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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...
NMR Spectrometers: Overview01:20

NMR Spectrometers: Overview

NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

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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Related Experiment Video

Updated: May 19, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Trajectory analysis of NMR structure calculations.

D Kohda1, F Inagaki

  • 1Department of Molecular Physiology, the Tokyo Metropolitan Institute of Medical Science, 18-22, Honkomagome 3-chome, Bunkyo-ku, 113, Tokyo, Japan.

Journal of Biomolecular NMR
|August 23, 2012
PubMed
Summary

Analyzing NMR structure calculations reveals how molecular structures move in conformational space. This trajectory analysis helps understand random sampling and optimize calculation protocols for better macromolecular structure determination.

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Last Updated: May 19, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Published on: September 17, 2017

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

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Nuclear Magnetic Resonance (NMR) and X-ray crystallography determine macromolecular structures at atomic resolution.
  • NMR structure calculation uses initial random structures to generate coordinates compatible with experimental data.

Purpose of the Study:

  • To analyze the conformational space trajectories of structures during NMR structure calculation.
  • To assess the utility of trajectory analysis for understanding random sampling and optimizing calculation protocols.

Main Methods:

  • Employed metric multidimensional scaling to obtain coordinates of structures in conformational space.
  • Calculated root-mean-square deviation (RMSD) to measure distances between structures.
  • Analyzed trajectories using a simulated annealing protocol with XPLOR on μ-Conotoxin GIIIA.

Main Results:

  • The 3D solution from multidimensional scaling adequately describes overall trajectory configurations.
  • Comparing full and converged calculation trajectories clearly distinguishes random sampling.
  • Individual trajectory examination aids in optimizing NMR structure calculation protocols.

Conclusions:

  • Trajectory analysis provides insights into the conformational landscape explored during NMR structure calculations.
  • This method can identify random sampling and guide the refinement of computational protocols for improved structural accuracy.