What is the best method for calculating partial charges and protonation/deprotonation states of a small molecule such as phenol or caffeine, depending on the pH? For instance, it is well known that above pH=10 or so phenol is deprotonated, but there is data about its protonation around pH=2. For more complex molecules such as caffeine, similar things happen. So I am more interested in calculating partial charges of protonated and deprotonated forms than on pKas (sometimes, experimental data is available).

I head about Gaussian and the like, but I also wonder about software or methods that are easy to use.

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    $\begingroup$ What are partial charges, really? The charge of your molecule is 0 when protonated or -1 when deprotonated (that's for phenol; +1 and 0, correspondingly, for caffeine). What portion of the molecules will be at either state under given pH, is determined by pKa. That's just about it. If you want to know the atomic charges within any molecule or ion, well, these may be calculated, but it really takes some heavy quantum chemistry to find the figures that will be anywhere near reliable. $\endgroup$ – Ivan Neretin Sep 13 '15 at 8:28

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