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100 protocols using av 500 spectrometer

1

Synthetic Methodology for Novel Compounds

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Unless otherwise noted, materials were obtained commercially and used without further purification. All the solvents were treated according to general methods. Flash column chromatography was performed over silica gel (300 to 400 mesh). See Supplementary Materials and Methods for experimental details.
1H nuclear magnetic resonance (NMR) spectra were recorded on a Bruker AV-400 spectrometer and a Bruker AV-500 spectrometer in chloroform-d3. Chemical shifts are reported in parts per million (ppm) with the internal tet-ramethylsilane (TMS) signal at 0.0 ppm as a standard. The data are being reported as [s, singlet; d, doublet; t, triplet; m, multiplet or unresolved; brs, broad singlet, coupling constant(s) in hertz, integration). 13C NMR spectra were recorded on a Bruker AV-400 spectrometer and a Bruker AV-500 spectrometer in chloroform-d3. Chemical shifts are reported in ppm with the internal chloroform signal at 77.0 ppm as a standard. Mass spectra were recorded with Micromass QTOF2 Quadrupole/Time-of-Flight Tandem mass spectrometer using electron spray ionization.
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2

Nuclear Magnetic Resonance Spectrometry

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The 1 H and 13 C spectra were recorded on a Bruker AV 500 spectrometer at 500 MHz for 1 H and 125.43 MHz for 13 C. The NMR experiments involving 31 P were recorded on a Bruker AV 500 spectrometer equipped with a switchable probe. The chemical shifts were recorded in ppm. All spectra were recorded at room temperature and the concentration of L1•6HCl, L2•6HCl, AMP, GMP, UMP and CMP was 2 × 10 -3 M in D 2 O. The pD was adjusted using a concentrated solution of DCl or NaOD in D 2 O.
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3

Characterization of Organic Compounds

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Reagents and solvents were purchased
from commercial sources and used directedly. Flash chromatography
was performed using 300-mesh silica gel. Reactions were monitored
by thin-layer chromatography using silica gel plates with fluorescence
F254 and UV light visualization. Low-resolution electrospray
ionization mass spectrometry (ESI-MS) was performed on an Agilent
1200 high-performance liquid chromatography (HPLC)-mass selective
detector mass spectrometer and high-resolution ESI-MS on an Applied
Biosystems Q-STAR Elite ESI-LC-MS/MS mass spectrometer. 1H NMR spectra were performed on a Bruker AV-400 spectrometer at 400
MHz or a Bruker AV-500 spectrometer at 500 MHz. 13C NMR
spectra were performed on a Bruker AV-500 spectrometer at 125 MHz.
Coupling constants (J) were expressed in hertz (Hz).
Chemical shifts (δ) of NMR were reported in parts per million
units relative to an internal standard (tetramethylsilane). Purity
of the compounds was determined by reverse-phase high-performance
liquid chromatography (HPLC) analysis to be >95%. HPLC instrument:
Dionex Summit HPLC (column: Diamonsil C18, 5.0 μm, 4.6 ×
250 mm2 (Dikma Technologies); detector: PDA-100 photodiode
array; injector: ASI-100 autoinjector; pump: p-680A). A flow rate
of 1.0 mL/min was used with mobile phase of MeOH in H2O
with a 0.1% modifier (ammonia, v/v).
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4

Purification and Characterization of Organic Compounds

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Unless otherwise noted, materials were obtained commercially and used without further purification. All the solvents were treated according to general methods. Flash column chromatography was performed over silica gel (300 to 400 mesh). See Supplementary Materials and Methods for experimental details.
1H NMR spectra were recorded on a Bruker AV-400 spectrometer and a Bruker AV-500 spectrometer in chloroform-d3. Chemical shifts are reported in parts per million (ppm) with the internal tetramethylsilane (TMS) signal at 0.0 ppm as a standard. The data are reported as follows: s = singlet, d = doublet, t = triplet, m = multiplet or unresolved, brs = broad singlet, coupling constant(s) in hertz, integration. 13C NMR spectra were recorded on a Bruker AV-400 spectrometer and a Bruker AV-500 spectrometer in chloroform-d3. Chemical shifts are reported in ppm with the internal chloroform signal at 77.0 ppm as a standard. Mass spectra were recorded with a Micromass quadrupole/time-of-flight tandem mass spectrometer using electron spray ionization.
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5

