Melting points were measured in the open capillaries with a Stuart SMP3 melting-point apparatus (Bibby Scientific Limited, Staffordshire, UK). Two FT-IR spectrometer (Perkin-Elmer, Waltham, MA, USA) using the frustrated total internal reflection accessory with a diamond crystal. The 1H and 19F NMR spectra were registered on a Bruker DRX-400 spectrometer (400 or 376 MHz, respectively) or a Bruker AvanceIII 500 spectrometer (500 or 470 MHz, respectively) (Bruker, Karlsruhe, Germany). The 13C NMR spectra were recorded on a Bruker AvanceIII 500 spectrometer (125 MHz). The internal standard was SiMe4 (for 1H and 13C NMR spectra) and C6F6). The 13C chemical shifts were calibrated using the solvent signal DMSO-d6 (δC 39.5 ppm). For compounds 4a-d , 8a-d , 5 , 5’ , 11a , 11b signals in 1H and 13C spectra were assigned based on 2D 1H-13C HSQC and HMBC experiments. The high-resolution mass spectra (HRMS) were recorded on a Bruker maXis impact mass spectrometer (ESI) (Bruker, Karlsruhe, Germany). The column chromatography was performed on silica gel 60 (0.062–0.2 mm) (Macherey-Nagel GmbH & Co KG, Duren, Germany). The initial ethyl-2-hydroxy-4-methyl-4-oxo-2-(trifluoromethyl)butanoate (aldol 6a ) [35 (link),36 (link)] and diethyl 2,6-dihydroxy-4-oxo-2,6-bis(trifluoromethyl)heptanedioate (bis aldol 7a ) [35 (link)] were synthesized by referring previously published methods.
Avance 3 500 spectrometer
Manufactured by Bruker
Sourced in Germany, United States, Switzerland
The Avance III 500 spectrometer is a high-performance nuclear magnetic resonance (NMR) system designed for analytical and research applications. It provides a magnetic field strength of 500 MHz, enabling researchers to conduct advanced NMR experiments and analyze a wide range of samples.
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Lab products found in correlation
Acquity uplc beh c18 column, by Waters Corporation (7 mentions)
J 815 spectropolarimeter, by Jasco (5 mentions)
Agilent 1200 infinity series hplc, by Agilent Technologies (5 mentions)
Amazon speed esi iontrap ms, by Bruker (5 mentions)
Lichroprep rp 18 gel, by Merck Group (5 mentions)
Uv 2450 uv vis spectrophotometer, by Shimadzu (4 mentions)
Ultimate 3000 series uhplc, by Thermo Fisher Scientific (4 mentions)
3 acetylpyridine, by Thermo Fisher Scientific (4 mentions)
Cary 5000, by Agilent Technologies (4 mentions)
Microtof q 2 mass spectrometer, by Bruker (4 mentions)
Kieselgel 60 f254, by Merck Group (4 mentions)
Rp 18 f254, by Merck Group (4 mentions)
Agilent 6520 q tof mass spectrometer, by Agilent Technologies (4 mentions)
Spectrum 100 ftir spectrometer, by PerkinElmer (3 mentions)
Uatr two, by PerkinElmer (3 mentions)
Sephadex lh 20, by Cytiva (3 mentions)
Uv 1800 spectrophotometer, by Shimadzu (3 mentions)
Lichroprep rp 18 40 63 μm, by Merck Group (3 mentions)
L dihydroxyphenylalanine l dopa, by Merck Group (3 mentions)
P 1010 polarimeter, by Jasco (3 mentions)
108 protocols using avance 3 500 spectrometer
1
Synthesis and Characterization of Aldol Compounds
2
Spectroscopic Characterization of Substances
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UV–Vis spectra were recorded using a Perkin-Elmer Lambda 35 UV–Vis spectrophotometer. FTIR spectra of KBr pellets of substances were recorded using a Perkin–Elmer spectrum 100 FTIR spectrometer. 1H NMR spectra were recorded on a Bruker Avance III 500 spectrometer at 25 °C. Solid-state 13C cross-polarization/magic-angle spinning (CP/MAS) NMR was also carried out in the same Bruker Avance III 500 spectrometer; the broad band channel was tuned to 125 MHz (the resonance frequency of 13C), and a 4 mm MAS probe was used for the experiment at a spinning speed of 10 KHz; a typical 13C value of pulse length was used for 4 µs and relaxation delay of 20 s was used.
