Pyridine d5

Manufactured by Cambridge Isotopes

Sourced in United States

Pyridine-d5 is a deuterated form of the organic compound pyridine. It is used as a solvent and reagent in various analytical and chemical applications.

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Lab products found in correlation

10 protocols using pyridine d5

Endothelial Cell Molecular Pathway Analysis

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Materials were purchased respectively as follows: EGM-2 medium kit from Lonza Cambrex (Nottingham, UK), enhanced chemiluminescence (ECL) reagent from AbClon (Seoul, South Korea), Griess reagent from Promega Co. (WI, USA), LeGene Premium Express 1st Strand cDNA Synthesis System from LeGene Biosciences (CA, USA), polyvinylidene fluoride (PVDF) membranes from Millipore (MA, USA), pyridine-d5 from Cambridge Isotope Laboratories Inc. (MA, USA), RNAiso PLUS from TAKARA Korea Biomedical Co. (Seoul, South Korea), thin-layer chromatography (TLC) silica gel 60 F₂₅₄ from Merck (Darmstadt, Germany), and TOPreal™ qPCR 2× PreMIX SYBR green from Enzynomics (Seoul, South Korea). N(G)-nitro-L-arginine methyl ester (L-NAME), fetal bovine serum (FBS), and silica gel resin were purchased from Sigma-Aldrich (MO, USA). All other chemicals were of ultra-pure grade. The primary antibodies (eNOS, phospho-eNOS Ser¹¹⁷⁷, Akt, phospho-Akt Thr³⁰⁸, and GAPDH) and horseradish peroxidase (HRP)-conjugated secondary antibodies (anti-rabbit and anti-mouse) were obtained from Merckmillipore (CA, USA). All other chemicals were of ultra-pure grade.

Lee Y.S., Kim H., Kim J., Seol G.H, & Lee K.W. (2019). Lancemaside A, a major triterpene saponin of Codonopsis lanceolata enhances regulation of nitric oxide synthesis via eNOS activation. BMC Complementary and Alternative Medicine, 19, 110.

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Analytical Methods for Compound Characterization

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Deionized water was used throughout the study. Ethanol was analytical grade. ¹H and ¹³C NMR spectra were collected on an Avance III 600 spectrometer (Bruker, Switzerland) with tetramethylsilane (TMS) as an internal standard in pyridine-d₅ (Cambridge Isotope Laboratories, Inc.). An ultra-high-performance liquid chromatograph connected to a triple quadrupole tandem mass spectrometer (UPLC-Xevo TQ MS, Waters, United States) was used to obtain electrospray ionization–mass spectrometry (ESI-MS) data. Silica gel (200–300 mesh, Qingdao Haiyang Chemical Co., Ltd., Qingdao, China), a macroporous resin column (D101, Jiangsu Donghong Chemical Co., Ltd., China), and thin-layer chromatography (TLC) plates (Qingdao Haiyang Chemical Co., Ltd., China) were used to monitor the compound. The TLC spots were visualized under ultraviolet (UV) light at 254 nm and stained by spraying the TLC plates with 5% (v/v) H₂SO₄ in alcohol followed by heating. Semi-preparative high-performance liquid chromatography (HPLC) analysis was performed on an Agilent 1260 series system (Agilent Technologies, United States) equipped with a diode array detector, and preparative HPLC was conducted with a Hanbon series system (Jiangsu Hanbon Science & Technology Co., Ltd., China) equipped with a UV detector, using two types of C18 columns produced by Agilent (Zorbax SB-C18 column, 5 μm; ϕ 9.4 × 250 mm and ϕ 4.6 × 250 mm).

Yan X.X., Zhao Y.Q., He Y., Disayathanoowat T., Pandith H., Inta A, & Yang L.X. (2023). Cytotoxic and pro-apoptotic effects of botanical drugs derived from the indigenous cultivated medicinal plant Paris polyphylla var. yunnanensis. Frontiers in Pharmacology, 14, 1100825.

