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My understanding is that hydrogen bonds formed by proteins require the NH2 / COOH to be neutral. Hence to find out when the hydrogen bonds are the strongest will depend on the absolute charge of the protein and not the net charge. Hence how do you calculate this absolute charge or is there another way to determine when the strongest hydrogen bonds will be formed when changing the pH condition?

Note: For absolute charge I do not need the actual charge in coulombs but more of the relative charge the NH2 / COOH will bear when changing the pH conditions

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    $\begingroup$ Free -COOH/-NH2 groups in proteins ( like in glutamic acid or lysin) are too acidic/basic to stay neutral, so very majority of them is in their ionic form. So there would be rather ionic pair bonding R - COO- ... NH3+ - R // For the charge of the protein, you need pH and detailed aminoacid sequence. $\endgroup$
    – Poutnik
    Commented Dec 24, 2022 at 10:33
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    $\begingroup$ You might want to start by asking whether the premise of your post here is correct: "My understanding is that hydrogen bonds formed by proteins require the NH2 / COOH to be neutral. " <-- is this true? How did you come to this conclusion? What atoms in proteins commonly form H-bonds? $\endgroup$
    – Buck Thorn ♦
    Commented Dec 24, 2022 at 11:09
  • $\begingroup$ I recommend starting learning about proteins form beginning, maybe go back to aminoacids... $\endgroup$
    – Mithoron
    Commented Dec 24, 2022 at 18:56
  • $\begingroup$ You are asking a number of questions based on a false assumption. It leads to confusing sentences like this one: "Hence how do you calculate this absolute charge or is there another way to determine when the strongest hydrogen bonds will be formed when changing the pH condition?" The question in the title can be answered, however, and there are theoretical and experimental approaches to determine the total charge of a protein. $\endgroup$
    – Buck Thorn ♦
    Commented Dec 31, 2022 at 10:36

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