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Related Concept Videos

Thermal Sigmatropic Reactions: Overview01:16

Thermal Sigmatropic Reactions: Overview

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Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in 1,5-hexadiene, referred...
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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...
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¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

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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...
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¹H NMR: Pople Notation01:09

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The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
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¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

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A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
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π Electron Effects on Chemical Shift: Overview01:27

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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,...
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Methyl group assignment using pseudocontact shifts with PARAssign.

Mathilde Lescanne1, Simon P Skinner1,2,3, Anneloes Blok1

  • 1Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.

Journal of Biomolecular NMR
|November 29, 2017
PubMed
Summary
This summary is machine-generated.

The PARAssign program effectively assigns methyl group NMR resonances in proteins using protein structure and pseudocontact shifts (PCS). Optimal assignments depend on tag placement and resonance pairing, with two tags yielding 60% reliable assignments.

Keywords:
AssignmentHeat shock proteinMethyl groupsNMR spectroscopyParamagnetic tagPseudocontact shift

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Area of Science:

  • Structural Biology
  • Biophysics
  • Nuclear Magnetic Resonance (NMR) Spectroscopy

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structure and dynamics.
  • Assigning resonances, especially for methyl groups in amino acids like leucine, isoleucine, and valine, is a key challenge in NMR analysis.
  • Paramagnetic tagging with lanthanoids offers a method to generate pseudocontact shifts (PCS) aiding resonance assignment.

Purpose of the Study:

  • To evaluate a new version of the PARAssign program for assigning methyl group NMR resonances.
  • To assess the impact of protein structure and pseudocontact shifts (PCS) from paramagnetic tags on assignment accuracy.
  • To investigate factors influencing the reliability of resonance assignments using paramagnetic tagging.

Main Methods:

  • Utilized the PARAssign program to assign NMR resonances of methyl groups in a 25 kDa protein.
  • Employed protein structure data and pseudocontact shifts (PCS) generated from lanthanoid tags at up to three attachment sites.
  • Analyzed the dependence of assignment reliability on the orientation of magnetic susceptibility tensors and the fraction of assignable resonances.

Main Results:

  • A reliable assignment was achieved for 60% of methyl groups using data from two tag positions.
  • With a single tag, reliable assignments were limited to methyl groups with large PCS near the tag.
  • For remaining resonances, the number of possible assignments was often reduced to two or three.

Conclusions:

  • Paramagnetic tagging combined with PARAssign is a valuable tool for methyl group resonance assignment in proteins.
  • Optimal assignment results depend on strategic placement of paramagnetic tags to avoid correlated PCS and maximize resonance pairing.
  • Integrating paramagnetic tagging with other experimental data, such as mutagenesis or NOE-based experiments, can further enhance assignment accuracy.