I do mass spectroscopy and all the detected fragments are charged and often unusual or uncharacterized species. I use energy calculations on optimized or suspected geometries to gauge their possible validity.
Yep! While the default in the draw tool is to auto-adjust hydrogens, you can turn this off (e.g., to create \ce{CH3*} or other radicals / charged species.
You can always adjust the total charge or spin when generating calculations.
The big catch is that force fields often like charged species, so you may run into weird geometries or problems if you optimize the geometry in Avogadro (which defaults to MMFF94 or UFF).
My group performs charged / radical calculations fairly frequently using Avogadro.
Please feel free to post if you run into problems…
Thank you, ghutchis. I have previously done much modelling for charged and radical species in the Chemdraw Office Suite Gaussian program. Charges do make weird geometries, but I think sometimes these make sense, or are at least suggestive of the reality. But when I tried modelling zwitterions, the energy results were probably much too low (good stability). Putting separated charges in seems to always get high stability, the closer the charges, the better the stability calculation, but the less real likelyhood. Zwitterions certainly exist, but the modelling I have seen was likely wrong. Likewise for radicals, the singly occupied MO’s seem poorly modelled, but its better than the math I’m capable of !
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