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Related Concept Videos

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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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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
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Related Experiment Video

Updated: Jul 24, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Locating Hydrogen Positions for COF-300 by Cryo-3D Electron Diffraction.

Wenjia Sun1, Pohua Chen1, Mingxuan Zhang1

  • 1College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, P.R. China.

Angewandte Chemie (International Ed. in English)
|July 5, 2023
PubMed
Summary

This study shows that 3D electron diffraction (3D ED) can locate hydrogen atoms in covalent organic frameworks (COFs). This technique clarifies host-guest interactions, crucial for understanding COF functions and applications.

Keywords:
Covalent Organic FrameworkDynamical RefinementElectron DiffractionHydrogen AtomsKinematical Refinement

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Area of Science:

  • Materials Science
  • Crystallography
  • Nanotechnology

Background:

  • Covalent organic frameworks (COFs) are vital materials with diverse applications.
  • Host-guest interactions within COFs are critical for their functionality.
  • Determining hydrogen atom positions is essential for understanding these interactions but challenging due to synthesis difficulties.

Purpose of the Study:

  • To demonstrate the capability of 3D electron diffraction (3D ED) for locating hydrogen atoms in COFs.
  • To investigate host-guest interactions in COFs by precisely determining atomic positions.
  • To overcome limitations in crystal quality for structural analysis of COFs.

Main Methods:

  • Utilized continuous precession electron diffraction tomography (cPEDT) under cryogenic conditions.
  • Applied 3D ED to analyze the structure of a COF.
  • Focused on the identification of light atoms, specifically hydrogen.

Main Results:

  • Successfully located hydrogen atoms within both the COF framework and guest molecules for the first time.
  • Provided precise structural information, including hydrogen positions.
  • Enabled a clear understanding of host-guest interactions through atomic-level insights.

Conclusions:

  • 3D ED, particularly cPEDT, is a powerful technique for the structural determination of COFs, including light atoms.
  • This method offers novel insights into host-guest interactions, advancing COF research.
  • The findings pave the way for more detailed investigations into COF properties and applications.