Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ion Exchange01:17

Ion Exchange

Ion exchange chromatography separates charged molecules from a solution by reversibly exchanging them with mobile, or 'active', ions associated with the oppositely charged stationary phase. This method can be used to separate ions, soften and deionize water, and purify solutions. The polymers comprising the ion-exchange column are high-molecular-weight and chemically stable polymers, crosslinked to be porous and essentially insoluble. They are also functionalized with either acidic or basic...
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...
¹H NMR of Labile Protons: Deuterium (²H) Substitution00:48

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

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.
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the others.
¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
In chiral compounds such as 2-butanol, replacing the methylene hydrogens at C3 produces a pair of...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Nature Counts to Three: Universal Mg-Pinch Motif Polarizes the Cleaved Bond in NTP-Processing Enzymes.

Journal of the American Chemical Society·2026
Same author

A lattice Monte Carlo model for amyloid fibril formation.

Biophysics and physicobiology·2026
Same author

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
Same author

Machine Learning-Driven Drug Repurposing for KRAS G12C and KRAS G12D Inhibition.

ACS omega·2026
Same author

Multiscale machine learning molecular mechanics for mechanism and stereoselectivity of Diels-Alderase catalysis.

Nature communications·2026
Same author

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Journal of chemical information and modeling·2026

Related Experiment Video

Updated: May 28, 2026

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
09:18

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Published on: April 17, 2017

pH replica-exchange method based on discrete protonation states.

Satoru G Itoh1, Ana Damjanović, Bernard R Brooks

  • 1Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi, Japan.

Proteins
|October 18, 2011
PubMed
Summary

We introduce a pH replica-exchange method (PHREM) for accurate proton titration curves. PHREM improves sampling and precision for pK(a) values and Hill coefficients in biomolecular simulations.

More Related Videos

Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions
08:40

Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions

Published on: June 23, 2022

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex
10:52

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Published on: July 27, 2022

Related Experiment Videos

Last Updated: May 28, 2026

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
09:18

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Published on: April 17, 2017

Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions
08:40

Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions

Published on: June 23, 2022

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex
10:52

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Published on: July 27, 2022

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Modeling

Background:

  • Proton titration curves are crucial for understanding protein function.
  • Existing constant pH methods can be computationally intensive and may lack sampling efficiency.

Purpose of the Study:

  • To develop and validate a novel pH replica-exchange method (PHREM) for calculating proton titration curves.
  • To compare the performance of PHREM against the established PHMD algorithm.

Main Methods:

  • PHREM algorithm: replicas are simulated at different pH values with pH exchange.
  • Application to a blocked amino acid and two protein systems (snake cardiotoxin, turkey ovomucoid third domain).
  • Utilized a generalized Born implicit solvent model.

Main Results:

  • PHREM provides more accurate Hill coefficients in single simulation sets.
  • PHREM demonstrates superior sampling of protonation states and reduced scatter in titration points.
  • Achieves comparable accuracy to PHMD with multiple simulation sets, but with better precision.
  • Exhibits faster convergence of individual simulations compared to PHMD.

Conclusions:

  • PHREM offers enhanced precision and sampling for determining pK(a) values and Hill coefficients.
  • The method shows improved efficiency and accuracy in biomolecular simulations.