How to measure intramolecular and intermolecular distances, angles and torsions in Mercury

0 views

|

February 1, 2024

  • Share
  • In this video, Aimee LeBrun demonstrates how to measure intermolecular and intramolecular distances, angles, and torsion in molecules and crystal structures using the CCDC's visualisation software Mercury. This functionality could be used in the study of molecular geometry, and interactions in the solid form, such as hydrogen bonds. Measuring distances, angles, and torsions functionality is available in the free version of the visualization software Mercury. Find out more and download free Mercury here: https://www.ccdc.cam.ac.uk/solutions/software/free-mercury/ To view the structures used in this video, you can type the following refcodes in the Structure Navigator, or download these CIF files from Access Structures (https://www.ccdc.cam.ac.uk/structures/): ABAHUI and HXACAN for the demonstration, and HOFGEO, ABAGIV, GUKTUD and IBPRAC for the suggested exercises. In this video: - 00:13 Introduction to measuring distances, angles and torsions in CCDC's Mercury - 00:34 How to select a structure from the Cambridge Structural Database (CSD) in the Structure Navigator or upload a file. - 00:55 How to turn on atom labels to easily identify atoms. For more details about using labels in Mercury, watch the how to video https://www.youtube.com/watch?v=FvKgc42Xik0 - 01:11 How to measure distances in Mercury, exemplified for a bond. - 01:39 How to measure angles. - 02:14 How to measure torsions. - 02:47 How to visualise and save the list of the measurements taken. - 03:24 Example of measuring distances and angles for hydrogen bonds. This part briefly cover how to display hydrogen bonds in Mercury, but you can learn more in this video https://www.youtube.com/watch?v=bd8k0grYid8&t=57s - 05:07 Examples of measuring other interactions. - 05:18 Try it yourself! You can grow your skills with using Mercury for visualizing structures using the free CSDU module “Visualization 101 – Visualizing structural chemistry data with Mercury” here: https://www.ccdc.cam.ac.uk/community/training-and-learning/csdu-modules/visualization-101/

    Chemistry

    Keep up to date with all your favourite videos and channels.

    Get personalised notifications on new releases and channel content by subscribing to the LabTube eNewsletter.