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Related Concept Videos

Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

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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...
1.6K
NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

4.1K
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...
4.1K
¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

5.2K
Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...
5.2K
Inductive Effects on Chemical Shift: Overview01:27

Inductive Effects on Chemical Shift: Overview

2.6K
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...
2.6K
π Electron Effects on Chemical Shift: Overview01:27

π Electron Effects on Chemical Shift: Overview

1.9K
An applied magnetic field causes loosely bound π-electrons in organic molecules to circulate, producing a local or induced diamagnetic field over a large spatial volume. As the molecules tumble in solution, the field generated by π-electrons in spherical substituents results in a zero net field. However, the net field generated by π-electrons in non-spherical substituents is not zero. The effect of this induced field depends on the orientation of the molecule with respect to B0,...
1.9K
π Electron Effects on Chemical Shift: Aromatic and Antiaromatic Compounds01:14

π Electron Effects on Chemical Shift: Aromatic and Antiaromatic Compounds

2.1K
In aromatic compounds, such as benzene, the circulation of (4n + 2) π-electrons sets up a diamagnetic or diatropic ring current around the perimeter of the molecule. This current induces a magnetic field that opposes the external field inside the ring and reinforces it on the outside. The protons in benzene are deshielded and exhibit high chemical shifts in the range 6.5–8.5 ppm. The shielding effect at the center of the ring is evident in complex aromatic molecules, such as...
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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PPM_One: a static protein structure based chemical shift predictor.

Dawei Li1, Rafael Brüschweiler

  • 1Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA.

Journal of Biomolecular NMR
|June 21, 2015
PubMed
Summary
This summary is machine-generated.

A new protein chemical shift predictor, PPM_One, uses 3D structures to estimate backbone and side-chain proton shifts. This tool improves accuracy for assessing protein stereospecific assignments and protein dynamics.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Accurate prediction of protein chemical shifts is crucial for structural biology.
  • Existing methods have limitations in accuracy and scope.

Purpose of the Study:

  • To develop and evaluate a novel empirical knowledge-based chemical shift predictor for protein backbone and side-chain atoms.
  • To assess the predictor's ability to emulate protein dynamics and aid in stereospecific assignment.

Main Methods:

  • Mined BioMagResDataBank and Protein Data Bank for parametrization.
  • Developed linear and artificial neural network models for prediction.
  • Incorporated interatomic steric contacts to emulate local protein dynamics.

Main Results:

  • The PPM_One predictor accepts single 3D structures.
  • Prediction accuracy for side-chain protons is sufficient for independent stereospecific assignment assessment.
  • Achieved overall improvement compared to current top-performing chemical shift prediction programs.

Conclusions:

  • PPM_One offers an improved method for predicting protein chemical shifts.
  • The predictor has potential applications in structural biology and protein assignment.
  • Emulating protein dynamics through steric contacts enhances prediction accuracy.