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You can probably tell I'm not really a chemist (hi from physics!), but I've suddenly found myself having to draw some structural formulae, hence the stupid question.

I've drawn a diagram of the four DNA bases:

DNA bases

I don't care what they're attached to, and I don't fancy drawing an entire DNA molecule, but I'd like to show where they bond to the rest of the nucleotide. I've used \cdots ($\cdots$) currently, but that doesn't feel right. I considered R, but I'm not sure if an entire DNA molecule really counts as an R group. I saw a wavy bond once, but it feels like those are confined to stereochemistry.

What's the convention in cases like this? (And what do I Google to find it next time I want to know?)

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According to the Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008), in the structure diagram of the parent structure, variable substituents should be indicated by an unambiguous label.

This label should be chosen so that it cannot easily be confused with other valid element symbols or fragment abbreviations. Traditionally, the letter “R” is widely used, followed by a superscripted number (R1, R2, etc.) or prime(s) (R', R", etc.) if necessary to distinguish different groups. It is not acceptable to use a letter followed by a subscripted number, since subscripted numbers are more commonly used to indicate repeat counts, and confusion between the two is inevitable. Other common symbols include X, Z, and G. (…)

The label may be used with or without an explicit list of allowed substituents (e.g. in tabular form).

The wavy line is preferred in structure diagrams of the variable substituents, in cases where the external connection points must be indicated for the variable substituents.

Variable substituents

Therefore, if you consider nucleobases with variable substituents, you may use labels such as “R”. However, if you consider the nucleobases to be the variable substituents of another (larger) parent structure, you may use a wavy line.

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Just as a side note, I think it is easier to use ChemDraw to make the graphics then import them into your LaTeX file, rather than using the chemfig package which (I find) is cumbersome. Obviously it's entirely your choice.


I don't think there is an established convention per se.

If you wrote $\ce{R}$, nearly everybody would understand it, especially if you also mention at the side that $\ce{R}$ refers to the deoxyribose sugar. In chemistry, $\ce{R}$ is used for anything and everything.

I haven't seen $\cdots$ being used for this purpose in chemistry before.

A wavy line parallel to a bond isn't used for indicating stereochemistry. It is usually used to show that a group or moiety connects to something else. For example, if I was too lazy to write this reaction out in full

Hypothetical

I would instead write

Lazy

In your case it would be acceptable as well.

Examples

With that said, I went to look up some textbooks.

Berg & Stryer, Biochemistry, 7th ed.: Nothing

enter image description here


Clayden et al., Organic Chemistry, 2nd ed.: R

enter image description here


Blackburn et al., Nucleic Acids in Chemistry and Biology, 3rd ed.: Nothing

enter image description here


McMurry, Organic Chemistry, 8th ed.: Wavy lines

enter image description here


TL;DR: You can probably get away with anything you like.

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  • $\begingroup$ Thanks! I'm impressed by how quickly you managed to show me textbooks. ChemDraw probably would be easier, but I don't have a copy (yet) and I'm comfortable enough with LaTeX to be able to manage the relatively simple diagrams I'm working with. I'll at least change the ChemFig settings to match ChemDraw (with wider double-bond spacing and such) at some point. $\endgroup$ – georgewatson Sep 12 '16 at 11:11
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    $\begingroup$ Nothing is obviously the worst choice since it looks like a methyl group. $\endgroup$ – Jan Sep 12 '16 at 15:20
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    $\begingroup$ @Jan Yes, it is certainly strictly wrong, but I think it is fine as long as the context is established. Every book describes the structure of a deoxyribonucleotide before going on to talk about Watson-Crick base pairing, so there is little opportunity for misinterpretation. $\endgroup$ – orthocresol Sep 12 '16 at 16:27
  • $\begingroup$ That’s why I said worst choice — it takes me two looks minimum to establish the content that that is not a methyl group ;) But yeah, with context it’s not wrong ^^ $\endgroup$ – Jan Sep 12 '16 at 16:31
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    $\begingroup$ @dendodge As a side note: taking into consideration your background mentioned in your profile (exposure to different operating systems, HTML), ChemDoodle represents an interesting alternative to ChemDraw. $\endgroup$ – Buttonwood Sep 12 '16 at 19:33

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