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Related Concept Videos

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

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

1.0K
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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¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

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

1.3K
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...
1.3K
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

1.7K
A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
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Spin–Spin Coupling Constant: Overview01:08

Spin–Spin Coupling Constant: Overview

1.2K
In bromoethane, the three methyl protons are coupled to the two methylene protons that are three bonds away. In accordance with the n+1 rule, the signal from the methyl protons is split into three peaks with 1:2:1 relative intensities. The methylene protons appear as a quartet, with the relative intensities of 1:3:3:1.
Qualitatively, any spin plus-half nucleus polarizes the spins of its electrons to the minus-half state. Consequently, the paired electron in the hydrogen–carbon bond must...
1.2K
IR Spectrum Peak Broadening: Hydrogen Bonding01:23

IR Spectrum Peak Broadening: Hydrogen Bonding

1.9K
The vibrational frequency of a bond is directly proportional to its bond strength. As a result, stronger bonds vibrate at higher frequencies, while weaker bonds vibrate at lower frequencies. The stretching vibration of the strong O–H bond in alcohols and phenols (very dilute solution or gas phase) appears as a sharp peak at 3600–3650 cm−1.
However, the extent of hydrogen bonding influences the observed stretching frequency and band broadening. Intermolecular or intramolecular...
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Related Experiment Video

Updated: Apr 27, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
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A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+.

Jimmy C Kromann1, Anders S Christensen1, Casper Steinmann2

  • 1Department of Chemistry, University of Copenhagen , Denmark.

Peerj
|July 16, 2014
PubMed
Summary

We introduce PM6-D3H+, a new computational chemistry method that improves geometry optimizations. This enhanced method offers better accuracy for hydrogen bonds and dispersion interactions in molecular modeling.

Keywords:
BiochemistryComputational biochemistryComputational chemistryMolecular modelingProteins

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Area of Science:

  • Computational Chemistry
  • Quantum Chemistry
  • Molecular Modeling

Background:

  • The semi-empirical PM6 method is widely used for molecular modeling.
  • Accurate treatment of dispersion and hydrogen bonding is crucial for reliable predictions.
  • Existing corrections may have limitations in certain computational workflows.

Purpose of the Study:

  • To develop and implement an improved version of the PM6 method, named PM6-D3H+.
  • To incorporate advanced dispersion and hydrogen bond corrections for enhanced accuracy.
  • To evaluate the performance of PM6-D3H+ in geometry optimizations and vibrational analysis.

Main Methods:

  • The PM6-D3H+ method combines the DFT-D3 dispersion correction with a modified H+ hydrogen bond correction.
  • Implementation of PM6-D3H+ in the GAMESS computational chemistry program.
  • Comparison of PM6-D3H+ with existing methods (PM6-DH2, PM6-DH+) using interaction energies and geometry optimizations.

Main Results:

  • PM6-D3H+ shows interaction energies very similar to PM6-DH2 and PM6-DH+ (RMSD/MAD within 0.02 kcal/mol).
  • Geometry optimizations with PM6-D3H+ in GAMESS yield significantly fewer imaginary frequencies (82% with 0 imaginary) compared to PM6-DH+ in MOPAC (54% with 0 imaginary).
  • The GAMESS implementation is computationally feasible for small protein geometry optimizations, despite being slower for larger systems.

Conclusions:

  • PM6-D3H+ provides a robust and accurate method for molecular modeling, particularly for systems requiring vibrational analysis.
  • The GAMESS implementation of PM6-D3H+ is a valuable alternative to MOPAC's PM6-DH+ for specific computational needs, such as LBFGS optimization and vibrational free energy calculations.
  • PM6-D3H+ enhances the reliability of computational predictions in chemistry and related fields.