Proton NMR (1H NMR) spectra were acquired with a Bruker Avance-500SB (Bruker, Wissembourg, France) operating at 500.13 MHz and equipped with a 5 mm broadband inverse probe with non-spinning samples and thermostated at 298 K. Spectra were collected into 32 K points with a spectral width of 5,000 Hz (10 ppm). Acquisition of the spectra was performed with a presaturation of the water signal during 2 s after a relaxation delay of 8 s. A total of 128 transients were accumulated for a total acquisition time of 28 min and 24 s. Spectra were phased, baseline corrected, and referenced to TSP manually with the XWIN-NMR software (version 3.5, Bruker, Karlsruhe, Germany).
Xwin nmr software
Manufactured by Bruker
Sourced in Germany
XWIN-NMR is a software package designed for the acquisition, processing, and analysis of nuclear magnetic resonance (NMR) data. It provides a comprehensive suite of tools for NMR spectroscopy experiments and data management.
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Lab products found in correlation
Topspin 3, by Bruker (2 mentions)
Drx 500 spectrometer, by Bruker (2 mentions)
5 mm nmr tube, by Bruker (1 mentions)
Avance 600 nmr spectrometer, by Bruker (1 mentions)
Txi probe head, by Bruker (1 mentions)
Matlab algorithm, by MathWorks (1 mentions)
Dpx 300 spectrometer, by Bruker (1 mentions)
8453 uv vis spectrophotometer, by Agilent Technologies (1 mentions)
Spd 10ad vp, by Shimadzu (1 mentions)
M 560, by Büchi (1 mentions)
Irprestige 21 fourier transform infrared ftir spectrophotometer, by Shimadzu (1 mentions)
Nmrpipe nmrdraw, by Bruker (1 mentions)
Drx 400 nmr spectrometer, by Bruker (1 mentions)
Avance 360, by Bruker (1 mentions)
Drx 500 mhz spectrometer, by Bruker (1 mentions)
13 protocols using xwin nmr software
1
Proton NMR Spectroscopy of Samples
2
NMR Analysis of Media Samples
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Media samples were prepared for NMR analyses based on protocols as described by Beckonert and colleagues [24 (link)]. Briefly, 300 μl media samples were mixed 1:1 with NMR phosphate buffer (50% v/v D20 (GOSS Scientific, UK, 0.01% v/v sodium 3-(trimethylsilyl) propionic acid 2,2,3,3-d4 ([TSP)], pH 7.4) and centrifuged at 12,470 × g for 5 minutes. Some 550 μl of sample was transferred into 5-mm NMR tubes (Bruker, Germany) and all samples from both studies were run on a Bruker Avance 600 NMR Spectrometer with TXI probe head (Bruker), using XWIN-NMR software (Bruker Biospin, Germany). 1H NMR data were acquired by applying a standard one-dimensional (1D) pulse programme for 128 scans (after eight dummy scans), that included water irradiation during the recycle delay, set at 2 seconds (s). The pulse sequence was set to: recycle delay-90°-t-90°-tm-90°-ACQ, whereby 90° pulse length was set to between 16.5 μs, t (short delay) = 2 s, tm (mixing time) = 100 ms and ACQ (acquisition period) = at 2.73 s per scan. Spectral data underwent baseline correction, internal reference (TSP) peak calibration and phasing, using an in-house MATLAB algorithm (version R2012b, Mathworks Inc, USA) and Topspin 3.1 software (Bruker BioSpin, Germany). Water regions and HEPES buffer peaks were removed followed by to automatic spectral alignment and probabilistic quotient normalization [25 (link)] in MATLAB.
3
Optimizing NMR Analysis of Cellular 19F Relaxation
4
Metabolic Changes in Traumatic Brain Injury
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Anesthesia induction was performed with an intraperitoneal injection of 1.0% ketamine in all TBI rats. The rats were then set in a 4.7-T Bruke r BioSpec Imager (Bruker Medical System, Karlsruhe, Germany). Brain MRI and MR spectroscopy were applied by a blinded researcher according to a previously described method [17 (link)]. Briefly, a T2-weighted image (T2WI) sequence with 4,500 repetition times (ms) and 80 echo times (ms) was applied. The slice thickness was 1.5 mm. The cross-sectional area was measured with ParaVision 3.0 software (Bruker Medical System). The lesion volume was calculated from the cross-sectional area and slice thickness.
