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Related Concept Videos

Hydrogen Bonds00:26

Hydrogen Bonds

131.4K
Hydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.
Hydrogen Bonds Control the World!
Because hydrogen has very weak electronegativity when it binds with a strongly electronegative atom, such as oxygen or nitrogen, electrons in the bond are unequally shared....
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Hydrogen Bonds01:04

Hydrogen Bonds

13.3K
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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Metal-Ligand Bonds02:51

Metal-Ligand Bonds

24.0K
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
24.0K
Ligand Binding Sites02:40

Ligand Binding Sites

14.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.9K
IR Spectrum Peak Broadening: Hydrogen Bonding01:23

IR Spectrum Peak Broadening: Hydrogen Bonding

1.8K
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...
1.8K
Valence Bond Theory02:42

Valence Bond Theory

11.2K
Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Hydrogen Bonds in Protein-Ligand Complexes.

Gabriela Bitencourt-Ferreira1, Martina Veit-Acosta1, Walter Filgueira de Azevedo2

  • 1Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.

Methods in Molecular Biology (Clifton, N.J.)
|August 28, 2019
PubMed
Summary

Accurate hydrogen bond energy calculation is vital for drug design. This study explores semi-empirical force fields in molecular docking programs like AMBER and AutoDock4 to predict binding affinity, aiding virtual screening.

Keywords:
Binding affinityDrug designHydrogen bond interactionsMolecular recognitionShikimate pathway

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Area of Science:

  • Computational chemistry
  • Drug discovery and development

Background:

  • Hydrogen bond potential energy evaluation is crucial for drug design.
  • Semi-empirical force fields are commonly used in molecular docking for binding affinity calculations.

Purpose of the Study:

  • To describe methods for predicting hydrogen bond potential energy using semi-empirical force fields.
  • To evaluate the 12-10 potential for assessing protein-ligand binding affinity.

Main Methods:

  • Utilized semi-empirical force fields within molecular docking programs (AMBER, AutoDock4, TreeDock, ReplicOpter).
  • Applied the 12-10 potential model.
  • Evaluated binding affinity against crystallographic structures with experimental data.

Main Results:

  • Demonstrated the application of semi-empirical force fields for hydrogen bond potential energy prediction.
  • Successfully applied the 12-10 potential to assess binding affinity in various protein-ligand systems.

Conclusions:

  • Semi-empirical force fields provide a reliable method for evaluating hydrogen bond potential energy in drug design.
  • The 12-10 potential is effective for predicting protein-ligand binding affinity in virtual screening.