Hydrogen bonds XH...Y

Dear users/developers,

Please advise if there is a way to visualize hydrogen bonds like PH…Br (between any polarized hydrogen and any electronegative element), I see only most standard bonds like NH…O.

I would like to create nice publication figures using Avogadro2 but without setting up hydrogen bonds I would need to use another software :frowning:

Thank you in advance.

At the moment, the hydrogen bond is set for the “standard” set of first row (NOF donor/acceptor).

I understand the need, but my experience is that such generalized hydrogen bond interactions trigger VERY STRONG FEELINGS in some chemists. (lol)

I can probably create a pull request build for a patched version, but I’m less sure if I would want to merge it into a release. What OS do you use?

Dear Geoff,

Thanks for yr reply.

True about strong feelings :))
But even decades ago there were reports, e.g., on hydrogen bond between metal non-bonded e-pairs and water H (even in metal complexes where they are ‘electropositive’, see https://doi.org/10.1002/anie.201001892 and others).

I an using Ubuntu-like system (Tuxedo OS) and precompiled avogadro (using alias avogadro=‘/home/al_chem/…/avogadro/Avogadro2-x86_64.AppImage’).

In case this functionality will be available I will be happy to create publication figures (and cite Avogadro2). But it will be possible only with high resolution figures, *png now are not that great, maybe I am missing something about resolution options?

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Yes, I’m just referring to “hydrogen bonding” as one of those concepts like “aromaticity” that create huge debates at conferences.

The default is to export at the resolution of your screen / window, since many systems are now using 4K or similar high resolution screens.

It’s possible to export at other resolutions, but even an image at 1024 pixels is ~3 inches at 300 dpi. What resolution do you want for the publication?

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Oh, I just realized that I was using big monitor in my office (I connect my small laptop to it) not with full resolution. Fixed this and now Avogadro2 figures are awesome. H-bonds I will draw for now with GIMP/LibreImpress.

Thanks for reminding about monitor resolution.

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For an (adjustable) identification of H-bonds in a 3D structure CCDC’s Mercury program* could provide a cross check. (This can run separately from displaying «short distances» just less than the sum of the van der Waals radii.) The systematic description (including a proper nomenclature) was popularized by Magret Etter (see for instance 1990ACR120, or Acta Cryst B46) for small molecule crystallography. Beside .cif, the program equally can process e.g., .pdb, .mol, .mol2 files)


* Already within the CSD-Community version.

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I’ll note that even CCDC Mercury doesn’t offer PH as a donor. That’s the point … there’s a pretty wide debate about what is and what is not a hydrogen bond.

As @al_chemist noted - there’s definitely a benefit to a wider list, but the other point is the ability to “draw in” annotated interactions in Avogadro (e.g., so you don’t need to go to an image program)