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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.3K
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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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...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.8K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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¹H NMR of Labile Protons: Deuterium (²H) Substitution00:48

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This lesson illustrates the role of deuterium substitution in simplifying the NMR spectrum of compounds comprising labile protons. One method employed is the use of deuterium. Amongst the three isotopes of hydrogen, deuterium (2H) has a nucleus composed of one proton and one neutron. When the D2O solvent is added to a pure dry ethanol solution, its labile proton is substituted with deuterium.
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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RNA structure refinement using NMR solvent accessibility data.

Christoph Hartlmüller1,2, Johannes C Günther1,2, Antje C Wolter3

  • 1Center for Integrated Protein Science Munich, Department Chemie, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.

Scientific Reports
|July 16, 2017
PubMed
Summary
This summary is machine-generated.

Solvent paramagnetic relaxation enhancements (sPRE) offer a new method for RNA structural studies. This technique provides quantitative solvent accessibility and distance information, improving RNA structure determination accuracy and model scoring.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biophysics

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for studying ribonucleic acids (RNAs), which play vital roles in cellular functions.
  • Despite advancements in NMR techniques, RNA structural determination remains challenging.

Purpose of the Study:

  • To introduce and validate solvent paramagnetic relaxation enhancements (sPRE) as a method for RNA structural analysis.
  • To demonstrate the utility of sPRE in improving the accuracy and convergence of RNA structure determination.

Main Methods:

  • Utilizing the soluble paramagnetic compound Gd(DTPA-BMA) to induce sPRE.
  • Acquiring sPRE data for RNAs with various isotope labeling schemes.
  • Integrating sPRE data as restraints in RNA structure determination.

Main Results:

  • sPRE provides a quantitative measure of RNA solvent accessibility and distance-to-surface information.
  • sPRE data correlate well with known RNA structures, enhancing accuracy and convergence.
  • sPRE is advantageous for sample preparation, stability, and recovery, with a large dynamic range.
  • sPRE data reflect the global fold of the RNA.

Conclusions:

  • sPRE is a valuable and versatile tool for RNA structural studies.
  • sPRE data can effectively identify interaction surfaces and score structural models.
  • sPRE enhances the accuracy and efficiency of RNA structure determination using NMR.