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Related Concept Videos

NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

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...
Inductive Effects on Chemical Shift: Overview01:27

Inductive Effects on Chemical Shift: Overview

The protons in unsubstituted alkanes are strongly shielded with chemical shifts below 1.8 ppm. Methine, methylene, and methyl protons appear at approximately 1.7, 1.2 and 0.7 ppm, while the proton signal from methane appears at 0.23 ppm. An electronegative substituent, such as chlorine, withdraws the electron density from the protons, increasing their chemical shift. Progressive substitution of the hydrogens in methane by chlorine shifts the proton signals increasingly downfield, to 3.05 ppm in...
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
Proton (¹H) NMR: Chemical Shift01:07

Proton (¹H) NMR: Chemical Shift

Organic molecules primarily contain carbon and hydrogen atoms. While all the hydrogen isotopes are NMR-active, protium or hydrogen-1 is the most abundant. It has a significant energy separation between its nuclear spin states due to its large gyromagnetic ratio. As per Boltzmann's distribution, an increase in the energy separation implies a greater excess population of nuclei available for excitation, resulting in a strong NMR absorption signal.
Absorption signals of all the protium nuclei in a...
¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
In chiral compounds such as 2-butanol, replacing the methylene hydrogens at C3 produces a pair of...
Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

SHIFTX2: significantly improved protein chemical shift prediction.

Beomsoo Han1, Yifeng Liu, Simon W Ginzinger

  • 1Department of Computing Science, University of Alberta, Edmonton, AB, Canada.

Journal of Biomolecular NMR
|March 31, 2011
PubMed
Summary

SHIFTX2 is a new program that accurately predicts protein chemical shifts from coordinate data. It is faster, more comprehensive, and more accurate than previous methods, aiding protein structure determination.

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Last Updated: Jun 3, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Published on: September 17, 2017

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Accurate prediction of chemical shifts is crucial for understanding protein structure and function.
  • Existing methods for protein chemical shift prediction have limitations in accuracy, speed, and coverage.

Purpose of the Study:

  • To introduce SHIFTX2, a novel computer program for rapid and accurate prediction of protein chemical shifts.
  • To evaluate the performance of SHIFTX2 against existing chemical shift prediction tools.

Main Methods:

  • Development of SHIFTX2 utilizing a large database of training proteins (>190).
  • Application of advanced machine learning techniques and incorporation of diverse features (e.g., angles, solvent accessibility, H-bond geometry, pH, temperature).
  • Combination of sequence-based and structure-based chemical shift prediction approaches.

Main Results:

  • SHIFTX2 demonstrates substantially improved accuracy (up to 26% better correlation coefficient, up to 3.3x smaller RMS error) compared to existing programs.
  • Achieves high correlation coefficients for backbone chemical shifts (e.g., 0.9992 for (13)Cβ) and side chain shifts (0.9787 for (13)C).
  • Offers increased coverage (up to 10% more) and speed (up to 8.5x faster) for predicting a wider range of chemical shifts.

Conclusions:

  • SHIFTX2 represents a significant advancement in protein chemical shift prediction accuracy and efficiency.
  • The program's capabilities are expected to facilitate long-anticipated applications in protein structure determination, refinement, and validation.
  • SHIFTX2 is accessible as a standalone program and a web server.