Jul 17, 2010

Quick and easy flash column fix

Have u just broken the end of your favourite flash column? Is your glassblower over worked and won't get to your column for a few months?

Here is a quick and dirty fix for the end of your column. Simply find an appropriately sized disposable nalgene syringe (polypropylene types only, otherwise you will extract out nasty plasticisers, don't use the Terumo ones with the black plunger tips), cut the end off and CAREFULLY (with thick gloves) put the cut syringe on the end of the broken column. I do stress that u wear thick garden or oven gloves as that broken column will be mighty sharp and will slice through your hand/finger like butter if you slip. Make sure it's a snug fit - gentle heating of the syringe with a heat gun before application will help.

 The end product is a column that will fit any size test-tube. This trick is also handy for those columns that don't fit into the ends of small tubes.

Jun 1, 2010

The news of our death has been greatly exaggerated.

Although it has been a while since we have posted anything on the blog, I assure you, our select few followers that we are not dead, merely overworked. As we approach the middle of the year a number of us are approaching that penultimate point in our PhDs which requires our focus on the lab (and our boss has cracked the whip). I hope to continue blogging sporadically and hope that MSG will do the same when he has time. Keep checking in, we will hopefully be posting again soon.

In the meantime:

Apr 30, 2010

RBF Teaches: Drying solvents

So, when you do real chemistry and are able to use a manifold appropriately you can start to look at some genuinely difficult chemistry requiring dry conditions. The dry (or anhydrous) reaction is quite commonplace in synthetic labs and you will most likely come across it in your career, probably very early on. Once again, I suggest reading APOC as it details the use and setup of a manifold, the ways in which to perform anhydrous reactions and also how to dry solvents. I will hopefully be able to outline a few key steps in how we dry solvents in the lab at present and the few tricks I have picked up along the way.

  1. So to start you need to select your solvent and identify the ideal way of drying it. A great companion for any lab monkey is Purification of Laboratory Chemicals. This book will also show you ways in which to purify any other chemical in your lab inventory (some are not there but a lot are). So, find your solvent in this book and it is generally ideal to look for the rapid purification and drying methods. In our case we will use THF as an example.
  2. The next step is to set up your equipment so that the solvent stays dry. First, wash your glassware with acetone to remove any water and also some pure diethyl ether to remove any crud from the acetone.  DO THIS IN A HOOD and remove as much solvent from the glassware as possible. Next, I suggest putting your glassware (Distilation apparatus, collecting RBF etc.) in a hot oven overnight to ensure any solvent or water is well and truly gone. When you assemble the equipment the next day, take it out of the oven while hot, assemble and put under vacuum to ensure no condensation occurs (You may have to use another empty RBF to get vacuum ;)). Once dry and cool put the glassware under argon. You should also use a second RBF to use initially to catch the first fractions of the distilation as some impurities or lighter solvents can come through. Next, our book tells us a number of ways to dry a solvent but in our lab we use a still to distill this solvent. However, the use of a distilation bridge can just as easily work when you have no space for a still.
  3. The use of activated molecular sieves or some other innocuous dried material (e.g. KOH for TEA) can be placed in your dry collection flask to prevent the solvent becoming wet over time. It is also a good idea to grease the farthest part of all joints lightly with silica grease to ensure an airtight seal.
  4. Now it is time to dry our solvent. The drying agent used is usually sodium metal (either wire or pressed) and benzophenone as an indicator (benzophenone turns blue when complexed with Na in an atmosphere free of oxygen and water). The benzophenone undergoes a reaction with sodium to give non-volatile products that appear blue (due to the nature of the complex) when the solvent is dry and the atmosphere free of oxygen. If the solution is wet the sodium forms NaOH and takes the water out of solution as this salt. As an option another still can be set up to pre-dry the THF using CaH2. This prevents excess consumption of the sodium and benzophenone. N.B. Not a good idea to dry chlorinated solvents with sodium. Always make sure you read the procedure.
  5. Once you have your solvent you wish to dry, add your drying agent. In the case of sodium it is a good idea to have your solvent under argon and to crush the benzophenone onto the sodium. Try to be quick as the sodium can catch fire in the air, ensure you have a lot of the mineral oil on the sodium so that it is not exposed to air. Place the sodium with crushed benzophenone on it into the solvent and attach this flask to your distilation apparatus.
  6. Begin your distilation at the required temperature making sure you have a sufficient cooling system in place (i.e. if your solvent boils at lower temperatures then cool it well with ice water, but if it boils high or freezes at low temps then r.t. water is not a problem). Do not boil the still dry, this is dangerous, simply leave enough solvent to cover the drying agent completely.
  7. Once the distilation is complete, disconnect your collection flask ensuring that it is kept under argon, stopper (using a small amount of grease at the top of the neck) and place to one side.
  8. Quenching: Scary stuff if you don't do it right. Initially to quench something like CaH or Na you want to use something that will react with the agent but in a controlled way, for these two agents iPrOH (isopropyl alcohol) is a good choice. iPrOH is hindered and will not react quickly with the agent. First, cool the remaining solution on ice. Next slowly add iPrOH (add a decent amount, usually around 50-100mL) and allow to stir for 15min or so. Now you can add EtOH or MeOH (DO NOT ADD WATER) and continue to stir it on ice for a time. Eventually, you can start to add water dropwise to completely quench the solution but be mindful of the temperature of the solution and the development of bubbles. This is a warning that the quench is occuring and usually occurs quite rapidly. Then you can dispose of your waste in an appropriate waste drum and glory in your dry solvent.
I hope this helps you I will add some pics next time I see someone doing a distilation. Keep safe and don't blow yourselves up in the meantime. Read APOC and get the purification book (don't download it via torrent ;) ). Next I hope to write about schlenk lines or what we call a manifold.