To measure the metabolites with MR spectroscopy, the volume of interest was selected over the perilesional area with a cubic volume of 2×2×2 mm3 in the injured hemisphere in T2WI. Bruker’s XWIN-NMR software was used to process all raw spectroscopic data. The metabolites were identified according to their chemical shift, as observed in the MR spectroscopy, in parts per million values: choline (Cho), 3.2; creatine (Cr), 3.03; N-acetylaspartate (NAA), 2.0; and lactate (Lac), 1.3; 0.9. The Cho, NAA, Lac, and 0.9 peak areas were quantitated as relative ratios to Cr, which was the internal reference for each rat, to allow the comparison of metabolite levels over time and between different animals [18 (link)].
To measure the metabolites with MR spectroscopy, the volume of interest was selected over the perilesional area with a cubic volume of 2×2×2 mm3 in the injured hemisphere in T2WI. Bruker’s XWIN-NMR software was used to process all raw spectroscopic data. The metabolites were identified according to their chemical shift, as observed in the MR spectroscopy, in parts per million values: choline (Cho), 3.2; creatine (Cr), 3.03; N-acetylaspartate (NAA), 2.0; and lactate (Lac), 1.3; 0.9. The Cho, NAA, Lac, and 0.9 peak areas were quantitated as relative ratios to Cr, which was the internal reference for each rat, to allow the comparison of metabolite levels over time and between different animals [18 (link)].
5
Comprehensive Analytical Characterization of Novel Compounds
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All chemicals were obtained from Sigma-Aldrich or Merck. NMR Spectra were registered on Bruker DPX 300 spectrometer at room temperature (298K) on a using DMSO-d6 as the solvent and processed using Bruker XWinNMR software. LC/MS was developed by means of chromatography with PHENOMENEX GEMINI NX C18 110Å 4.61 × 150 mm column (0.05% TFA, gradient MeCN/H2O), UV-detector SHIMADZU SPD-10AD VP (registered absorption at 254 nm), ELSD (evaporative light scattering detector) SEDEX-75 and API-150EX mass-spectrometer. Elution started with 0.1 M solution of TFA in water and ended with 0.1 M solution of TFA in acetonitrile used a linear gradient at a flow rate of 0.15 mL/min and an analysis cycle time of 25 min. FT-IR spectrum was registered in KBr pellet with Shimadzu IR Prestige-21 Fourier Transform Infrared (FTIR) Spectrophotometer. UV/Vis spectrum was registered in acetonitrile with Agilent 8453 UV-Vis Spectrophotometer. Melting point was registered with Buchi M-560. Elemental analysis was performed on EuroEA-3000 CHNS-O Analyzer.
6
Quantitative Analysis of Organic Compounds in Stillage
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Proton resonances
from organic compounds in stillage were measured during fermentation
by a proton nuclear magnetic resonance (1H NMR) spectroscopy
with a water suppression pulse sequence. The compounds α-GPC,
ethanol, lactic acid, acetic acid, succinic acid, betaine, glycerol,
and PEA were measured quantitatively by resonance signals at 3.05,
1.07, 1.25, 1.95, 2.5, 3.09, 3.45, 7.2 ppm, respectively. The strong
water resonance present in the spectra was suppressed using double
pulse field gradient spin echo, as provided by the Bruker XWIN-NMR
software (Bruker, Mississauga, ON, Canada). The samples were collected
every 24 h for seven days of incubation, and before analysis, samples
were centrifuged (Beckman Coulter Canada Inc., Mississauga, ON, Canada)
at 10,000 rpm for 10 min, and supernatant samples were filtered with
0.45 μm PTFE filters (Pall Corp, Ann Arbor, MI). Finally, filtered
samples (0.5 mL) were added to clean NMR tubes. Deuterium oxide (50
μL, D2O, 99.8%) was mixed with each sample to provide
a locking signal, 40 μL of pyrazine (C4H4N2) was added as an internal standard, and 500 μL
of filtered samples were pipetted into each NMR tube. 1H NMR was used to record spectra (16 scans), and the concentration
was determined by comparison with the internal standard resonance
at 8.5 ppm.
