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Molecules! - helen-louise
baratron
baratron
Molecules!
I have ChemDraw! The standard price for ChemDraw Pro is £640.00, but students can buy it for £90. Yay.

To celebrate this, I have drawn the structures of every psychoactive drug I have ever taken.
Drugs I have taken
I've checked the structures against several different sites, but venlafaxine in particular doesn't seem to reach consensus. Something about the exact 3D shape of the cyclohexane ring at the top.

When more time exists, I will draw the structures of every painkiller and antibiotic I've ever taken. Opioids have incredibly weird structures which will test my understanding of the software. (I think they're a bit beyond me today.)

Yay hexagons!

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Current Mood: excited excited

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Comments
(Deleted comment)
baratron From: baratron Date: 20th March 2009 16:11 (UTC) (Link)
It does a lot more than draw hexagons. It draws pentagons and heptagons as well!

No, seriously - see my reply to Ian below.
(Deleted comment)
emperor From: emperor Date: 20th March 2009 07:47 (UTC) (Link)
Shiny pictures.


The part of me that needs a life ever so desperately wonders what the free software to do this is
nmg From: nmg Date: 20th March 2009 08:02 (UTC) (Link)
Such a geek. Such a geek. :)
hiddenpaw From: hiddenpaw Date: 20th March 2009 08:09 (UTC) (Link)
This is art. Remake it out of pasta and newspaper Magazing cuttings (Prefferably Nuts) on black and submit it to the Royal accademy of art for thier summer exhibition.
lovingboth From: lovingboth Date: 20th March 2009 08:40 (UTC) (Link)
Yep. Hand-drawing it would be another option.

(Oh, and another 'eek' at the full price. A small market to be sure, but what is so special that a CAD program couldn't do?)
barakta From: barakta Date: 20th March 2009 11:19 (UTC) (Link)
Making it do it by proper chemistry rules probably. i.e valency and other scarier 'rules' which I never understood. I gave up when the electrons got complicated.

There used to be a freeware one but it was a bit like the difference between Ms Paint and Photoshop.
baratron From: baratron Date: 20th March 2009 16:10 (UTC) (Link)
There is also ChemDraw Ultra which is £970 for commercial users and £360 for academic users. I don't know the student price because my cookie has expired now. I assume that the full versions include multiple licenses. Mine can only be installed on one machine.

As for what it does that CAD programs don't:
1) It contains a large number of built-in molecules and molecular fragments. Carbohydrates, amino acids and DNA fragments are all non-trivial to draw.
2) "Check structure" - errors in valency, bonds in the wrong place etc. are pointed out.
3) "Clean up structure" - the structure is "snapped" to correct bond angles and errors are fixed.
4) Auto-carbon chain tool - choose how long you want it and the zigzag appears.
5) Trivial (one click) to change bond order from single to double to triple, and to align the double bond in the correct place in the structure.
6) Information about compounds. Once you've drawn something you can click on it to be told the molecular formula, relative molecular mass etc.
7) Mass spectrometry tools - you can draw a molecule then split it to find out the masses of the fragments.
8) 3D structure tools - when you rotate a molecule, bonds change from wedged to normal to dashed as they go in or out of the plane of the screen, to preserve stereochemistry.
...um, and that's just what I've found so far.
lovingboth From: lovingboth Date: 21st March 2009 09:35 (UTC) (Link)
Ah, OK :)

Annoyingly, the deadline for this year's Summer Exhibition was just over a week ago.
From: fluffymormegil Date: 20th March 2009 08:20 (UTC) (Link)
Ooh. Shiny! Molecules are fun.
barakta From: barakta Date: 20th March 2009 08:21 (UTC) (Link)
Geek! :) These are ace.
judiff From: judiff Date: 20th March 2009 08:44 (UTC) (Link)
shiny!
purplerabbits From: purplerabbits Date: 20th March 2009 09:46 (UTC) (Link)
That would make an awesome poster - or maybe a make-your-own poster that people could enter drugs and text on :-)


mjl From: mjl Date: 20th March 2009 09:54 (UTC) (Link)
Cool. This is all rather beyond my mostly forgotten A-level though (and I didn't do well in the organic bit of it at the time). I don't remember drawing anything more complicated than benzene. The points without any letters on are carbon, right? And there are lots of hydrogens that aren't shown?

What are those weird bonds to the fluorine in flupentixol doing? And why does has it have "pent" in the name when there doesn't seem to be 5 of anything?

(There is no need to actually answer these questions - I don't really need to know, and I could probably Google the answers if I tried...)
baratron From: baratron Date: 20th March 2009 20:17 (UTC) (Link)
Yup - skeletal formulae show only the carbon skeleton + any atoms that aren't hydrogens. You assume that every C atom has as many H atoms as it needs to make it up to 4 bonds. (Rule zero of organic chemistry: Carbon always has 4 bonds in compounds).

The "weird" bonds to the fluorines are showing the 3D shape: the black wedge shows a bond coming out of the plane of the screen and the dashed line shows a bond going into the plane of the screen. To be honest, they're not needed as 3 of the 4 bonds are to identical atoms, therefore there isn't any interest in the stereochemistry about that carbon. You'll notice that with Prozac I wrote the same group as simply -CF3. I wasn't going to go back and remove something interesting that I'd already worked on ;)

No freaking idea what the "pent" part of the name is supposed to signify. There happen to be 5 loose carbon atoms that aren't part of either the thioxanthene (3 rings at the bottom with S in) or the piperazine (ring at the top with two Ns in), but they don't form a continuous chain, being a propylene (3Cs with a C=C double bond) and an ethanol (2Cs with -OH) fragment respectively. Could it refer to them? I don't know. Wikipedia claims that the systematic IUPAC name is 2-[4-[3-[2-(trifluoromethyl)thioxanthen-9-ylidene] propyl]piperazin-1-yl]ethanol, but Wikipedia doesn't always get things right.

The "thix" part shows the presence of sulphur, which is why I'm so pissed off that someone decided to standardise the name to "tix" - that doesn't tell me that there's a sulphur present! Grrr. See also amoxicillin (which used to have a nice "oxy" in to tell us about the oxygen) and beclametasone (which used to have a "metha" to refer to the methyl groups). Standardising of drug names that destroys chemistry MAKES ME ANGRY.
rhialto From: rhialto Date: 20th March 2009 22:38 (UTC) (Link)
Giving the IUPAC name is apparently then a feature the program doesn't have. Or you haven't found it yet (or maybe it is in a more expensive version).
taimatsu From: taimatsu Date: 20th March 2009 10:13 (UTC) (Link)
Wow :) That's pretty amazing. Go you! :)
From: skibbley Date: 20th March 2009 10:29 (UTC) (Link)
Ooooooh! Wellcome Gallery here you come!
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