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Related Concept Videos

Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
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Spin–Spin Coupling Constant: Overview01:08

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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...
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Spin–Spin Coupling: One-Bond Coupling01:17

Spin–Spin Coupling: One-Bond Coupling

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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,...
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Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)01:22

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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...
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¹H NMR: Long-Range Coupling01:27

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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...
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Cooperative Allosteric Transitions01:58

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Quantifying the Cooperativity of Backbone Hydrogen Bonding.

You Xu1,2,3, Jing Huang1,2,3

  • 1Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.

Journal of Computational Chemistry
|May 19, 2025
PubMed
Summary

We developed a new method to quantify hydrogen bond cooperativity in proteins. Polarizable force fields show promise for simulating these cooperative effects, improving biomolecular modeling accuracy.

Keywords:
N‐methylacetamide (NMA)cooperativityforce fieldshydrogen bondnoncovalent interaction

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Structural Biology

Background:

  • Hydrogen bonds (H-bonds) are crucial for protein stability, structure, and dynamics.
  • Cooperative effects, where aligned H-bonds enhance each other, are observed in protein secondary structures like alpha-helices and beta-sheets.

Purpose of the Study:

  • To introduce a novel physical quantity for evaluating the cooperativity of intermolecular interactions.
  • To assess the cooperativity of protein backbone H-bonds using computational methods.

Main Methods:

  • Utilized N-methylacetamide molecules as a model system for aligned H-bonds.
  • Employed quantum chemistry (QM) calculations at the MP2/aug-cc-pVTZ level.
  • Benchmarked various protein force fields against QM results.

Main Results:

  • QM calculations revealed cooperative energies for H-bonds ranging from 2 to 4.3 kcal/mol.
  • Additive force fields failed to capture H-bond cooperativity.
  • Polarizable force fields (Drude, AMOEBA) reproduced the QM trend, though with lower magnitude.

Conclusions:

  • The proposed formula effectively quantifies H-bond cooperativity.
  • Accurate simulation of biomolecular systems can be advanced by incorporating cooperative energy into polarizable force fields.
  • This research provides a pathway for improved force field parameterization.