d, by PerkinElmer (1 mentions)
2 hydroxy 5 methoxybenzoic acid, by Merck Group (1 mentions)
2 hydroxy 3 methoxybenzaldehyde, by Merck Group (1 mentions)
2 hydroxy 4 methoxybenzaldehyde, by Merck Group (1 mentions)
400 mhz instrument, by Bruker (1 mentions)
Avance 3 500, by Bruker (1 mentions)
Evolution 300 spectrophotometer, by Thermo Fisher Scientific (1 mentions)
Labmaster pro, by MBraun (1 mentions)
B 545, by Büchi (1 mentions)
Ftir spectrophotometer 1000, by PerkinElmer (1 mentions)
Uv vis spectrometer, by PerkinElmer (1 mentions)
Ct dna, by Merck Group (1 mentions)
Cary eclipse fluorescence spectrometer, by Agilent Technologies (1 mentions)
16 protocols using esquire 3000 spectrometer
1
Synthesis of Benzylidene Cyclopentanone Derivatives
2
Synthesis and Characterization of Compound 10
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All reactions were performed under an argon atmosphere by standard Schlenk techniques. Amine 1 was prepared as reported previously. 10 Benzene and chloroform were dried by standing over sodium metal and CaH 2 , respectively, and distilled under argon. Dimethyl sulfoxide was distilled under vacuum. Methanol was dried with an in-house PureSolv MD5 a For definitions, see the footnote to Table 2. solvent-drying system (Innovative Technology, USA). A solution of sodium methoxide was prepared by dissolving the appropriate amount of sodium metal in anhydrous methanol. Other chemicals and solvents were obtained from commercial suppliers (Sigma-Aldrich or Lachner, Czech Republic) and were used without any additional purification. NMR spectra were recorded at 25 °C on a Varian Unity INOVA spectrometer operating at 399.95 MHz for 1 H, 100.58 MHz for 13 C, and 161.92 MHz for 31 P. The chemical shifts (δ in ppm) are given relative to internal tetramethylsilane ( 1 H and 13 C) or to external 85% aqueous H 3 PO 4 ( 31 P). IR spectra were obtained on a Nicolet Magna 6700 FTIR spectrometer in the range of 400-4000 cm -1 . Electrospray ionisation mass spectra (ESI MS) were acquired with a Bruker Esquire 3000 spectrometer using samples dissolved in HPLC-grade methanol.
3
Characterization of Organic Compounds by Mass Spectrometry
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ESI mass spectra were recorded using an Esquire 3000 spectrometer from Bruker or an Acquity UPLC/MS system from Waters equipped with an SQ Detector 2 and a column heater set at Organic & Biomolecular Chemistry Paper 60 °C. MALDI-TOF mass spectra were recorded using an Autoflex Bruker with hydropiccolinic acid (HPA) (45 mg, ammonium citrate (4 mg) in 500 mL H 2 O/CH 3 CN) as the matrix. Peptides were analyzed in the positive mode and oligonucleotides and conjugates in the negative mode.
4
Synthesis and Purification of Organic Compounds
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Before use, solvents were distilled under positive pressure of dry argon by standard methods. Acetonitrile and tetrahydrofuran were distilled over calcium hydride and stored over 4Å molecular sieves. All starting materials and reagents were either commercially available or previously synthesized. Unless otherwise noted, chemicals were obtained from local suppliers and were used without further purification. All reactions were monitored by thin-layer chromatography (250 μm Silica Gel 60 F254 glass plates). Nuclear magnetic resonance (NMR) spectra were recorded on Bruker 600 MHz instruments (Bruker Corporation, Billerica, MA, USA), and the chemical shifts were presented in terms of parts per million, with tetramethylsilane as the internal reference. Electron-spray ionization mass spectra in positive mode (ESI-MS) data were obtained with a Bruker Esquire 3000+ spectrometer. Column chromatography purifications were carried out on Silica Gel 60 (E. Merck, 70–230 mesh [EMD Millipore, Billerica, MA, USA]).
5
Synthesis and Characterization of Benzaldehyde Derivatives
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All synthetic procedures were performed under normal atmospheric conditions. Fourier transform infrared (FTIR) spectra were recorded with a IRAffinity-1S Shimadzu spectrophotometer. High resolution electron spray ionisation mass spectra were recorded on a BrukerDaltronics Esquire 3000 spectrometer by Dr. Lisa Haigh (Imperial College London). UV-Vis absorption spectra were recorded on a Cary100 UV-Vis spectrophotometer. Elemental analysis of the compounds prepared was performed commercially by London Metropolitan University. 2-(Methylthio)ethan-1-amine, 2-hydroxy-3-methoxybenzaldehyde, 2hydroxy-4-methoxybenzaldehyde, 2-hydroxy-5-methoxybenzoic acid, and 2-hydroxy-6-methoxybenzaldehyde were purchased from Sigma Aldrich and used as received. For the high concentration UV studies (250 µM), a 10 mM stock solution of 4 in DMSO was initially prepared. The copper concentration of the stock solution was determined by inductively coupled plasma mass spectrometry (ICP-MS, PerkinElmer NexION 350D). The stock solution was diluted in PBS to the working concentration.
