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Not such a science genius girl. - helen-louise
Not such a science genius girl.
Things that are incredibly embarrassing if you're a postgraduate chemistry student: When you show your results to your supervisor and he says "What stereochemistry did you use?", and you're left blinking and saying "Stereochemistry...?!". I totally forgot that inhibitor 1 (and by extension, 2) has a chiral centre! Oh dear. It turns out that I'd been working with the R- isomer, so now I need to go and repeat the molecular docking with the S- isomer. To be honest, looking at the results, I don't think that it'll make any vital difference - but it's still important to try both!

Results from today are exciting in a good way - they seem to be confirming that the method is valid. Philip & I had been mystified by a hydrogen bond that both PBD Ligand Explorer and GOLD were showing in the X-ray structure from the original research group. It appears to be linking an ether group in the ligand to the O=C of the residue Asn 51, which is strange because you can't have hydrogen bonds without hydrogen - but we didn't think that either the amide or the ether oxygens would get protonated at pH 6.5. The joy of having two supervisors is that when I showed it to Katherine, she suggested it could be tautomerism - something like keto-enol. I just looked it up and there's such a thing as amide-imidic acid tautomerism. I can't find anything more useful from a quick Google search, but I'll add it to the list of things to look up in the huge 11-volume heterocycle book OF DOOM.

I'm feeling a bit better emotionally today. It took me forever to settle down to work, but I've eventually got quite a bit done. Yay.

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Current Mood: okay okay

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nmg From: nmg Date: 5th May 2010 20:33 (UTC) (Link)
This post makes me happy (or to be more specific, you being happy and upbeat about your PhD makes me happy). Rar!
baratron From: baratron Date: 5th May 2010 20:49 (UTC) (Link)
Thanks. I'm quite pleased :) In my previous research, at this stage I was still blundering around without the first clue about what I was supposed to be doing. Didn't understand the background material, didn't know how to use the computer programs I was supposed to be working with, didn't really know or get on with anyone else in the department - probably didn't even know what my research topic actually was!

It's all going a lot better this time. I understood what my research topic might be months before I committed to the project. And I've done all the background reading, and learnt how to do the computer stuff. (It helps that this time I'm using commercial software with known quirks, so you can find tutorials online on other universities' websites). People here do what I'd always expected at a university - when we get together over the coffee machine we talk about work, or cool geeky science news, not football or TV. I never fitted in my research group at Imperial because I don't like football, and wouldn't go to the bar to drink and get smoke blown over me.

It seems odd that a small non-science specialist University of London college could have more geeks than somewhere like Imperial, but I suppose that's the difference between self-funding and doing a PhD because you can't be bothered to get a "real" job... :X
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