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Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
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Related Experiment Video

Updated: Mar 29, 2026

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
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Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange.

Jason A Wallace1, Jana K Shen1

  • 1Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States.

Journal of Chemical Theory and Computation
|November 26, 2015
PubMed
Summary
This summary is machine-generated.

This study introduces a novel computational method combining implicit and explicit solvent models for accurate pKa calculations and protonation dynamics. This approach enhances understanding of biological energy transduction processes.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Biophysics

Background:

  • Accurate pKa values and protonation-coupled dynamics are crucial for understanding biological energy transduction.
  • Existing computational methods face limitations in accurately capturing these phenomena.

Purpose of the Study:

  • To develop a new computational technique for precise pKa determination and analysis of protonation-coupled conformational dynamics.
  • To improve the accuracy and efficiency of molecular dynamics simulations for biological systems.

Main Methods:

  • Embedding continuous constant pH molecular dynamics within an explicit-solvent representation.
  • Utilizing the generalized-Born (GB) model for solvation free energy estimation.
  • Employing a pH-based replica exchange scheme for enhanced sampling.

Main Results:

  • Achieved an average absolute deviation of 0.53 and RMSD of 0.74 from experimental data for five benchmark proteins.
  • Demonstrated increased accuracy compared to GB-only methods by preserving native structure and improving conformational flexibility description.
  • Successfully modeled solvent-mediated ion-pair interactions.

Conclusions:

  • The new technique provides a practical tool for capturing ionization equilibria and conformational dynamics.
  • Offers an intimate view of ionization-coupled dynamics, complementing experimental techniques.
  • Enhances the accuracy of molecular simulations for biological processes.