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Related Concept Videos

NMR Spectrometers: Overview01:20

NMR Spectrometers: Overview

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NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
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NMR Spectroscopy of Aromatic Compounds01:14

NMR Spectroscopy of Aromatic Compounds

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Aromatic compounds can be identified or analyzed using proton NMR and carbon‐13 NMR. Typically, aromatic hydrogens or hydrogens directly bonded to the aromatic rings are strongly deshielded by the aromatic ring current. Therefore, they absorb in the range of 6.5–8.0 ppm in proton NMR spectra. For instance, aromatic hydrogens directly bonded to the benzene ring absorb at 7.3 ppm. However, aromatic hydrogens of larger rings absorb farther upfield or downfield than the ideal range.
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NMR Spectroscopy and Mass Spectrometry of Aldehydes and Ketones01:15

NMR Spectroscopy and Mass Spectrometry of Aldehydes and Ketones

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In aldehydes, the hydrogen atom connected to the carbonyl carbon helps distinguish aldehydes from other carbonyl compounds using ¹H NMR spectroscopy. The closeness of aldehydic hydrogen to the electrophilic carbonyl carbon highly deshields the hydrogen atom causing its signal to appear around 10 ppm in the ¹H NMR spectra. α hydrogens split the aldehydic proton signal, which helps identify the number of α hydrogens in the molecule. For instance, one α hydrogen creates a...
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NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

3.5K
The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...
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Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy
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CASMDB: An Open-Source Database of Metabolite Annotation Data for 1D 1H NMR-Based Metabolomics.

Morgan W Hayward1, Luca G Mureddu1, Gary S Thompson2

  • 1Division of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7HN, United Kingdom.

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Summary

This study introduces the CcpNmr Analysis Simulated Metabolomics Database (CASMDB) to improve NMR metabolomics. CASMDB provides accurate metabolite identification across various experimental conditions, enhancing data analysis.

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Area of Science:

  • Metabolomics
  • Nuclear Magnetic Resonance (NMR) Spectroscopy
  • Bioinformatics

Background:

  • Metabolomics relies on databases for metabolite identification.
  • Existing NMR metabolomics databases lack comprehensive experimental condition data (pH, temperature, field strength) and contain annotation errors.
  • These limitations hinder accurate analysis of experimental samples, especially across different NMR field strengths.

Purpose of the Study:

  • To develop a robust, curated database for NMR-based metabolomics.
  • To address the shortcomings of existing public databases regarding experimental conditions and data accuracy.
  • To facilitate accurate spectral simulations for metabolite identification.

Main Methods:

  • Collected, remediated, and integrated annotation data from HMDB, BRMB, and GISSMO databases.
  • Built the CcpNmr Analysis Simulated Metabolomics Database (CASMDB).
  • Ensured CASMDB contains fully annotated metabolite entries for spectral simulation.

Main Results:

  • CASMDB comprises 1932 unique, fully annotated metabolite entries.
  • The database enables accurate simulation of NMR spectra at arbitrary field strengths.
  • CASMDB is available as a versioned repository on GitHub and can be expanded.

Conclusions:

  • CASMDB significantly enhances the accuracy of NMR metabolomics studies.
  • It provides a valuable resource for visualizing experimental and simulated metabolite references.
  • The database supports 1D 1H NMR-based metabolomics across diverse experimental conditions.