Apr 29, 2010

Damn bureaucrats! Damn lab monkeys!

So lately, I have been super duper frustrated at life in the lab, so much so that I just couldn't stand to voice anything on this wonderful venting point. Anyway, it all started after I got back from a nice little holiday to Bali. The lab I came back to was a filthy mess and I had worked so damn hard to get it clean before I left that I was devastated to say the least. Anyway, the trend continued in a downward spiral and I have been getting more and more angry with the way things in the lab and around uni have been getting. More paperwork, more running around to get work done, more finxing things in the lab, more organising people to send chemicals or come and demo a new piece of lab equipment.

Anyway, I have been a good little gopher recently and have been rushing around trying to get things done but the amount of go between trying to get people to send items they said they would send or do things they said they would do has been so frustrating. I have decided that this all stems from the damn bureaucrats who need us to file 8 forms just to get one bottle of compound. I don't particularly like sitting behind a desk calling people or emailing them to get something done, it's time consuming and seems pointless. 

On a chemical side not unrelated, our CEM microwave has failed with a power supply error and the damn thing just came back with a replacement power supply. WTF!?!?! I have tried to run some reactions on the damn thing and it fails after 5min. Our water pumps that have lasted for years have all decided to trip all the fumehoods and die all at the same time. We have a brand new MPLC that we can't use and I really want to play with it :P. All in all what a crazy start to this semester......

And they have started up a repetition of Modern Talking again *GROAN*

Mar 31, 2010

It is SO holiday time!

Oh yeah! It's holiday time. That time in the year when you just CBF doing any work whatsoever and you just need a week or so off to get your act together. As it is I am sure some people have considered a holiday and others have taken them and I plan to do similarly.

I honestly cannot wait. I am plodding around the lab procrastinating any work and I just want to leave. Unfortunately, the bossman knows this and keeps giving me work to do. DAMN! Oh well, I will do what I can, then go and finish up the odd job or two when I get back with renewed vigour and fervour and such. Hooray! 

I must also mention that tomorrow is April Fool's Day. I haven't played a decent prank in a long time and I dearly wish I had a good one this year but, alas, I don't. I serious have no originality when it comes to a planned prank. I am pretty good at the spontaneous prank but the ones that take the planning just never work out as awesome as I had planned. You would think being in a place filled with chemicals and other things I could rustle up some cool pranks but I always think that people will hate me afterwards.If you have any ideas I am open to suggestions though.

