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I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file.

QuantumATK provides a function like this. However, this is not an option at the moment.

If there is no such software, how do you create passivated structures?

Edit: To clarify what I mean when I say "passivate": I mean just adding e.g. H atoms to the dangling bonds.

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  • $\begingroup$ Can you define what you mean by passivate the structure? Just terminate with H+ or OH- etc? $\endgroup$
    – Tristan Maxson
    Commented Feb 1, 2021 at 1:31
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    $\begingroup$ @TristanMaxson Yes, exactly. $\endgroup$
    – random01
    Commented Feb 2, 2021 at 10:15
  • $\begingroup$ Are there language restrictions (e.g. you don't want to work with FORTRAN, etc.)? There are a few exhaustive lists already though they aren't exactly searchable re: support for passivity, e.g. opensourcemolecularmodeling.github.io, en.wikipedia.org/wiki/…, and en.wikipedia.org/wiki/…. Heck, nanohub.org might even be useful. $\endgroup$
    – TylerH
    Commented Feb 2, 2021 at 15:22
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    $\begingroup$ @TylerH No there are no language restrictions. I am open to working with any program that is open source and solves the problem. $\endgroup$
    – random01
    Commented Feb 2, 2021 at 16:05
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    $\begingroup$ @NikeDattani: Open-source would be better, but free is okay as well. $\endgroup$
    – random01
    Commented Feb 3, 2021 at 19:12

1 Answer 1

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There are actually quite a number of tools that can be used to passivate a structure. They all work differently, and none are perfect at what they do. If you're dealing with organic molecules, these codes will work far better than if you're dealing with inorganic complexes.

Here is a list of some tools you may be interested in:

  • PyMOL has an H Add function. PyMOL accepts many kinds of formats. Commercial software with a free academic license.

  • Avogadro has an option for automatically adding H atoms to a structure, as described here. Free and open-source.

  • Olex has a similar command as PyMOL called hadd, as described here. This program is widely used when dealing with CIFs. Free software.

  • Reduce, Chimera, and MOPAC can all be used to automatically add H atoms to PDB structures. Free software (for non-commercial users).

  • Quantum ATK has a passivate option. Commercial software.

  • CrystalMaker has an option for automatically adding H atoms in its Molecule Builder utility, as listed here. Commercial software.

  • Materials Studio has an option for automatically adding H atoms. Commercial software.

There are likely many, many others.

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  • $\begingroup$ Thank you. I will look at the free software from the list. Commercial software is not an option at the moment as stated in the question. $\endgroup$
    – random01
    Commented Feb 10, 2021 at 16:14
  • $\begingroup$ There was some discussion here of merging these two questions. I think the other question is formulated a little more clearly so I considering having that one as the master question. Do you have any objection to this? The OP hasn't been on the site in several months, so I'll take your opinion as the deciding factor on whether to merge them or leave them alone. $\endgroup$
    – Tyberius ♦
    Commented Oct 19, 2021 at 20:54

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