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Related Concept Videos

Hydrogen Bonds01:04

Hydrogen Bonds

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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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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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IR Spectrum Peak Broadening: Hydrogen Bonding01:23

IR Spectrum Peak Broadening: Hydrogen Bonding

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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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Intermolecular Forces03:13

Intermolecular Forces

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Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
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Van der Waals Interactions01:24

Van der Waals Interactions

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Atoms and molecules interact with each other through intermolecular forces. These electrostatic forces arise from attractive or repulsive interactions between particles with permanent, partial, or temporary charges. The intermolecular forces between neutral atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively known as van der Waals forces.
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Covalent Bonds01:08

Covalent Bonds

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Overview
When two atoms share electrons to complete their valence shells, they create a covalent bond. An atom's electronegativity—the force with which shared electrons are pulled towards an atom—determines how the electrons are shared. Molecules formed with covalent bonds can be either polar or nonpolar. Atoms with similar electronegativities form nonpolar covalent bonds; the electrons are shared equally. Atoms with different electronegativities share electrons unequally,...
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
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Coarse-grained potential for hydrogen bond interactions.

Justyna D Kryś1, Dominik Gront1

  • 1Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.

Journal of Molecular Graphics & Modelling
|June 9, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to describe hydrogen bonds using only Cα positions for protein simulations. The novel energy function accurately identifies hydrogen bonds and protein structures like β-sheets in simulations.

Keywords:
Coarse grain methodsHydrogen bondMean field force filedProtein modeling

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Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Protein structure and dynamics are vital for biological processes.
  • Hydrogen bonds are key to protein folding but complex to model, especially in reduced models.
  • Accurate mathematical formulation of hydrogen bonds remains a challenge.

Purpose of the Study:

  • To propose a novel hydrogen bond energy function for coarse-grained simulations.
  • To define this function based solely on Cα positions.
  • To assess its accuracy in recognizing hydrogen bonds and protein structures.

Main Methods:

  • Developed a new hydrogen bond energy function using only Cα atom positions.
  • Applied the function in coarse-grained simulations of protein models.
  • Evaluated the function's accuracy in identifying hydrogen bonds and secondary structures.

Main Results:

  • The novel hydrogen bond energy function achieved over 80% accuracy in recognizing hydrogen bonds.
  • Successfully identified β-sheet structures in simulations of β-amyloid peptide.
  • Demonstrated the utility of Cα-based energy functions in coarse-grained protein simulations.

Conclusions:

  • The proposed Cα-based hydrogen bond energy function is effective for coarse-grained simulations.
  • This method simplifies modeling while maintaining accuracy in predicting protein structure.
  • Offers a promising approach for studying protein folding and dynamics.