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Related Concept Videos

Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
X-ray Crystallography02:18

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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.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...

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Crystallization and In Situ Room Temperature Data Collection Using the Crystallization Facility at Harwell and Beamline VMXi, Diamond Light Source
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Published on: March 8, 2024

Validating and understanding ring conformations using small molecule crystallographic data.

Simon J Cottrell1, Tjelvar S G Olsson, Robin Taylor

  • 1Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK. cottrell@ccdc.cam.ac.uk

Journal of Chemical Information and Modeling
|March 1, 2012
PubMed
Summary
This summary is machine-generated.

Analyzing ring conformations is key for drug design. Mogul software now efficiently extracts geometrical preferences from the Cambridge Structural Database (CSD), aiding in understanding molecular structures.

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Area of Science:

  • Chemical Crystallography
  • Computational Chemistry
  • Drug Discovery

Background:

  • Understanding small molecule conformational preferences is crucial for structure-based drug design.
  • The Cambridge Structural Database (CSD) contains extensive data on molecular geometries, but manual analysis is time-consuming.
  • Existing tools for extracting geometrical preferences from the CSD can be enhanced for specific applications.

Purpose of the Study:

  • To extend the Mogul program for analyzing and comparing ring conformations.
  • To leverage a comprehensive library of over 900,000 ring fragments from the CSD.
  • To provide a rapid method for understanding conformational preferences in various molecular contexts.

Main Methods:

  • Development of an extended Mogul program incorporating a new library of ring conformations.
  • Utilizing a large dataset of over 900,000 ring fragments from the Cambridge Structural Database (CSD).
  • Application of the enhanced Mogul tool to analyze crystal lattice structures and protein-bound molecules.

Main Results:

  • The extended Mogul program can efficiently analyze and compare diverse ring conformations.
  • A comprehensive library derived from the CSD enables detailed geometrical preference analysis.
  • Demonstrated utility in understanding conformational preferences of molecules within crystal lattices and protein binding sites.

Conclusions:

  • The enhanced Mogul program offers a powerful and efficient solution for analyzing ring conformations.
  • This tool facilitates a deeper understanding of molecular structure-activity relationships in drug design.
  • The findings contribute to more accurate structure-based drug design by providing insights into conformational preferences.