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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...
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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.
Transition State Theory01:25

Transition State Theory

Transition-state theory, also known as activated-complex theory, provides a molecular-level explanation of reaction rates in both gas-phase and solution-phase reactions. It extends earlier kinetic models by considering the formation of a short-lived, high-energy configuration during a reaction.The progress of a chemical reaction can be represented using a reaction profile, which plots potential energy against the reaction coordinate. As two reactant molecules approach one another, their...
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Using generalized ensemble simulations and Markov state models to identify conformational states.

Gregory R Bowman1, Xuhui Huang, Vijay S Pande

  • 1Biophysics Program, Stanford University, Stanford, CA 94305, USA.

Methods (San Diego, Calif.)
|May 5, 2009
PubMed
Summary

This study introduces MSMBuilder, a tool for identifying long-lived molecular states from simulations. It helps build Markov State Models to understand molecular dynamics and transitions between states.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Statistical Mechanics

Background:

  • Understanding molecular conformational dynamics is crucial for various scientific disciplines.
  • Identifying long-lived molecular states is a key step in modeling these dynamics.
  • Existing methods may not fully capture the complex transitions between molecular states.

Purpose of the Study:

  • To present MSMBuilder, a software package for constructing Markov State Models (MSMs).
  • To demonstrate the utility of MSMs in identifying metastable states from simulation data.
  • To provide tools for evaluating and visualizing these models.

Main Methods:

  • Utilizing Generalized Ensemble (GE) simulations and other simulation datasets.
  • Applying the MSMBuilder package to process simulation data.
  • Building Markov State Models to represent molecular conformational landscapes.

Main Results:

  • MSMBuilder successfully identifies dominant metastable states in molecular systems.
  • The package facilitates the analysis of transition rates between identified states.
  • Tools for model evaluation and visualization are integrated within MSMBuilder.

Conclusions:

  • MSMBuilder is an effective tool for analyzing molecular conformational dynamics.
  • Markov State Models provide a robust framework for understanding molecular behavior.
  • The package aids in creating comprehensive models of molecular systems.