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From Wikipedia, the IUPAC name for guanine is 2-amino-1,9-dihydro-6H-purin-6-one besides 2-amino-6-hydroxypurine and 2-aminohypoxanthine.

I have some difficulty understanding the 6H part in its name since there's a keto group at the 6th position unlike in cytosine (4-aminopyrimidin-2(1H)-one) where the 1H clearly refers to the hydrogen at the 1st position

What does 6H exactly mean?

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    $\begingroup$ So-called Indicated H goldbook.iupac.org/terms/view/I03004 $\endgroup$
    – Alchimista
    Dec 10, 2021 at 14:57
  • $\begingroup$ @Alchimista Thank you! But a thing still bugs me; the indicated hydrogen in cytosine gets added at position-1 which is also evident in its name. While in the case of guanine, it(hydrogen) apparently gets added at position-1 and not 6 as shown in its IUPAC name. Am I getting it right? $\endgroup$
    – Nex
    Dec 10, 2021 at 19:07
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    $\begingroup$ Related: chemistry.stackexchange.com/questions/110664/… $\endgroup$ Dec 11, 2021 at 10:07
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    $\begingroup$ @Nex the numbering fixes the double bonds with respect to purine numbering, guanine is named as a 1,9-dihydropurinone. The H in 1 isn't indicated H. See also Nilay Ghosh comment. $\endgroup$
    – Alchimista
    Dec 11, 2021 at 13:18

1 Answer 1

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The original parent structure purine ($\ce{C5H4N4}$) has the maximum number of noncumulative double bonds for this kind of structure. Compared to an ideal unsaturated compound, however, purine has one extra hydrogen somewhere. The position of this extra hydrogen must be indicated. A few different isomers are possible; for example, the original parent structure could be 9H-purine.

9H-purine

In the given compound, a double bond of the original purine is missing. Thus, the parent structure is a bit more saturated with the equivalent of two additional hydrogen atoms ($\ce{C5H6N4}$). Such saturation is described using ‘hydro’ prefixes. The locants of the original indicated hydrogen and the two additional hydrogens are 1, 6, and 9. The indicated hydrogen gets the lowest locant, so the name of the unsubstituted parent structure is 6,9-dihydro-1H-purine.

6,9-dihydro-1H-purine

In the substituted purin-6-one, however, the numbering is different because a double bond was removed to make room for the ketone. According to Rule P-58.2.3, the indicated hydrogen is placed at the position that will accommodate this principal characteristic group. Therefore, the name becomes 1,9-dihydro-6H-purin-6-one.

1,9-dihydro-6H-purin-6-one
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  • $\begingroup$ Am I right in thinking that there is no hydrogen at or near position six? If so, could someone add to the answer an acknowledgement of this and an explanation of what exactly is meant by "indicated hydrogen"? Is it in fact not a hydrogen atom at all, but a configuration of bonds? $\endgroup$ Dec 29, 2022 at 16:12
  • $\begingroup$ @MatthewChristopherBartsh IUPAC Gold Book: indicated hydrogen $\endgroup$
    – Loong
    Dec 30, 2022 at 17:31
  • $\begingroup$ Thanks for the link. I already read it after seeing it in Alchemista's comment. There is a slight problem with it, however. In all the examples given in the link there is an actual hydrogen atom at the position referred to. There is no example analogous to the "6H" of 2-amino-1,9-dihydro-6H-purin-6-one where, if I am correct, there is no actual hydrogen atom at position 6. The nearest hydrogen being attached to the nitrogen at position 5. Could someone please confirm that the nearest H to position 6 is attached to N5? $\endgroup$ Dec 30, 2022 at 20:34
  • $\begingroup$ @MatthewChristopherBartsh In the final product 2-amino-1,9-dihydro-6H-purin-6-one, three hydrogen atoms of 6,9-dihydro-1H-purine are substituted with other groups. So, yes, there is no hydrogen atom left at position 6. However, no, there is no hydrogen attached to position 5 and there is no nitrogen at position 5. $\endgroup$
    – Loong
    Dec 31, 2022 at 18:53
  • $\begingroup$ I meant to ask, "Could someone please confirm that the nearest H to position 6 is attached to N1?" You are right that there is no N5. I got confused about the numbering; my diagram has no numbering and left and right are reversed and I confused left and right I think. Thanks for confirming that there is no hydrogen at position 6. It sounds like "6H" refers to a hydrogen atom in a molecule that could be a precursor in a chemical process that synthesizes 2-amino-1,9-dihydro-6H-purin-6-one or perhaps in a "parent" molecule in a taxonomy of molecules. I find it very hard to understand. $\endgroup$ Dec 31, 2022 at 21:04

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