[zuriel]

Hey everyone.

So, I'm starting postgraduate research soon and I'm very excited.
I'll be working in the area of medicinal chemistry/synthetic organic chemistry and I'm wondering have any of you got any tips for me?

How do you organise your workbench if you're a synthetic chemist?

What search engines do you use for checking chemical references?

What online facilities do you avail of to search through scientific journals?

Any hints and tips on how you organise your own lab notebook?

Just throw any advice at me whatsoever, I'm very keen to see how other fellow chemists organise things and work in a synthetic organic chemistry environment.

Thanks! 

[fledarmus]

SciFinder, head and shoulders above anything else for checking references and synthetic methods.

In your lab book, there are a few things that you need to have for every single reaction, or it will be worthless for anybody following you.

1) Where did you get your procedure from? Note a reference for each procedure, so when you go back to write up your research, you will know where to give credit and footnotes.

2) Where did you get your starting materials? If commercial, that should be noted, but if they are products from previous reactions or were obtained from labmates, make sure that you can trace them back through your notebooks! I label all my compounds in the format ([lab notebook name]-[page number]-[product on page]) so they can always be traced back. For example, a crude product for a reaction might be MLC25-136-1, and after a chromatography that isolated three spots, I would have products MLC25-136-2, MLC25-136-3, and MLC25-136-4. That becomse the name of the compound whenever I use it again, so I can always trace back every batch of compound to its source from commercial materials.

3) How did you identify your products? It helps to have a standard set of analytical data for every compound, but at the very least you should have whatever data you based your identification of the compound on. If you compared it to literature values, be sure to include the reference for those values as well.

The rest of the lab notebook record is all that stuff they taught you when you were taking organic chemistry - the reaction you were trying to carry out, a table of the amounts of each compound you used to carry out the reaction, a brief description of how the reaction was run and how each product was isolated, purified, and characterized, and the identification and yield of the product(s).

Organizing the workbench - that is about as individual as it can possibly be. Take care to follow the OSHA guidelines if you are working in the US, and keep an eye out for Murphy's law. Pay attention when you are working to times when you almost break or almost drop something, and try to move things to avoid those problems.

And some beginner safety tips, although you didn't ask this one. When you start, make a practice of understanding the possible risks and remedies for every compound you are using. Know where to find the eyewash fountain, safety shower, and fire extinguisher. Keep everything clean - if you spill something, clean it up immediately, and be aware of places that other people might have spilled things. Bad accidents aren't usually caused by a single mistake, but by a whole series of little things neglected. Resting a hand on a bench, you accidentally press onto a glass sliver that wasn't cleaned up when somebody broke a beaker last week, and when you jerk your hand back you spill a flask of strong acid that shouldn't have been there into a sink full of water, which sprays up into your eyes because you had just taken off your safety glasses, and now that you can't see, you can't remember where the eyewash fountain is and when you make it to the safety shower you can't figure out how to turn it on...

Best of luck - you're entering a fun world!

[zuriel]

Thank you so much, fledarmus! The advice on organising the lab notebook is great. I just want to make sure that I have everything ready on the organisation front for when I start so as to avoid all the weeks of trial, error and "finding my own best system."

I'm starting in Ireland but I'm sure some OSHA guidelines will still apply - at least subtle variations of them will remain.

Do you have any advice for organising references? Would you advise the paper title, author and page number or else the DOI instead?

[fledarmus]

Heh - for references, whatever makes it easiest for you to find it again. You're going to need the entire reference anyway when you start to write up your book, so be sure it is enough to let you find the original work. If you've got one of those reference organizers like End Note, now would be a good time to figure out how to use it.

For most of the references, though, at least in the beginning, you will probably be following somebody else's procedure in your lab. Make sure you have these references as well, notebook number and page! You have no idea how frustrating it is to look at a reaction months later and think to yourself, "Now why did I do that?" And for reactions that you repeat from your own notebook, again, be sure to reference the notebook number and page, so you can compare later reactions to previous ones.

[curiouscat]

I second the advice about End Note. There's no excuse not to use a Refrence Manager software any more. If you can't afford EndNote there's tons of free ones: JabRef, BibTex, RefMan etc.

What works for me is to enter the Ref. the moment I download a Ref. ; oftentimes websites will have a free plugin that makes this a breeze. Link the pdf to the ref. citation; it's amazing how often you'll end up with duplicate papers on your hard-drive otherwise.

One trend I notice is more n more people using an electronic lab notebook. Not everyone's cup of tea but some researchers love it. Give it a shot.

[408]

I have a big folder of references, subcategorized by projects, I then name the reference for the reason I saved it
"bonding in...."
"how to make..."
"applications of..."

Back when I was more organized (first year of phd) I had a word table with two collumns "citation" and "when to cite"  Immeasurably helpful, but I got lazy and never updated it as I was reading references.

Never used reference software.  I had hundreds of refs before starting my phd and could not be bothered to go around spending time putting them all into software. 


Don't take any advice from me on organizing lab books.  Mine sucks.  Big time.  I have to publish soon after the experiment is completed because otherwise I have no idea what I have done.

Bench.  Wipe it down once and a while.  Don't just put paper towels down on top of mess and work on top of the paper towels.  Pisses off the safety people.

[zuriel]

Thanks everyone, keep the advice coming!

I know this might be a stupid question but how do you folks deal with organising compounds you've synthesised? Do you label the round bottomed flask which holds the final product and store it sealed or do you transfer the contents to a glass vial and label that instead? I know some final products can only be about <100mg strong after rotavap or whatever...not sure what's practical to do about those.

[fledarmus]

100 mg? For me, that much material would be a large scale synthesis! If I make more than 10 mg of most products, I am wasting material. Occasionally I will have an early intermediate that is a gram or more, but not often.

Don't let yourself get into the habit of storing products in round bottoms. They take up way too much space and are far too expensive and useful to be wasted on long term storage. Transfer the compounds to vials or bottles as soon as the last step of your purification, and do all your characterizations and weighing out materials for new reactions from there. Put paper labels on the vials with at the minimum a tare, a structure, and a full notebook reference number so even your professor, who never comes into the lab, will be able to identify the compound and find exactly how much is in the bottle and how it was made.

[408]

I work with things most people dislike working with, and small scale starts at 200 mg.  Most things I work with I have around half a gram of lying around.

Do you just do mass spec and NMR or?

But scale will depend on what sort of chem you do.

Yeah, don't be the guy who stores products in round bottoms.  No one likes that guy. 

[zuriel]

Thanks fledarmus! Your advice is great.

408 - I haven't started yet but I'm sure mass spec. and NMR are the typical characterisation techniques I'll be using. From reviewing past papers of the research group related to my project it seems that final product quantities range from between 40 mg - 180 mg.