3
Analytical Characterization of Degraded Products
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The degraded products were identified by NMR experiments. Compounds were analyzed by UPLC-Q-TOF-MS/MS in positive ion mode. 1D and 2D-NMR spectra were acquired using solvent signals (CD3OD: δH 3.31/δC 49.9; C3D6O: δH 2.05/δC 49.9; Pyridine-d5: δH 8.74, 7.58, 7.22/δC 150.4, 135.9, and 123.9) on a Bruker 600 spectrometer (1H: 600 MHz) and a Bruker Avance III 500 spectrometer (1H: 500 MHz; 13C: 125 MHz) (Bruker, Rheinstetten, Germany).
4
NMR Analysis of Unknown Metabolite
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The purified compound from the cell extract was dissolved in 0.5 mL of D2O and placed in 10-mm-diameter NMR tubes for the NMR analysis. The 1H-NMR, 13C-NMR and 2D-NMR (heteronuclear multiple bond coherence, HMBC) spectra were measured on a Bruker AVANCE III 500 spectrometer with a 5 mm CPPBBO probe head to determine the preliminary structure and confirm the identity of the unknown compatible solute. 3-(trimethylsilyl)-2,2,3,3-d4 propionic acid sodium salt (abbreviated as TMSP) served as the internal reference.
5
Kinetics of Acyl Hydrazide Reactions
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Powder of any one of the acyl hydrazides
RC(=O)NHNH2 (0.21 mmol) was added to a solution
of ZnCl2 (0.021
mmol) in (CD3)2SO (0.4 mL) or (CD3)2CO (0.4 mL) placed in an NMR tube, whereupon 10-fold
excess R2′NCN (2.1 mmol) was added to the mixture. The NMR tube was closed,
and the obtained homogeneous solution was kept at 60 °C for 2
h in the NMR spectrometer. Assuming that the reaction is pseudo first-order,
the reaction rate constant k could be estimated from
the slope of the initial time dependence of the concentration of the
product. In this work, the reaction kinetics was monitored by measuring 1H NMR spectra every 48 s (4 scans, repetition time 4 s), following
the initial equilibration period of 5 min. The 1H NMR spectra
were measured on a Bruker Avance III 500 spectrometer (operating frequency
500.13 MHz for 1H). The rate constant k was estimated by measuring the logarithms of the relative (normalized)
integrated intensities of the product’s ortho-CH proton signal, fitting their initial time dependence (300–800
s) by a straight line, and calculating the slope.
RC(=O)NHNH2 (0.21 mmol) was added to a solution
of ZnCl2 (0.021
mmol) in (CD3)2SO (0.4 mL) or (CD3)2CO (0.4 mL) placed in an NMR tube, whereupon 10-fold
excess R2′NCN (2.1 mmol) was added to the mixture. The NMR tube was closed,
and the obtained homogeneous solution was kept at 60 °C for 2
h in the NMR spectrometer. Assuming that the reaction is pseudo first-order,
the reaction rate constant k could be estimated from
the slope of the initial time dependence of the concentration of the
product. In this work, the reaction kinetics was monitored by measuring 1H NMR spectra every 48 s (4 scans, repetition time 4 s), following
the initial equilibration period of 5 min. The 1H NMR spectra
were measured on a Bruker Avance III 500 spectrometer (operating frequency
500.13 MHz for 1H). The rate constant k was estimated by measuring the logarithms of the relative (normalized)
integrated intensities of the product’s ortho-CH proton signal, fitting their initial time dependence (300–800
s) by a straight line, and calculating the slope.
