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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...
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...
NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
Atomic Nuclei: Magnetic Resonance01:05

Atomic Nuclei: Magnetic Resonance

The number of nuclear spins aligned in the lower energy state is slightly greater than those in the higher energy state. In the presence of an external magnetic field, as the spins precess at the Larmor frequency, the excess population results in a net magnetization oriented along the z axis. When a pulse or a short burst of radio waves at the Larmor frequency is applied along the x axis, the coupling of frequencies causes resonance and flips the nuclear spins of the excess population from the...
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

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 first.
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the others.

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Related Experiment Video

Updated: Jul 10, 2026

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex
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Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Published on: July 27, 2022

Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method.

Mikolai I Fajer1, Hongzhi Li, Wei Yang

  • 1Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.

Journal of the American Chemical Society
|October 24, 2007
PubMed
Summary

We developed a novel simulated scaling approach for efficient protein spin label simulations. This method accurately predicts spin label behavior and aids in interpreting EPR measurements for protein conformation and dynamics.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • Simulating spin label behavior is crucial for understanding protein dynamics.
  • Accurate conformational sampling is essential for reliable molecular modeling.

Purpose of the Study:

  • To develop an efficient computational approach for simulating spin label behavior attached to protein backbones.
  • To enhance local conformational sampling for improved accuracy in molecular dynamics.
  • To validate the method against experimental data and explore its application in interpreting EPR measurements.

Main Methods:

  • Developed the simulated scaling (SS) approach, coupling a potential scaling parameter random walk with molecular dynamics within a hybrid Monte Carlo framework.
  • Ensured the method retains thermodynamic detailed balance for accurate relative free energy calculations.
  • Validated the approach using the X-ray crystal structure of spin-labeled T4 lysozyme.

Main Results:

  • The SS approach enables efficient barrier crossings between conformations, enhancing sampling.
  • Potentials of mean force (PMF) for spin label torsion angles were consistent across various protein environments (surface, semiburied, buried).
  • An implicit solvent model showed excellent agreement with explicit solvent treatment, offering computational efficiency.

Conclusions:

  • The developed SS approach accurately simulates spin label behavior and provides insights into protein conformation and dynamics.
  • The method is effective in diverse protein environments and supports the interpretation of Electron Paramagnetic Resonance (EPR) data.
  • Implicit solvent models are computationally viable alternatives for spin label modeling.