How to define and visualize hydrogen bonds in Mercury - video tutorial



September 1, 2023

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  • In this Mercury software tutorial, you will learn the basics of visualizing hydrogen bonds. Using CCDC's Mercury, you can personalise the H bond definition, which includes the list of hydrogen bond donors and acceptors, you can display intermolecular and intramolecular H bonds, and expand the contacts around a molecule (H bond donors and acceptors) to display the hydrogen bonding network created. You will see how to do so in this video. You can visualize hydrogen bonds in structures from the Cambridge Structural Database (CSD), the free CSD Teaching Subset (already loaded in CCDC's Mercury), and in your own crystal structures (first, you can simply upload them to CCDC's Mercury from the top menu File, then Open). By gaining a better understanding of the intermolecular interactions such as hydrogen bonds and and the hydrogen bonding network, we can learn more about the stability of a solid form and it can thus help us design new materials. This video will get you started to effectively displaying hydrogen bonds in Mercury and you can then move on to more advanced analysis functionality from the CSD Software (e.g., Full Interaction Maps, Hydrogen Bonds Propensity, etc.). If you are a chemistry student or educator, exploring H bonds with CCDC's Mercury and the CSD Teaching Subset, will help you visualize in 3D and contextualise interactions to enhance learning. You might find helpful to complement this video with more resources from our teaching modules: For more Mercury software tutorials visit the CCDC (Cambridge Crystallographic Data Centre) website and explore CSDU modules and our self-guided workshops: - - (CSD-Community and CSD-Core for H bonds display, CSD-Materials for advanced functionality). In this video: - 00:00 Welcome and learning outcomes - 00:27 Open CCDC's Mercury visualization software and open structure BITZAF, pyridoxine, a form of vitamin B6. - 00:51 Which atoms do you think are H bond donors and which acceptors in this pyridoxine molecule? How many hydrogen bonds do you think it forms in this crystal structure? - 01:01 See and edit and personalise the H bonds definition: select hydrogen donors and acceptors, set distances, select to intermolecular H bonds or intramolecular ones or both, and more. - 02:39 Visualize the hydrogen bonds for your molecule in the crystal structure under examination. - 03:08 Expand and explore the hydrogen bonding network. Hydrogen bonds visualization can be done with both the free version of CCDC's Mercury and the more advanced licensed one. Read about the functionality available in free Mercury and how to download it, and how to enquire for licenses here: Follow us on social media: Instagram: @ccdc_cambridge Twitter: @ccdc_cambridge Facebook: Cambridge Crystallographic Data Centre (CCDC)

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