Mar 26, 2010

Farewell old friends

Well, it has been a sad evening. Tonight we were saying goodbye to two members of the group, Z and W, who were both very valued members as well as friends. Regardless of the time we spent with these people I find it very difficult to accept that they are leaving. It really does seem that we never really got to know them as well as we could while at the same time know them very well and would be proud to call them both friends. On behalf of the group and our little online community I would dearly like to wish both of you very well in your future endeavours and hope that your yields be high and your Rfs separable. Tonight was, for me, a great night out, I have had such a great time with you both and I hope to continue our friendship outside of the lab and in person, rather than this cyberspace.

Hopefully, W will remember the small details of Rugby League that I tried to pass on and Z will land safely every time you are jumping out of those planes. Travel safely, enjoy the sights and sounds and make sure you take the time to smell the roses.

Good luck and farewell.

From MSG:
Just want to add some of my own words to this farewell. It's been awesome having both of you around, both as colleagues and as friends. One of the lasting legacies (at least until our cohort graduates) of W will definitely be infecting our brains with Modern Talking madness. And to A: thanks for letting us pick on you in the lab ;) and thanks for all the good times. In terms of chemistry, without your pioneering work I would not have been able to complete my total syntheses.

Hope you both enjoy your farewell presents. A: hope the Cook's Companion will bring you much joy in the kitchen for many days to come, and W, World Cup jokes aside, I really hope the gift brings you fond memories of your time in Australia every time you put the shirt on.

All the very best - MSG

Mar 11, 2010

Late nights in lab

So normally I am prety casual about staying back in the lab to finish some work. Most of the time I have done enough during the day to not really need to stay back and pound through another experiment. However, sometimes, when I am slack or stupid I find myself back in the lab in the dark pushing litres of solvent through a column. 

That was the story last night, but fortunately, for some reason a lot of my workmates were keen to work back late too. So, after the new girl T broke a few pieces of glassware and had had no luck with her experiment we decided it was time to crank up the angry oldskool neu-metal and have a bit of angry lab time.

Needless to say, it didn't last long, I was getting pestered to finish up because I was really late getting home and T and P both wanted to finish the reaction up. So, when my lift arrived it was pretty late and I was just finished with my column. 

I seriously hate late nights in the lab. To me there is always some sort of fear that if something goes wrong noone will be around to mop you up off the floor till the next morning. Hopefully, I won't have to go through that too many more times in my PhD.

Mar 9, 2010

RBF Teaches: Common Sense

Today, young ones, I thought I would go through a little thing I like to call common sense. Some of you have it, others (most) do not. It is something that can be developed however, by using that thing scientists call "the Brain". First, an explanation of why this is important (not the brain, common sense). 

Initially, when I started tutoring I taught 1st year science and engineering students very basic chemistry, mostly organic. However, a number of frequently asked questions came up. Most notably, "can I pour this down the sink?" and "which bin do I throw this in?". Well, after a while I started adding the answers to a short intro speech I gave at the start of the practical session. Unfortunately, people tend not to listen intently and I, admittedly, do ramble on occasion. So, in the hopes of saving some other poor sod the hassle, here we go.

  • Typically, if you wouldn't eat it or drink it normally, don't tip it down the sink. If in doubt, put it in a  waste container. Most typically, put it in the waste container labelled with your said waste.
  • Next, gloves always go in a toxic/hazardous waste bin simply because its safer for you and the cleaners (if you have them) and these things have a habit of coming around again. Don't whinge or ask why, just do it.
  • Washing you glassware - First, ask yourself, "am I going to use this for a dry (anhydrous) reaction?". If yes, then wash with water then acetone and dry it in the oven. If it's a burette for a titration, don't go washing it with acetone, rinse it with distilled water and then rinse it a couple of times with your solution. If you are going to use water in your reaction why the hell would you wash your flask with water, then acetone? Unless of course you see lumps of organic solids still stuck to the flask (unlikely).
  • If it stinks, keep it in the fumehood. Noone else wants a whiff. If you have to rotavap it do that on a rotavap that is isolated and preferable also in a hood. This includes gloves.
  • If you are doing an extraction, hold the stopper. If you hold the stopper pressure with build up, so release the pressure every so often. Once you are done, take the stopper off.
  • Use a funnel to pour liquids. This avoids spills *rolls eyes*.
  • Drying salts (MgSO4 NaSO4) are kept in the oven so they stay dry and therefore work more efficiently. Don't take them out and walk them back to your fume hood. Take a container or test tube, get some drying salt and then take it back.
  • When you take a flask off the rotavap, occassionally it sticks, a slight, gentle twist will usually get it off without too much effort and you won't have broken your flask on the water bath. Oh and it's usually a good idea to make sure the vacuum is released properly too.
  • Put things back where they belong. It makes it easier to find when you are looking for it next time.
  • Wear gloves and lab coat at all times in the lab, that will save you wondering when you should and shouldn't need gloves.
  • Wash your hands, even with gloves you don't want to risk it. Imagine going to the toilet and putting all those lab goodies on to your goodies. Not so goody.
  • If you break some glassware, use a dustpan to clean it up so that you don't get cut with contaminated glass.
  • Only tighten clamps to the point at which the glassware stops moving, any more is redundant and will probably result in breakages.
That is probably a little too much and some a little too obvious, but seriously, all of these things I have been asked or witnessed. Take some time, think, pray, then think again, then do. That should  eliminate some of the basic mistakes you will make until you are reach the super 1337 levels. Even then we are all human and we can just have bad days. There are most likely a dozen other things that I haven't gone through but I will put them in when I think of them.

