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I'd like to be able to convert zwitterions to neutral form in Avogadro if possible. How do I do this?

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  • $\begingroup$ What's the purpose? $\endgroup$ – Abel Friedman Jan 1 '15 at 0:30
  • $\begingroup$ To create 3D models of these molecules in neutral form. $\endgroup$ – BH2017 Jan 1 '15 at 0:41
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    $\begingroup$ Let's write down the amino acids in the proper zwitterionic form. We won't put wrong the wrong ideas into the students' heads if we do that. $\endgroup$ – Abel Friedman Jan 1 '15 at 1:57
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    $\begingroup$ @AbelFriedman Neutral forms are lower in energy over zwitterionic species in the gas phase according to theory. Besides, it is nice to model both neutral and zwitterionic to compare/contrast the forms in visual form... $\endgroup$ – LordStryker Jan 5 '15 at 19:32
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    $\begingroup$ @AbelFriedman The "fact" you stated needs evidence, and I also doubt that very much since absolute statements are almost never true. After all we are dealing with an equilibrium here and in aqueous solution all four forms will be present. $\endgroup$ – Martin - マーチン Jan 6 '15 at 6:51
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I don't think the neutral protomer of an amino acid can be generated in Avogadro. What can be done is adjusting the protonation state for different values of pH. That option is in the Build menu - Build-> Add Hydrogens for pH.

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    $\begingroup$ Well, you could do it manually, or protonate the end groups using Build -> Add Hydrogens $\endgroup$ – Geoff Hutchison Jan 5 '15 at 18:33

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