smaerd
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Hexamine Chemical Drawing Question
So I'm just having fun drawing some more complex compounds in ACD labs chem draw tool. I looked at hexamine just for kicks on wikipedia and wondered
how I'd go about drawing it.
So I drew it up. Then I used the, "Clean Structure", tool to see if it would even out some of my lines. Instead it gave me this pretty cool looking
hexagon with a triskelion-eque shape in the middle.
I used the tool to "generate chemical name" and they both showed up as hexamine's chemical name(as expected). I was just wondering if both of these
are proper ways to display the compound?
Are there any good resources or links where I can learn more about the format for chemical drawing?
Thank you for your time.
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Nicodem
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Any way of drawing a compound is valid as long as the connectivity and configuration are correct. Drawing variations in conformation is quite
acceptable as long as you don't draw some overly weird angles and overpositions. Nevertheless, it not polite to draw structures in higher energetic
conformations (for example, if you draw a cyclohexyl ring, you draw it in the chair conformation rather than boat, etc.). Obviously, facilitating the
comprehensiveness of the drawing is encouraged and ultimately is also the only thing that matters (structures should not be ambiguous - they should
represent only one unique compound rather than a range of isomers). Therefore it does not really matter if you draw hexamine in perspective or
flattened, because the connectivity remains the same and only one configuration is possible anyway. Some people have difficulties in comprehending 3D
drawings and to them a flattened structure will be more comprehensive. On the other hand structures implying three dimensions via perspective have
more realistic depictions of bond angles and present a much better picture of the structure, so those that have less troubles comprehending them will
find them much more preferable. Yet, it is important to present them properly. The view angle should be such as to make all the carbons visible. For
example, in your depiction you used a view angle that makes it difficult to understand if the nitrogen at the top is directly conected with the
nitrogen at the bottom or is there a methylene group in between them. As you see, the view angle of the structure makes the connectivity ambiguous.
Rotating the structure by just a few degrees would have showed that methylene group properly. Note how this is taken care in the scheme presented at
the wikipedia entry for hexamine:
…there is a human touch of the cultist “believer” in every theorist that he must struggle against as being
unworthy of the scientist. Some of the greatest men of science have publicly repudiated a theory which earlier they hotly defended. In this lies their
scientific temper, not in the scientific defense of the theory. - Weston La Barre (Ghost Dance, 1972)
Read the The ScienceMadness Guidelines!
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smaerd
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Thanks for such a nice and comprehensive explanation. I really appreciate it.
I see what you mean, I did hide that methylene group on accident.
Thanks again  !
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Paddywhacker
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If you use the "search for structure" on the Chemspider site you can crudely draw your structure and then have the software tidy it up. Then you can
rotate and zoom it to get a nice picture.
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