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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

847
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...
847
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.1K
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: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.0K
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...
1.0K
¹H NMR of Labile Protons: Temporal Resolution01:10

¹H NMR of Labile Protons: Temporal Resolution

1.1K
Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding between the proton and the heteroatom in other molecules. The extent of hydrogen bonding affects the electron density around the proton, thereby giving different chemical shift values for the protons in the proton NMR spectrum.
The –OH proton in alcohols typically appears in the range of δ 2 to 5 ppm but can vary depending on the specific...
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Time-Resolved Graphs of Polymorphic Cycles for H-Bonded Network Identification in Flexible Biomolecules.

Ylène Aboulfath1, Sana Bougueroua2, Alvaro Cimas2

  • 1Université Paris-Saclay, Univ Versailles Saint Quentin, DAVID, 78035 Versailles, France.

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Summary

This study introduces a novel graph-based method to analyze molecular dynamics (MD) of hydrogen-bonded biomolecules. The approach effectively captures dynamic structural changes and polymorphism in biomolecules, offering insights beyond atomic-level analysis.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding biomolecular behavior.
  • Analyzing complex changes in hydrogen-bonded (H-Bonded) flexible biomolecules remains challenging.
  • Existing methods often struggle to capture subtle dynamic and polymorphic information.

Purpose of the Study:

  • To develop a novel, coarse-grained approach for analyzing MD trajectories of H-Bonded flexible biomolecules.
  • To represent biomolecules using topological graphs of hydrogen-bonded cycles.
  • To distinguish conformational changes from polymorphic variations within the H-bond network.

Main Methods:

  • A coarse-grained representation of topological graphs is employed.
  • Biomolecules are modeled using their H-Bonded cycles and a graph of these cycles.
  • A minimum cycle basis represents each conformer/isomer.
  • "Polycycles" are utilized to differentiate cycles with similar polymorphic roles from those causing conformational changes.

Main Results:

  • The proposed method successfully analyzes MD trajectories of gas-phase biomolecules.
  • Polygraphs and their temporal evolution reveal the dynamicity of H-Bonded biomolecule metastructures.
  • Polymorphic information on cycles is provided, highlighting changes in the H-bond network dynamics.

Conclusions:

  • The novel graph-based approach offers a powerful tool for analyzing H-Bonded flexible biomolecules.
  • It provides insights into molecular dynamics and polymorphism not easily obtainable at the atomic level.
  • This method enhances the understanding of structural changes and H-bond network dynamics in biomolecules.