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NMR Analysis of Organic Compounds

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Dried compound 2 (10 mg) was exchanged into methanol-d4, 99.8 atom% D, containing 0.05% (v/v) Tetramethylsilane (TMS) (Cambridge Isotope Laboratories Inc., Andover, MA, USA). Dried compounds 5 and 6 (10 mg each) were exchanged into pyridine-d5, 99.5 atom% D (Cambridge Isotope Laboratories Inc.). Spectra were determined by one-dimensional (¹H NMR, ¹³C NMR and dept-135) and two-dimensional COrrelated SpectroscopY (COSY), Heteronuclear Multiple Bond Correlation (HMBC) and Heteronuclear Multiple Quantum Coherence (HMQC) NMR using a Bruker 500 MHz NMR (Bruker Daltonics SPR, Hamburg, Germany).

Saiki P., Kawano Y., Ogi T., Klungsupya P., Muangman T., Phantanaprates W., Kongchinda P., Pinnak N, & Miyazaki K. (2020). Purified Gymnemic Acids from Gymnema inodorum Tea Inhibit 3T3-L1 Cell Differentiation into Adipocytes. Nutrients, 12(9), 2851.

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NMR Analysis of Carbohydrates and Amino Acids

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All chemical solvents were acquired from Fisher Scientific (Columbus, OH, USA). ¹H NMR spectra were collected at 300 K on a NMR spectrometer Bruker AVIII400HD NMR spectrometer and ¹³C NMR spectra were recorded on Bruker Ascend 700 MHz equipped with a 5 mm autotune broadband (BBFO) smart probe with z-gradient and a TXO cryoprobe (CN/H) when needed. Pyridine-d₅ was purchased from Cambridge Isotope Laboratories, Inc. (Tewksbury, MA, USA). Monosaccharides (D- and L-glucoses, -galactoses, -mannoses, -fucoses, -arabinoses, -apioses, -riboses, and L-rhamnose), D- and L-cysteine methyl ester hydrochloride, salicin and adenosine were purchased from Sigma Aldrich (St. Louis, MO, USA).

Inagaki M., Iwakuma R., Kawakami S., Otsuka H, & Rakotondraibe H.L. (2021). Detecting and Differentiating Monosaccharide Enantiomers by 1H NMR Spectroscopy. Journal of natural products, 84(7), 1863-1869.

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NMR Spectroscopic Analysis of Samples

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All NMR experiments were performed using a Bruker Avance III-800 or Bruker Avance III-600 spectrometer at the School of Molecular Biology, University of Sydney. Dried HPLC purified samples were resuspended in chloroform-d (Sigma) with 0.5% (v/v) pyridine-d5 (Cambridge Isotope Laboratories, Inc).

Loughlin P.C., Willows R.D, & Chen M. (2014). In vitro Conversion of Vinyl to Formyl Groups in Naturally Occurring Chlorophylls. Scientific Reports, 4, 6069.

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Spectroscopic Analysis of Purified Compounds

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Chemical structures of the purified compounds were determined by spectroscopic analyses and comparison with previous literature data. High-resolution electrospray ionization mass spectrometry (HRESIMS) data were obtained by the Synapt G2 system (Waters, Milford, MA, United States). The 1D and 2D nuclear magnetic resonance (NMR) spectra were recorded by a Bruker Advance 500 MHz spectrometer (Rheinstetten, Germany) in chloroform-d, methanol-d₄, or pyridine-d₅ (Cambridge Isotope Laboratories, Andover, MA, United States). Chemical shifts were referenced to the solvent peaks (δ_H 7.26 and δ_C 77.2 for chloroform-d; δ_H 4.87 and δ_C 49.0 for methanol-d₄; δ_H 8.71 and δ_C 149.9 for pyridine-d₅).

Ngo M.T., Van Nguyen M., Han J.W., Kim B., Kim Y.K., Park M.S., Kim H, & Choi G.J. (2021). Biocontrol Potential of Aspergillus Species Producing Antimicrobial Metabolites. Frontiers in Microbiology, 12, 804333.