Mar 3, 2010

Lab Duties

So, after one great cleanup and me and MSG getting fed up with the standard (or lack thereof) of the lab, we decided to go nuts and purge the lab of its hopeless situation. I was sick of finding items missing or moved and things left messed up because someone couldn't find something so decided to toss the place just to find it and then leave it as it was because it was someone elses fault that they had to toss the place.

So, after a nice little hold hands session in which we all decided we would keep the lab in order and assign each other duties (some of which were not desireable but had to be done) we came up with a few jobs that people in the lab were responsible for.

  1. Solvents - Someone to keep a nice level of distilled solvents on the shelves so that we didn't run out and save a bit of time for everyone else in the lab.
  2. Stock manager - Responsible for keeping lab supplies at a manageable level (e.g. gloves, paper towel), mainly consumables but this means one person that knows where stuff is and can get it without tearing the place apart.
  3. Lab Nanny/Handyman - Responsible for general upkeep and running of the lab. Keep benches clean, keep glassware where it belongs, get liq N2 in the morning and most importantly look after any lab equipment (e.g. microwave, MPLC, fridges) and fix it if it needs fixing)
  4. Stills - Someone to look after the solvent stills (THF and DCM). Keep them clean (every few months) and dry and not rooted when someone forgets about them. 
We figured this was the best way to go. Everyone has a responsibility, everyone knows their job and knows who to ask when they need something. Also, everyone knows who to blame when things go awry and therefore keep that person attentive on their job. So, we are trialing this for now and we will see how it goes, there are still a few glassware hoarders in the lab *puts own hand up* but it's getting much better.

Onward, upward and all that crap.

Mar 1, 2010

Damn I hate undergrads sometimes

So today it is raining and I was up late last night writing a paper for pblication. I slept in this morning and after slogging it out in chock-a-block traffic finally made it to uni. I rolled down the road where I usually park only to find my parking spots are all taken, and after doing a full lap find that there are no parking spots at all in the university. Stupid undergrads. I spose I should have remembered it was their first day back at uni and that most of them, especially the noobs would all be coming in to classes. And, because they are all super soft would all drive in rather than be shoved onto a bus full of other noobs lest they all be grouped in the sam noob category, because nobody wants to be called similar to someone else. Heaven forbid they lose their individuality. 

Anyway, there was only really one thing for it. I couldn't just drive home. I have work to do, as much as I loathe it sometimes. No, I had to get in to work, be it late or whatever. So, I drove to the local shopping centre, parked and caught the noob bus. Which, I may have expressed earlier, also irks me to no end. It was the same b.s. people pushing to get into the bus first. Which always amuses and frustrates me. It's like they can't stand to be outside one second longer after standing outside for 15-30min previously. Anyway, after waiting patiently in a line which was more like a cone and not really like a line at all, I step on the bus and find a completely empty seat straight away. I have no idea what the noobs are pushing for, but next time I might throw a few elbows in just to see whose nose gets broken. It might be entertaining, most of them only come up to about my elbows anyway. 
Anyway, if the same happens tomorrow I will take a picture and show just how stupid these people really are. That way my words really aren't that meaningless. Then again, if it happens again tomorrow, I will be the one too stupid to wake up early and get a (ludicrously overpriced) parking spot.