6
Purification and Characterization of Organic Compounds
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Solvents were distilled under the positive pressure of dry argon before use and dried using standard methods. Chemicals were obtained from local suppliers and were used without further purification. All reactions were monitored by thin-layer chromatography (silica gel 60 F254 glass plates). NMR spectra were recorded on Bruker 400 MHz instruments, and the chemical shifts were presented in terms of parts per million with TMS as the internal reference. Electron-spray ionisation mass spectra in positive mode (ESI-MS) data were obtained with a Bruker Esquire 3000+ spectrometer. Flash column chromatography was performed on silica gel (200–300 mesh, Adamas, China).
7
Inert Atmosphere Synthesis and Characterization
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All syntheses and manipulations were performed under an inert gas (Ar or N2) atmosphere using standard Schlenk techniques and an MBraun LABmaster Pro glovebox. THF, n-hexane, and o-xylene were dried over NaK, distilled prior to use, and stored over 3 Å molecular sieve. Melting points were measured using a Büchi B-545 melting point apparatus. NMR spectra were recorded using a Bruker Avance III 500 or a Bruker Avance III 500HD NMR spectrometer. Chemical shifts are given in δ ppm and are referenced to the solvent residual peaks:24 DMSO-d6 (1H, δ = 2.50 ppm and 13C, δ = 39.52 ppm), C6D6 (1H, δ = 7.16 ppm and 13C, δ = 128.06 ppm). ESI mass spectra were recorded with a Bruker Esquire 3000 spectrometer. UV-visible spectra were recorded using a ThermoFisher Evolution 300 spectrophotometer.
8
Characterization of Organic Compounds
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Melting points were determined on a Fisher–Johns melting apparatus and are uncorrected. UV spectra were recorded on UV-VIS spectrophotometer model of type Genesys 10s and expressed in nm. FT-IR spectroscopic studies were carried out on a FTIR spectrophotometer 1000, model Perkin Elmer, at a room temperature of 25 °C. KBr pellets were dried in an oven and scanned for calibration purposes. 1H-NMR spectra of compounds were recorded on a Bruker Ascend TM 600 MHz machine. The chemical shifts (δ) are presented with reference to CDCl3 (δ: 7.25) and tetramethylsilane (TMS) (δ: 0.00) as the internal reference. Electron-spray ionization mass spectra in positive mode (ESI-MS) data were recorded on a Bruker Esquire 3000+ spectrometer. Column chromatography purifications were carried out on a Silica Gel 60 (Merck, 70–230 mesh). The purity of compounds was checked by thin-layer chromatography (TLC) and 1H-NMR. All the chemicals were purchased from Sigma-Aldrich (Saint Louis, MO, USA). Other reagents were purchased from Sinopharm Chemical Reagent Co. Ltd., (Shanghai, China).
9
Characterization of Fluorescent Dyes and Oligonucleotides
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All chemicals were used as purchased from commercial sources unless stated otherwise. Solvents were distilled over an appropriate drying agent and degassed prior to use. 1H and 13C NMR spectra were recorded by using a 400 or 500 mhz Bruker Avance Ultrashield NMR spectrometer at 296 K, respectively. Chemical shifts are referenced to residual deuterated solvent. Mass spectra were obtained by using electrospray ionisation (ESI) by Mrs. L. Haigh (Imperial College London) on a Bruker Daltronics Esquire 3000 spectrometer. Compound microanalysis was performed by Mr. A. Dickerson (Cambridge University). Absorption measurements were made on a Perkin–Elmer UV/Vis spectrometer. Emission spectra were obtained on a Varian Cary‐Eclipse fluorescence spectrometer. The oligonucleotides used were purchased RP‐cartridge purified from Eurogentec. CT‐DNA was obtained from Sigma–Aldrich. TOTA , TMPA‐M , ADOTA‐M ,DAOTA‐M2 ,11 and 1,13‐dimethoxy‐5,9‐bis (propyl)‐5H‐quinolino[2,3,4‐kl]acridin‐9‐ium tetraflouroborate13 were prepared by previously reported procedures.
10
Anhydrous Organic Synthesis Techniques
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All reactions were carried out under anhydrous conditions in an argon atmosphere with dry, freshly distilled solvents. Analytical thin-layer chromatography was performed on SiO2 (Merck silica gel 60 F254), and the spots were located with 1% aqueous KMnO4. Chromatography, referring to flash chromatography, was carried out on SiO2 (SDS silica gel 60 ACC, 35–75 mm, 230–240 mesh ASTM). Drying of organic extracts during workup of reactions was performed over anhydrous MgSO4 except where stated otherwise. Evaporation of solvent was accomplished with a rotatory evaporator. NMR spectra were recorded in CDCl3 or MeOD on a Varian VNMRS 400 (Varian, Palo Alto, CA, USA). Chemical shifts of 1H and 13C NMR spectra are reported in ppm downfield (δ) from Me4Si. Electron-spray ionization mass spectra in positive mode (ESI-MS) data were recorded on a Bruker Esquire 3000 + spectrometer (Bruker Daltonics Inc., Billerica, MA, USA).
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