from organic compounds in stillage were measured during fermentation
by a proton nuclear magnetic resonance (1H NMR) spectroscopy
with a water suppression pulse sequence. The compounds α-GPC,
ethanol, lactic acid, acetic acid, succinic acid, betaine, glycerol,
and PEA were measured quantitatively by resonance signals at 3.05,
1.07, 1.25, 1.95, 2.5, 3.09, 3.45, 7.2 ppm, respectively. The strong
water resonance present in the spectra was suppressed using double
pulse field gradient spin echo, as provided by the Bruker XWIN-NMR
software (Bruker, Mississauga, ON, Canada). The samples were collected
every 24 h for seven days of incubation, and before analysis, samples
were centrifuged (Beckman Coulter Canada Inc., Mississauga, ON, Canada)
at 10,000 rpm for 10 min, and supernatant samples were filtered with
0.45 μm PTFE filters (Pall Corp, Ann Arbor, MI). Finally, filtered
samples (0.5 mL) were added to clean NMR tubes. Deuterium oxide (50
μL, D2O, 99.8%) was mixed with each sample to provide
a locking signal, 40 μL of pyrazine (C4H4N2) was added as an internal standard, and 500 μL
of filtered samples were pipetted into each NMR tube. 1H NMR was used to record spectra (16 scans), and the concentration
was determined by comparison with the internal standard resonance
at 8.5 ppm.
7
NMR Spectroscopy of Organic Compounds
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Nuclear magnetic resonance (NMR) spectra were acquired at 283 K on a Bruker DRX-500 spectrometer equipped with a triple resonance probe with an x, y, and z-shielded pulsed-field gradient coil. Two-dimensional (2D) NMR spectra were recorded in a phase-sensitive mode using time proportional phase increment for quadrature detection in the t1 domain. Total correlation spectroscopy (TOCSY)22 using a dipsi-2 spinlock pulse sequence with a mixing time of 70 ms and nuclear overhauser enhancement spectroscopy (NOESY)23 with mixing times of 250–600 ms were performed. All NMR spectra were acquired with 2048 complex data points in t2 and 256 increments in the t1 dimension, with 64 scans per each increment. All NMR data were processed using nmrPipe/nmrDraw or XWIN-NMR software (Bruker Instruments, Karlsruhe, Germany) and analyzed using the Sparky 3.95 program.
8
Pyruvate-to-Lactate Conversion Kinetics
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Serial spectra were phase and baseline corrected and integrated using the XWinNMR software (Bruker Biospin, Coventry, UK). The integrated peak areas from the pyruvate/lactate experiments were plotted as a function of time, and apparent reaction rates were obtained by least-squares fitting of the data to the modified Bloch equations using a two-site exchange model as previously described (Hill et al, 2013a (link), 2013b (link)). All apparent rate constants for the forward reaction of conversion of pyruvate-to-lactate (kPL) are presented as a mean concentration per second normalised to the number of cells.
9
NMR Spectroscopy of Deuterated DOPA
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DOPA-1 (30 mg) was dissolved in 99.9% deuterium oxide (0.5 mL). The sample was then freeze-dried three times. The 1H NMR spectra was recorded with a Bruker DRX-400 NMR spectrometer (Bruker, Rheinstetten, Germany) at 25 °C. Data processing was performed using standard Bruker XWIN-NMR software.
10
NMR Analysis of Procyanidins and Prodelphinidins
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NMR spectra of the tissue extracts and the purified CT fractions were obtained on an Avance 360 (1H 360.13 and 13C 90.55 MHz) instrument equipped with XWINNMR software (Bruker Corporation, Billerica, MA, USA) or on a BrukerBiospin DMX-500 (1H 500.13 and 13C 125.76 MHz) instrument equipped with Topspin 3.4 software (Bruker Corporation, Billerica, MA, USA). The ratios of procyanidin/prodelphinidin (PC/PD) and cis/trans stereochemistry and mDP were determined through integration of respective cross peak signals in the 1H–13C heteronuclear single quantum coherence (HSQC) NMR spectra according to the procedures previously reported (Zeller et al., 2015a (link); Fryganas et al., 2018 (link); Naumann et al., 2018 (link)).
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