In an attempt to calculate the pKa of the carboxylic acid group of Bacteriopheophorbide A (BPheo, Pubchem), I generated the structure in MarvinSketch (ChemAxon product) and I came across an interesting result. According to the software, the inner amine groups which are part of the resonance structure can become positively charged at relatively high pH. The photo below shows the calculated pKa of the groups in blue (groups of interest are highlighted in yellow). According to this software, this means that at pH 5.5 the groups will both be positively charged, whereas I was under the impression that these groups can only be altered using very strong acids such as TFA due to the aromatic ring.

pKa calculation of BPheo

Is this realistic? Or is this simply an issue with the software. I've tried looking into this myself but the literature on BPheo seems rather sparse.

Thank you in advance for your input.

  • $\begingroup$ The one on the right in your image makes sense, as the basic line pair is perpendicular to the pi system. Compare to pyridine. The one on the left doesn’t make sense to me, unless the 3D conformation breaks the conjugation. $\endgroup$ – Andrew Jul 30 '20 at 1:58
  • $\begingroup$ Also, this structure is a form of porphyrin ring, which will chelate metal ions very readily. Perhaps the strong acid experiments you are thinking of were needed to displace a metal, not just protonate a free porphyrin? $\endgroup$ – Andrew Jul 30 '20 at 21:04

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