I've googled repeatedly (with multiple search queries) to try and get an answer to this question but nothing comes up.

Embarrassingly, I seem to be the only person who is confused by:

  1. ATP with oxygen anions.

enter image description here

  1. ATP with $\ce{OH}$ groups.

ATP molecular structure showing OH groups in the phosphate groups

I looked at the $3$D view on PubChem - when I click 'show oxygens' they are indeed present as per image 2. ATP molecular structure showing oxygen anions in the phosphate groups

The chemical formula for ATP is $\ce{C10\underline{\mathrm H_{16}}N5O13P3}$: $16$ hydrogens, which means image $2$ fits the bill better than image $1$.

However, image 1 is more commonly found in tutorials about ATP.

Which representation is it best to go with?

  • 3
    $\begingroup$ It will depend on the pH of the solution $\endgroup$
    – Waylander
    Sep 9 '20 at 13:38
  • 1
    $\begingroup$ well you also have a basic centre present so at neutral pH it is likely a zwitterion $\endgroup$
    – Waylander
    Sep 9 '20 at 18:05
  • 1
    $\begingroup$ All 3 of the OHs are acidic. The adenosine heterocycle is basic so it will pick up a proton from one of the OH groups at neutral pH en.wikipedia.org/wiki/Zwitterion $\endgroup$
    – Waylander
    Sep 9 '20 at 21:07
  • 1
    $\begingroup$ That would be the case in basic solution beyond pH 12. $\endgroup$
    – Waylander
    Sep 10 '20 at 6:44
  • 1
    $\begingroup$ If your goal is to understand the ATP cycle in a cell, this level of detail is absolutely irrelevant and a distraction. Acidic protons can move around freely in aqueous solution, so you can include them in drawings or not. It makes no difference in the big picture of the function. $\endgroup$
    – Andrew
    Dec 4 '20 at 19:53

in vivo : ATP with oxygen anions.

in vitro : Depends on pH of solution


DNA = Deoxy Ribonucleic Acid. DNA is acidic , because its monomers contain three phosphates bound together and this so-called triphosphoric acid is extremely acidic.

In living organisms, DNA is always accompanied by histones(positively charged proteins) or sometimes by Mg+2 complexes. Therefore the dNMPs ( deoxyribo Nucleoside Mono Phosphates) that constitute the genetic material , are negatively charged .

For rNMPs (ribo Nucleoside Mono Phosphates) the negative charged form is also more preferable.

Generally speaking in living creatures , ATP = -4 , ADP = -3 , AMP = -2 charged. (It is worth mentioning that Pi which is a by-product in cellular energetics is HPO4(-2). )

You can see in Molecular Cell Biology Lodish et al 8th ed section 12.1 that the overall reaction of cellular respiration is: Overall

Notice the charges.

IMPORTANT : Sometimes during the metabolism of these compounds Proton(H+) may be added to oxygens of phosphate groups only because of the mechanism of the reaction which is temporary. But usually the charges are as I mentioned before.


If you purify ATP in a solution isolated from the cell, the number of acidic hydrogens attached to the molecule is related to the pH of solution. you can predict the molar concentration of each chemical species the same way you predict the [H3PO4] , [H2PO4 -] , [HPO4 2-] , [PO4 3-] , [H+] in a solution of H3PO4 and H2O (a typical analytical chemistry question) Either by a complex utilization of Henderson–Hasselbalch equation or by Charge and Mass equations.

Also Look at this awesome picture wiki

  • $\begingroup$ You are mixing up ATP with monophosphoric nucleosides and thoroughly ignoring adenine's basicity which may be ignored in DNA, but should not be in ATP. $\endgroup$
    – Mithoron
    Dec 6 '20 at 22:01
  • $\begingroup$ @Mithoron thank you , I'd totally forgotten about that. Still that wouldn't change anything. Pka for H3PO4 is 2.14 ,7.20 ,12.3 . It will be even more acidic in (PO4)3 form, while A/T/C/G base are aromatic bases , which as you know have weak basicity. $\endgroup$
    – Sam
    Dec 7 '20 at 6:50
  • $\begingroup$ Weak, but many orders of magnitude stronger then water. What you picture would be in much more basic solutions then found in vivo - otherwise one, or even two nitrogens would be protonated. Also I quite doubt H-H equation would do much good in cases like this. On the bright side, as OP recently mentioned all this isn't really important in practice. $\endgroup$
    – Mithoron
    Dec 8 '20 at 1:38

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