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17 protocols using mestrenova 9

1

NMR Spectral Data Processing

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On-dimensional NMR spectra were processed for phase correction, baseline correction and resonance alignment with the MestReNova 9.0 software (Mestrelab Research S.L., Santiago de Compostela, Spain). The spectra region of δ 5.15–4.85 (water resonance) was then excluded to eliminate the influence of the water peak on the spectral line integration, and the region of δ 9.5–0.8 was segmented into bins with a width of 0.001 ppm for statistical analysis. Peak integrals for each NMR spectrum were normalized by the TSP spectral integral to represent the relative levels of assigned metabolites.
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2

NMR Data Processing and Normalization

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Fourier transformation was executed after applying an exponential function with a 0.3-Hz line-broadening factor to free induction decay (FID) signals. Subsequently, phase correction, baseline correction and resonance alignment were conducted on all 1D 1H spectra with the MestReNova 9.0 software (Mestrelab Research S.L., Santiagode Compostela, Spain). Chemical shifts of the NMR spectra were referenced to the methyl resonance of TSP (δ 0.00). Spectral regions of δ 4.85–4.75 (water resonance) were removed from the spectra, then the regions of δ 9.5–0.75 were binned by 0.001 ppm in MATLAB R2014b (MathWorks, Natick, USA) to obtain a data matrix for the following multivariate analysis. For each spectrum of a given NMR sample, peak integrals were normalized based on both the peak integral of TSP and the number of cells.
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3

NMR-based Metabolomic Analysis of Plant Stress

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1H NMR spectra were acquired and aligned using the MestReNova 9.0 software (Mestrelab Research, Escondido, CA, USA). NMR spectra were normalized, phased and baseline corrected (Polynomial Fit method) before imported into SIMCA-12 (Umetrics, Umea, Sweden). Chloroform extract were referenced to TMS peaks (0.00 ppm), aqueous were referred to alanine (1.47 ppm). UV scaling was applied to the data and a score plot was generated to describe the data using PLS-DA. NMR peaks were then manually identified according to integration, chemical shift and peaks multiplicity by comparing to online databases such as Human Metabolome Database (HMDB) [17 (link)], Biological Magnetic Resonance (BMRB) [18 (link)] and Yeast Metabolome Database (YMDB) [19 ]. Fold changes between metabolites in treatment (tolerant vs control; susceptible vs control) at different time points respectively were detected by comparing average of spectra intensity from three biological replicates with t-test P<0.05. Statistical significance for antioxidant, RWC and ions were determined by ANOVA with Tukey HSD multiple comparison post-test with significant value of P<0.05.
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4

NMR Characterization of Organic Compounds

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All samples were dissolved in deuterated chloroform (CDCl3) and 1H NMR spectra were collected on a Bruker Avance III 500 MHz spectrometer (Bruker GmbH, Germany) at 298 K. For the NOESY study, the mixing time was set to 0.2 s, and a relaxation delay of 3 s was used between scans. All the NMR data were processed using MestReNova 9.0 software (Mestrelab Research S.L., Spain).
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5

Compound Identification via MS and NMR

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Identification of the CPC purified compounds was performed by ESI-MS with an Advion compact mass (Advion, Ithaca, NY, USA) and NMR. The ESI-MS spectra conditions were as follows: positive ion mode; mass range, m/z 100–1200; capillary temperature, 200 °C; capillary voltage, 150 V; source voltage offset, 30; source voltage span, 10; source gas temperature, 150 °C; and ESI voltage, 3500 V. 1H-NMR (400 MHz) and 13C-NMR (100 MHz) were measured on a Bruker model digital Avance III 400 NMR in CDCl3. The NMR spectra were processed by the MestReNova 9.0 software (Mestrelab Research, Santiago de Compostela, Spain).
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6