6
Comprehensive Analytical Techniques for Compound Characterization
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NMR spectra were recorded with an Avance III 700 spectrometer with a 5 mm TCI cryoprobe (1H 700 MHz, 13C 175 MHz) and an Avance III 500 spectrometer (1H 500 MHz, 13C 125 MHz) (both Bruker, Billerica, MA/USA). Optical rotations were taken with a MCP 150 polarimeter (Anton Paar, Graz, Austria) and UV spectra with a UV‐2450 UV/Vis spectrophotometer (Shimadzu, Kyoto, Japan). IR spectra were taken with a Spectrum 100 FTIR spectrometer (Perkin Elmer, Waltham, MA/USA) and ECD spectra were measured using a J‐815 spectropolarimeter (Jasco, Pfungstadt, Germany).
ESI mass spectra were recorded with an UltiMate 3000 Series uHPLC (Thermo Fisher Scientific, Waltman, MA/USA) by utilizing a C18 Acquity UPLC BEH column (50×2.1 mm, 1.7 μm; Waters, Milford, USA) connected to an amaZon speed ESI‐Iontrap‐MS (Bruker, Billerica, MA, USA). HPLC parameters were set as follows: solvent A: H2O+0.1 % formic acid, solvent B: acetonitrile (MeCN)+0.1 % formic acid, gradient: 5 % B for 0.5 min, increasing to 100 % B over 19.5 min, keeping 100 % B for a further 5 min, flow rate 0.6 mL min−1, and DAD detection 190–600 nm.
ESI‐HRMS was performed with an Agilent 1200 Infinity Series HPLC (Agilent Technologies, Böblingen, Germany; conditions as for ESI‐MS) connected to a maXis ESI‐TOF‐MS (Bruker).
ESI mass spectra were recorded with an UltiMate 3000 Series uHPLC (Thermo Fisher Scientific, Waltman, MA/USA) by utilizing a C18 Acquity UPLC BEH column (50×2.1 mm, 1.7 μm; Waters, Milford, USA) connected to an amaZon speed ESI‐Iontrap‐MS (Bruker, Billerica, MA, USA). HPLC parameters were set as follows: solvent A: H2O+0.1 % formic acid, solvent B: acetonitrile (MeCN)+0.1 % formic acid, gradient: 5 % B for 0.5 min, increasing to 100 % B over 19.5 min, keeping 100 % B for a further 5 min, flow rate 0.6 mL min−1, and DAD detection 190–600 nm.
ESI‐HRMS was performed with an Agilent 1200 Infinity Series HPLC (Agilent Technologies, Böblingen, Germany; conditions as for ESI‐MS) connected to a maXis ESI‐TOF‐MS (Bruker).
7
Synthesis and Characterization of Glycans
8
Characterization of organic compounds
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1H and 13C NMR spectra were recorded on a Bruker Avance iii -500 spectrometer (Bruker BioSpin AG, Fällanden, Switzerland) at 298 K. The 1H and 13C NMR chemical shifts were referenced with respect to residual solvent peaks (δ TMS = 0). A Shimadzu LCMS-2020 and a Bruker maXis 4G QTOF instrument (Bruker BioSpin AG, Fällanden, Switzerland) were used to record electrospray ionization (ESI) and HR-ESI mass spectra, respectively. PerkinElmer UATR Two (Perkin Elmer, 8603 Schwerzenbach, Switzerland) and Shimadzu UV2600 (Shimadzu Schweiz GmbH, 4153 Reinach, Switzerland) instruments were used to record FT-infrared (IR) and absorption spectra, respectively.
3-Acetylpyridine, 4-hydroxybenzaldehyde and 1-bromopropane were purchased from Acros Organics (Chemie Brunschwig AG, Basel, Switzerland) and were used as received. Ligands2 , 4 , 5 and 6 were prepared as previously reported [11 (link),20 (link),21 (link)].
