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Related Concept Videos

¹H NMR of Labile Protons: Deuterium (²H) Substitution00:48

¹H NMR of Labile Protons: Deuterium (²H) Substitution

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This lesson illustrates the role of deuterium substitution in simplifying the NMR spectrum of compounds comprising labile protons. One method employed is the use of deuterium. Amongst the three isotopes of hydrogen, deuterium (2H) has a nucleus composed of one proton and one neutron. When the D2O solvent is added to a pure dry ethanol solution, its labile proton is substituted with deuterium.
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Hydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.
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A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...
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Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds' structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other...
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Related Experiment Video

Updated: Apr 21, 2026

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
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Benchmarking all-atom simulations using hydrogen exchange.

John J Skinner1, Wookyung Yu2, Elizabeth K Gichana1

  • 1Departments of Biochemistry and Molecular Biology and.

Proceedings of the National Academy of Sciences of the United States of America
|October 29, 2014
PubMed
Summary
This summary is machine-generated.

Modern molecular dynamics simulations can fold proteins, but simulations of protein G reveal issues. Force fields may need improvement for accurately modeling protein unfolding and hydration.

Keywords:
HXdenatured statesmolecular dynamicsprotein foldingunfolded state

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Long-time molecular dynamics (MD) simulations can now achieve reversible protein folding.
  • Modern force fields accurately reproduce the energy surface near native protein structures.

Purpose of the Study:

  • To evaluate the accuracy of modern force fields in simulating protein unfolding.
  • To compare MD simulations with experimental data for protein G.

Main Methods:

  • Molecular dynamics (MD) simulations of a protein G variant.
  • Site-resolved hydrogen exchange (HX) experiments.
  • Comparison of simulation trajectories with biophysical measurements.

Main Results:

  • Simulated denatured states were overly collapsed with persistent secondary structure.
  • MD trajectories showed excessive intramolecular H-bonding in expanded conformations.
  • Discrepancies between simulations and HX data suggest limitations in force fields.

Conclusions:

  • Current force fields may require refinement for accurate H-bonding and hydration modeling.
  • The study provides a protocol for validating simulation accuracy in capturing rare structural fluctuations.
  • Discrepancies highlight the need for improved force fields in computational biophysics.