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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

995
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...
995
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

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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.
1.4K

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Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
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Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and

Zheng Yi1, Benjamin Lindner, Jan-Hendrik Prinz

  • 1University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O. Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA and Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, USA.

The Journal of Chemical Physics
|November 12, 2013
PubMed
Summary

This study introduces a new method using Markov State Models (MSMs) to link molecular dynamics simulations with neutron scattering data. This approach helps identify specific molecular movements responsible for observed dynamics, improving data interpretation.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Materials Science

Background:

  • Neutron scattering experiments reveal molecular dynamics on sub-picosecond to microsecond timescales.
  • Assigning observed relaxations to specific structural changes is challenging due to overlapping timescales.

Purpose of the Study:

  • To present a theoretical approach combining molecular dynamics (MD) simulations with Markov State Models (MSMs) for analyzing neutron scattering data.
  • To demonstrate a practical method for deriving an MSM from MD simulations.
  • To enable direct identification of structural transitions linked to molecular relaxations.

Main Methods:

  • Application of a Markov State Model (MSM) to analyze configurational dynamics from molecular dynamics (MD) simulations.
  • Development of a practical procedure for deriving an MSM from MD trajectories.
  • Analysis of the alanine dipeptide system using a 9-state MSM based on dihedral angles and methyl group configurations.

Main Results:

  • An excellent agreement was found between quasielastic neutron scattering spectra calculated directly from MD trajectories and those derived from the MSM.
  • The derived 9-state MSM accurately represents the configurational dynamics of the alanine dipeptide.
  • The wavevector dependence of individual Markov processes was successfully described.

Conclusions:

  • The developed MSM-based approach provides a practicable method for interpreting quasielastic neutron scattering spectra.
  • This method allows for the assignment of spectral features to well-defined intramolecular transitions.
  • It minimizes the need for a priori assumptions about the nature of molecular dynamics.