Synthesis and Characterization of Homoserine Lactone

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All commercial materials were used without further purification. Flash chromatography was carried out using Macherey-Nagel (Hoerdt, France) Kieselgel 60 M silica. Analytical thin layer chromatography was realized using aluminum-backed plates coated with Macherey-Nagel Kieselgel 60 XtraSIL G/UV254. Compounds were visualized under UV light (at 254 nm) or stained using KMnO4. Nuclear magnetic resonance (NMR) spectra were recorded on a Bruker AVL300 or a Bruker AV400 or a Bruker AV500 spectrometer (Billerica, MA, USA), operating respectively at 300, 400, and 500 MHz for the proton (1H) NMR. Carbon (13C) NMR spectra were recorded on a Bruker AVL300 or a Bruker AV400 spectrophotometer or a Bruker AV500 spectrometer, operating, respectively, at 75, 100, and 125 MHz. Chemical shifts were reported in parts per million (ppm) in the scale relative to residual solvent signals. Multiplicities are abbreviated as follows: s, singlet; d, doublet; t, triplet; dd, doublet of doublets; dt, doublet of triplts, m, multiplet; br, broad. Coupling constants were measured in Hertz (Hz). High-resolution mass spectra (HRMS) and low-resolution mass spectra were performed by the Centre Commun de Spectrométrie de Masse (CCSM), University of Lyon 1, Lyon, France. l- or d-homoserine lactone hydrobromide was synthesized as previously described [20 (link)].
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6

Comprehensive NMR and Spectroscopic Analysis of Compounds

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One-dimensional (1D) NMR (500 MHz for 1H NMR and 125 MHz for 13C NMR) and two-dimensional (2D) NMR (HSQC, HMBC, 1H-1HCOSY, ROSEY, or NOSEY) were measured on the Bruker AV-500 spectrometers (Bruker, Germany). The chemical shifts of 1H and 13C NMR data were given in δ (ppm) and referenced to the solvent signal (CD3OD, δH 3.31 and δC 49.00; DMSO-d6, δH 2.50 and δC 39.52). High-resolution electrospray ionization mass spectroscopy (HRESIMS) data were acquired on an Agilent 6210 time-of-flight LC-MS instrument (Agilent Technologies Inc., Palo Alto, CA, USA). Optical rotation values were measured by JASCO P-1020 digital polarimeter (JASCO, Tokyo, Japan). IR spectrum data were recorded on Nicolet 380 Infrared Spectrometer (Thermo Fisher, Waltham, MA, USA). The electronic circular dichroism (ECD) data were determined using JASCO J-715 Spectropolarimeter (Jasco, Tokyo, Japan). The semipreparative high-performance liquid chromatography (HPLC) was equipped with an ODS column (250.0 mm×10.0 mm, 5 μm, Thermo Fisher Scientific, Waltham, MA, USA). Column chromatography (CC) was performed on silica gel (60–80 mesh or 200–300 mesh; Qingdao Marine Chemical Inc., Qingdao, China), Sephadex LH-20 (PharmaciaBiotec, Uppsala, Sweden), and ODS (40–70 µm, Nacalai Tesque, Kyoto, Japan).
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7

Synthesis and Characterization of Novel Compounds

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All reagents and starting materials were obtained commercially and used as received without any further purification unless otherwise noted. Gas chromatographic (GC) analyses were performed using a Shimadzu GC 2010-Plus equipped with a flame ionization detector (FID) and an SPB-5 column (length = 30 m, inner diameter = 0.25 mm, and film thickness = 0.25 μm). The GC yield was calculated using diphenyl ether as the internal standard. GC-MS analyses were analyzed on a Shimadzu GCMS-QP2010Ultra with a ZB-5MS column (length = 30 m, inner diameter = 0.25 mm, and film thickness = 0.25 μm). MS spectra were compared with the spectra gathered in the NIST library. The 1H NMR and 13C NMR were recorded on Bruker AV 500 spectrometers using residual solvent peak as a reference. HR-MS spectra were recorded by an Agilent HPLC 1200 Series coupled to Bruker micrOTOF-QII. Molecular mass of elemental sulfur is 32 g mol−1, unless otherwise noted. Compounds 4a·HCl6a and 6 (ref. 7a ) were synthesized following the known procedures.
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8