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Spectroscopic Characterization of Natural Compounds

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HRESIMS data were acquired with electrospray ionization in negative ion mode on an UltrOTOF-Q instrument (Bruker Daltonics, Billerica, MA, USA). NMR spectroscopic data were recorded at room temperature in CDCl₃, acetone-d₆, CD₃OD, and/or pyridine-d₅ (Cambridge Isotope Laboratories, Andover, MA, USA) on a Bruker DPX-300 spectrometer (Bruker, Karlhue, Germany) operating at 300.13 MHz (¹H)/75.47 MHz (¹³C). Standard pulse sequences were used for homo- and heteronuclear correlation experiments. Optical rotation was determined on a Perkin Elmer 341 polarimeter (λ = 589 nm, PerkinElmer Inc., Waltham, MA, USA). Column chromatography procedures were performed on silica gel 60 (70–230 mesh, Merck, Darmstadt, Germany), silica gel 60 RP-18 (230–400 mesh, Merck, Darmstadt, Germany) and Sephadex LH-20 (Amersham Biosciences, Buckinghamshire, UK). Reversed-phase semipreparative HPLC separations were carried out with a Shimadzu (Shimadzu, Kyoto, Japan) LC-6AD pump using a Phenomenex Luna RP-18 column (5 µm, 21.6 × 250 mm) at flow rates of 12 or 14 mL/min, with monitoring at 210, 230 or 254 nm.

Bisoli E., Freire T.V., Yoshida N.C., Garcez W.S., Queiróz L.M., Matos M.D., Perdomo R.T, & Garcez F.R. (2020). Cytotoxic Phenanthrene, Dihydrophenanthrene, and Dihydrostilbene Derivatives and Other Aromatic Compounds from Combretum laxum. Molecules, 25(14), 3154.

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NMR and Mass Spectrometry Analysis

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NMR spectra were recorded on a Bruker Avance (400 and 500 MHz) spectrometer. A set of experiments was run including ¹H, ¹³C, COSY, HSQC, HMBC, HSQC-TOCSY and NOESY. Pyridine-D₅ (Cambridge Isotope Laboratories, Inc) was used as the NMR solvent and the obtained spectra were referenced using the internal signal from the solvent.
High resolution ESI-MS mass spectra for the isolated compound were obtained using Thermo-Finnigan LTQ Orbitrap (Thermo Scientific, Germany).

Raheem D.J., Tawfike A.F., Abdelmohsen U.R., Edrada-Ebel R, & Fitzsimmons-Thoss V. (2019). Application of metabolomics and molecular networking in investigating the chemical profile and antitrypanosomal activity of British bluebells (Hyacinthoides non-scripta). Scientific Reports, 9, 2547.

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Extraction and Isolation of Yucca Compounds

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Each of nine stems of Y. schidigera were extracted with water for 3 h under reflux. The water extracts were evaporated to give dried residues. These residues (200 mg) were loaded onto a Sep-Pak C18 Plus Short Cartridge (360 mg, Waters, Milford, MA) and separated by washing with H2O, then 50% aqueous MeOH, and eluted with MeOH (4 mL for each step). The methanol fractions were dissolved in pyridine-d5 (Cambridge Isotope Laboratories, Inc., Tewksbury, MA) at a concentration of 10 mg/mL for NMR measurements. The water extracts of yucca were also dissolved in 40% aqueous acetonitrile for HPLC analysis. Samples were filtered through a 0.45 m membrane before HPLC analysis.

Suzuki R., Ohno H., Murakami T, & Shirataki Y. (2020). Improving quality control of yucca extracts used as food additives by screening antimicrobial activity using NMR metabolomics. Journal of natural medicines, 74(1).

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Structural Elucidation of Compound 1

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The chemical structure of compound 1 was determined by nuclear magnetic resonance (NMR) spectroscopy and highresolution electrospray ionization mass spectrometry (HR-ESI-MS) analyses. 1 H-NMR spectra were measured in pyridine d 5 (Cambridge Isotope Laboratories, Inc., USA) with a Bruker Avance III HD 500 MHz instrument (Bruker Biospin GmbH, Germany) at 500 MHz. Chemical shifts were measured using tetramethylsilane as the internal standard. HR-ESI-MS was determined by a Synapt G2 HDMS quadrupole time-of-flight (QTOF) mass spectrometer equipped with an electrospray ion source (Waters, UK). Coupling constants are reported in Hertz unit. The chemical structure of compound 1 was analyzed on the basis of 1 H-NMR spectral data and HR-ESI-MS.

Nguyen H.T., Yu N.H., Park A.R., Park H.W., Kim I.S, & Kim J.C. (2017). Antibacterial Activity of Pharbitin, Isolated from the Seeds of Pharbitis nil, against Various Plant Pathogenic Bacteria. Journal of microbiology and biotechnology, 27(10).

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