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Related Concept Videos

Spin–Spin Coupling: One-Bond Coupling01:17

Spin–Spin Coupling: One-Bond Coupling

Coupling interactions are strongest between NMR-active nuclei bonded to each other, where spin information can be transmitted directly through the pair of bonding electrons. While nuclei polarize their electrons to the opposite spins, the bonding electron pair has opposite spins. Configurations with antiparallel nuclear spins are expected to be lower in energy. When coupling makes antiparallel states more favorable, J is considered to have a positive value. The one-bond coupling constant, 1J,...
Double Resonance Techniques: Overview01:12

Double Resonance Techniques: Overview

Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by...
Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)01:22

Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)

Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the involved orbitals. The...
¹H NMR: Long-Range Coupling01:27

¹H NMR: Long-Range Coupling

The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene π orbitals.
Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)01:20

Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)

Two NMR-active nuclei bonded to a central atom can be involved in geminal or two-bond coupling. Geminal coupling is commonly seen between diastereotopic protons in chiral molecules and unsymmetrical alkenes, among others.
The central atom need not be NMR-active because its electrons are affected by the electron polarization of the spin-active atoms. However, spin information is transmitted less effectively than in one-bond coupling, and 2J values are usually weaker than 1J values. The energy of...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Practical Aspects of Sample Preparation and Setup of 1H R1&#961; Relaxation Dispersion Experiments of RNA
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How well do time-averaged J-coupling restraints work?

D A Pearlman1

  • 1Vertex Pharmaceuticals Incorporated, 40 Allston Street, 02139-4211, Cambridge, MA, U.S.A..

Journal of Biomolecular NMR
|August 23, 2012
PubMed
Summary
This summary is machine-generated.

Time-averaged J-coupling restraints offer a more realistic conformational analysis in molecular dynamics than conventional restraints. This method better captures sugar ring dynamics, crucial for understanding molecular behavior.

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Biophysics

Background:

  • Molecular dynamics (MD) simulations are vital for studying molecular conformational dynamics.
  • Nuclear magnetic resonance (NMR) derived J-coupling restraints are used to refine MD models.
  • Accurate representation of conformational fluctuations is essential for biological insights.

Purpose of the Study:

  • To compare time-averaged and conventional vicinal J-coupling restraints in MD refinement.
  • To evaluate the ability of different J-coupling restraints to reproduce conformational dynamics.
  • To assess the impact of force constants on MD refinement using J-coupling restraints.

Main Methods:

  • Molecular dynamics (MD) refinement of an adenosine nucleoside model system.
  • Utilizing time-averaged and conventional vicinal (3)J-coupling restraints.
  • Deriving target restraint values from a 3-ns unrestrained MD simulation.

Main Results:

  • Both restraint types reproduce averaged parameter values acceptably.
  • Time-averaged J-coupling restraints provide a more realistic description of conformational fluctuations.
  • Conformational behavior of the sugar ring using time-averaged restraints aligns well with unrestrained simulations.
  • J-coupling restraints can induce a localized 'heating effect', enabling sampling of low-energy rotamers.

Conclusions:

  • Time-averaged J-coupling restraints offer a superior description of conformational dynamics compared to conventional restraints.
  • The 'heating effect' from J-coupling restraints can be advantageous for experimental data but requires careful interpretation.
  • Smaller force constants are preferable for MD refinement, with values around K(j)≥0.4 kcal s(2)/mol being sufficiently large.