Analytical Characterization of Compounds

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Ultraviolet spectral were obtained on a Waters 2695 high performance liquid chromatography (HPLC) instrument with a photo diode array detector (Waters, Massachusetts, USA). Preparative HPLC was carried out on a Shimadzu LC-6AD instrument (Shimadzu, Kyoto, Japan) with a UV–Vis detector (SPD-20A), using a YMC-Pack-ODS-A column (250 × 20 mm, 5 μm) (YMC, Kyoto, Japan). The carbohydrates were measured by ion chromatography using an amperometric detector (Metrohm, Herisau, Switzerland) with a Hamilton RCX-30 column (250 × 4.6 mm, 7 μm) (Hamilton, Nevada, USA). Nuclear magnetic resonance (NMR) spectra were obtained using Bruker AV-500 spectrometers (500 MHz for 1H NMR and 125 MHz for 13C NMR) (Bruker, Zurich, Switzerland). Chemical shifts (δ) are given in ppm, with TMS as an internal standard, and coupling constants (J) are in Hz. High-resolution electrospray ionisation-mass spectrometry (HRESIMS) spectra were obtained using an Agilent 6540 ultra-performance liquid chromatography (UPLC) with high-resolution quadrupole time-of-flight (Q-TOF) mass spectrometer (Agilent, California, USA), using an RRHD Eclipse Plus C18 column (150 × 2.1 mm, 1.8 μm) (YMC, Kyoto, Japan)36 (link).
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9

Comprehensive Chemical Characterization

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Optical rotations were analyzed using a Rudolph Research Autopol III automatic polarimeter. UV and mass spectra were obtained using a Shimadzu 2020 EV LC–MS (Kinetex 1.7 μm C18 100 Å, LC Column 100 × 2.1 mm) using positive-and negative-mode electrospray ionization with a linear gradient of 5–95% acetonitrile MeCN–H2O with 0.5% formic acid in 15 min followed by 95% MeCN for 3 min with a flow rate of 0.3 mL/min. Column chromatography was performed using a CombiFlash system using a HP CL18 reverse phase column. HPLC fractionation used a semi-preparative C18 column of Kinetics New column. IR spectra were obtained using the PerkinElmer® Frontier FIR spectrometer, annotated by the PerkinElmer® Spectrum software suite. 1D and 2D NMR spectra were obtained on Bruker AV500 spectrometers at the UCLA Molecular Instrumentation Center. High resolution mass spectra were obtained from Agilent 6530 Q-TOF ESI with a 1260 Infinity LC with Autosampler at the UCLA Molecular Instrumentation Center.
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10

Spectroscopic Characterization of Organic Compounds

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The optical rotations were measured with a Jasco P-1010 polarimeter. The UV spectra were recorded with a PerkinElmer UV–Vis spectrophotometer. Infrared (IR) spectra were recorded using a PerkinElmer Frontier Optica FT–IR spectrometer. The 1D and 2D NMR spectra recorded using a 500 MHz Bruker AV-500 spectrometer. Chemical shifts are reported in parts per million (δ) and coupling constants (J) are expressed in hertz. The HRESIMS were carried out on a QTOF 6540 UHD mass spectrometer (Agilent Technologies, Santa Clara, CA, USA). Chiral HPLC was performed on a CHIRALCEL OD-H column of 4.6ϕ—250 mm and attached to Agilent Technologies 1260 Infinity II. Silica gel G60 (60–200 µm, SiliCycle® Inc., Québec, QC G1P 4S6, Canada) was used to perform column chromatography (CC). Precoated plates of silica gel (60F254, Merck, Kenilworth, NJ, USA) were used for analytical purposes.
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