> No matter how acid I set the pH aniline (pKa 4.6) is never protonated It's not a general model of pH-dependent protonation. It has a set of rules, particularly for amino acids.
For more accurate pKa determination, you'll probably want semiempirical quantum calculations or a more complete model. Several people have suggested interest and I've given them some pointers, but no contributions yet. (It's not trivial.) -Geoff
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