Recrystallization and NMR Characterization of HEX D

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Approximately 50 mL of 1 M hydrochloric acid solution were heated at 100 ± 1°C using an Ikamag ® C-MAG HS 7 magnetic stirrer ceramic heating plate (IKA, Germany) equipped with an ETS-D5 electronic contact thermometer (IKA, Germany). HEX D was dissolved in the solution followed by stirring of the mixture and cooling (15 min). The flask was subsequently placed on ice for 30 min to allow recrystallisation of the product. Finally, crystals were recovered by means of vacuum filtration and dried at room temperature. Hydrogen-1 and carbon-13 nuclear magnetic resonance ( 1 H and 13 C NMR) spectroscopy were used to confirm the structure of the starting material and the product of the reaction. All spectra were acquired in dimethyl sulfoxide-d 6 on a Bruker Avance 400 MHz NMR spectrometer (Bruker Corporation, U.S.A.) and processed using MestReNova ® 9.0.1 (Mestrelab Research, Spain).
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7

Molecular Formula Identification by NMR

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Molecular formulas were searched in ChemSpider database32 by tolerating plus or minus one hydrogen mass in each formula: for example, C7H15NO3 is searched as C7H14-16NO3. The following six elements were considered for the generation of the molecular formula from exact masses: C, H, N, O, P, and S. 2D 13C-1H HSQC spectra of the returned structures are predicted by using MestReNova 9.0.1 (Mestrelab Research, Santiago de Compostela, Spain). HSQC prediction of each molecule takes about 10 seconds on a desktop computer. The comparison of each HSQC peak list of the experimental NMR spectra is performed by using the query algorithm of COLMAR 13C-1H HSQC web server.33 (link)
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8

Rapid NMR Profiling of Edible Oils

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For the sample preparation of all types of edible oils, only the addition of deuterated solvent was required as a single step. 600 μL of CDCl3 (containing 1% TMS, Tetramethylsilane) and 50 μL of oil were placed in a 5 mm NMR tube and mixed thoroughly during 10 s. The spectra were acquired using a Bruker DPX 300 MHz NMR spectrometer, equipped with a BACS-60 robotic autosampler (which allows for fully automated analysis of up to 60 samples at a time) and a 5 mm Z-gradient QNP probe. For the acquisition, 32 K complex points were recorded, the spectral width was set to 12 ppm, the frequency offset was set to 5 ppm, the recycle delay was set to 4 s, the acquisition time was 4.56 s, the excitation pulse was a 90° hard pulse, the number of scans was set to 8 and the number of dummy scans was equal to 2. The total experimental time was 1 min and 26 s. A temperature of 30 °C was chosen for the experiments. The data were acquired automatically using the software ICON-NMR (Bruker BioSpin, Rheinstetten, Germany).
The resulting spectra were processed manually and automatically with the software MestreNova 9.0.1 (Mestrelab Research SL, Santiago de Compostela, Spain) and Topspin 2.1 (Bruker Biospin, Rheinstetten, Germany). No window functions were applied. The chemical shift scale was referenced using the signal of the TMS (0 ppm).
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9

NMR Spectral Analysis Protocol

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NMR-spectra were recorded on a Bruker AV 300 (Bruker Corporation, Billerica, Massachusetts, USA). The measurements were performed in deuterated solvents at room temperature. MestReNova 9.0 (Mestrelab Research S. L., Santiago de Com-postela, Spain) was used for data analysis. The chemical shifts are given in parts per million ( ppm) relative to the residual solvent signals. The multiplicity of the signals is labeled as singlet (s), doublet (d), triplet (t), quartet (q), heptet (h), multiplet (m) and broad (br) and the coupling constant J is noted in Hz.
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10

Quantitative NMR Data Processing

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MestReNova 9.0 (Mestrelab Research, S.L., Santiago de Compostela, Spain) was used to process all the acquired raw data, including phase correction, baseline adjustment, and integration, which were conducted manually, as previously described [18 (link),23 (link)]. The average values from six times replicated processing were performed for all the phase correction and integration procedures to minimize analyst error [24 (link)]. The chemical shifts were referenced to the IS resonance (δ 5.86, s), and the obtained peak area was used for the quantitation. The calculation of the analytes was accorded to our previous work [18 (link)] using the formula below: Ws=Wr×AsAr×EsEr
where Ws stands for the weight of IS, As and Ar denote the peak area of analyte and ISTD, respectively, while Es and Er represent the ratios of molecular weight to nuclei number for analyte and IS, respectively.
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