3-Acetylpyridine, 4-hydroxybenzaldehyde and 1-bromopropane were purchased from Acros Organics (Chemie Brunschwig AG, Basel, Switzerland) and were used as received. Ligands
9
Spectroscopic Characterization of Pyridine Derivatives
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1H, 13C{1H} and 2D NMR spectra were recorded on a Bruker Avance iii -500 spectrometer (Bruker BioSpin AG, Fällanden, Switzerland) at 298 K. The 1H and 13C NMR chemical shifts were referenced with respect to residual solvent peaks (δ TMS = 0). A Shimadzu LCMS-2020 instrument (Shimadzu Schweiz GmbH, 4153 Reinach, Switzerland) was used to record electrospray ionization (ESI) mass spectra. A PerkinElmer UATR Two instrument (PerkinElmer, 8603 Schwerzenbach, Switzerland) was used to record FT-infrared (IR) spectra, and Shimadzu UV2600 (Shimadzu Schweiz GmbH, 4153 Reinach, Switzerland) or Cary 5000 (Agilent Technologies AG, 4052 Basel, Switzerland) spectrophotometers were used to record absorption spectra. 3-Acetylpyridine and 4-hydroxybenzaldehyde were purchased from Acros Organics (Fisher Scientific AG, 4153 Reinach, Switzerland), rac-4-(butan-2-yloxy)benzaldehyde, 4-(2-methylpropoxy)benzaldehyde and 4-(tert-butoxy)benzaldehyde from Fluorochem (Chemie Brunschwig AG, 4052 Basel, Switzerland), 1-bromo-2-methylpropane from Sigma Aldrich (Chemie Brunschwig AG, 4052 Basel, Switzerland), and were used as received. 4′-(4-Hydroxyphenyl)-3,2′:6′,3″-terpyridine was prepared as previously described [6 (link)].
10
Analytical Characterization of Compounds
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Electrospray mass (ESI-MS) spectra were recorded with an UltiMate® 3000 Series UHPLC (Thermofisher Scientific, Waltman, MA, USA) utilizing a C18 Acquity® UPLC BEH column (2.1 × 50 mm, 1.7 µm; Waters, Milford, MA, USA), connected to an amaZon speed® ESI-Iontrap-MS (Bruker, Billerica, MA, USA). HPLC parameters were set as follows: solvent A: H2O+0.1% formic acid, solvent B: acetonitrile (ACN)+0.1% formic acid; gradient: 5% B for 0.5 min, increasing to 100% B in 19.5 min, keeping 100% B for further 5 min; flowrate 0.6 mL/min, DAD detection 200−600 nm.
High resolution electrospray mass (HR-ESI-MS) spectra were obtained with an Agilent 1200 Infinity Series HPLC (Agilent Technologies, Santa Clara, CA, USA) connected to a maXis® electrospray time-of-flight mass spectrometer (ESI-TOF-MS; Bruker; HPLC conditions same as for ESI-MS measurements).
Nuclear magnetic resonance (NMR) spectra were recorded with an Avance III 500 spectrometer (Bruker, 1H NMR: 500 MHz, 13C NMR: 125 MHz). UV/vis spectra were taken with a UV-2450 spectrophotometer (Shimadzu, Kyoto, Japan).
High resolution electrospray mass (HR-ESI-MS) spectra were obtained with an Agilent 1200 Infinity Series HPLC (Agilent Technologies, Santa Clara, CA, USA) connected to a maXis® electrospray time-of-flight mass spectrometer (ESI-TOF-MS; Bruker; HPLC conditions same as for ESI-MS measurements).
Nuclear magnetic resonance (NMR) spectra were recorded with an Avance III 500 spectrometer (Bruker, 1H NMR: 500 MHz, 13C NMR: 125 MHz). UV/vis spectra were taken with a UV-2450 spectrophotometer (Shimadzu, Kyoto, Japan).
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