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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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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Updated: Sep 30, 2025

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
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Carbon-Centered Hydrogen Bonds in Proteins.

Juhi Dutta1,2, Akshay Kumar Sahu1,2, Abhijeet S Bhadauria1,2

  • 1School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.

Journal of Chemical Information and Modeling
|March 16, 2022
PubMed
Summary
This summary is machine-generated.

Researchers discovered novel hydrogen bonds (H-bonds) involving tetravalent carbon atoms in proteins. These carbon-centered H-bonds, distinct from classical types, play a role in substrate binding and C-H bond activation.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Classical hydrogen bonds (H-bonds) involve lone pair electrons or pi-electrons.
  • A recent concept explores H-bonding without these traditional electron donors.
  • H-bonds with less electronegative tetrahedral carbon atoms challenge conventional definitions.

Purpose of the Study:

  • To report the first instance of H-bonds involving tetravalent carbon atoms within protein structures.
  • To investigate the nature and strength of these novel carbon-centered H-bonds.
  • To explore their functional implications in protein-ligand interactions and C-H bond activation.

Main Methods:

  • Analysis of protein structures to identify potential carbon-centered H-bonds.
  • Quantum chemical calculations to assess H-bond characteristics and energies.
  • Development of an empirical equation to estimate C-H···C H-bond energy.

Main Results:

  • Identified H-bonds where sp3-hybridized carbon atoms act as acceptors, facilitated by bonded elements like As and Mg.
  • Determined these H-bonds to be weak to moderate in strength, with binding energies ranging from -5.4 to -14.0 kJ/mol.
  • Found that C-H···C H-bonds contribute significantly to substrate binding and C-H bond activation, comparable to C-H···π interactions.

Conclusions:

  • Tetravalent carbons can act as H-bond acceptors in proteins under specific bonding arrangements.
  • These novel H-bonds are crucial for protein function, influencing substrate binding and catalysis.
  • The study expands the understanding of non-classical H-bonding in biological systems.