Feb 26, 2010

MPLC vs Flash Chromatography

Yesterday an old argument reemerged in the lab. On discussing the use of an auto-column and the ways in which we can implement it in the lab and the ways in which time will be saved one of us mentioned that an auto-column MPLC would never be as good as a good ol' hand worked flash column. 

Well, this discussion, I am sure, has been brought up in a number of scientific circles since the emergence of these new-fangled contraptions. Most notably, the Biotage Isolera (Image 1) and the Teledyne CombiFlash (Image 2) as well as the Kyle Finchsigmate's MPLC for the people (Image 3). But, are they as good as the good ol' hand column.

Well, here are the pros and cons that I can think of and I am sure some equally chemically minded person will come through with many more.

  • Set it up and walk away (do another experiment in the time it takes to run)
  • Set up a solvent gradient to allow for greater separation.
  • In the case of the Industrial machines, use of software to duplicate Rf separation from TLC plates is reportedly possible.
  • Ready-made cartridge columns mean you don't have to worry about packing your column.
  • Loading the column requires little to no time and doesn't require you to reach high up in the hood under the sash and try load your column without disturbing the silica.
  • Small scale to large scale, it doesn't matter.
  • Auto collection of samples with ELSD tech to let you know where your compounds are and in which fractions.
  • Reusable columns (simply flush with methanol)
  • Reverse phase simply requires a different column pack.
  • Column can be set to not collect until it identifies a compound.
  • Can be networked and allow for notification of completion.
  • Higher pressure means faster run columns.
  • Some setup time required to start the column.(Probably simply comes with time and use of the machine the user should get faster.)
  • Works better with small Rf separations rather than large.
  • ELSD doesn't work without a chromaphore in your compound (duh).
  • TLC mimic tech doesn't always work.
  • Churns through a lot of solvent (but can be optimized with Isolera "Gradient Optimization").
  • Any blockage may cause detrimental effects and lots-o-mess. 
  • One column at a time for the basic apparatus and this can cause lab fights (grrr)
  • Someone's gotta look after the bloody thing or else it'll turn to sh!t.
Ol' Faithful
  • Usually able to be run fairly quickly once you are proficient.
  • Can usually get a good separation especially with large Rf differences
  • Close to hand and no wait time in the lab.
  • Can be relaxing and give you some time to reflect on some of the finer points in your thesis.

  • Time consuming running a big column and no free hands to do other work.
  • Silica is often not recycled and discarded.
  • TLCing your fractions only to find it hasn't come off yet is such a biatch.
  • No automatically made solvent gradients means you pretty much make up a solution of a certain polarity and run it like that.
  • Loose silica is bad for your lungs (like Cancer bad)
  • Loading columns can be tedious
  • Packing columns can be tedious
  • Exploding glass columns, rare but can happen
  • Ground joints on goose necks fusing to the joint on the column, so annoying
  • Tubes flying off from too much pressure

Feb 23, 2010

What the Heck...

I've always found ACIEE abstracts fascinating, not just because they describe exciting research but because they always have some quirky (and sometimes really lame) one-liners. For example this one (DOI 10.1002/anie.200906818):

I always thought "What the Heck" was my joke... apparently it was also one of Professor Weinreb's too. That's an impressive looking compound too, and I'll certainly take a closer look at this once I put this reduction/oxidation on.

Feb 18, 2010

Pushing hard

Well, over the last week or so I have been struggling to form this damn strecker product on a particularly bitchy aldehyde (read F@rking HORRIBLE). Anyway, after failing miserably numerous times I have decided to modify my aldehyde to make it a bit more stable and possibly allow me to follow some literature procedure a bit more closely.

Unfortunately, this means PCC (pyridinium chlorochromate) yummy! and the boss wants me to use this due to the literature. I am seriously not cool with the whole thing. I mean seriously, Ley's oxidation was working quite well on the less stable compound and is a bit less nasty. But anyway, I have to admire the simplicity in setting up a reaction of this sort. Reminds me of cooking a little bit.

Not that I taste my reaction or anything but I mean the whole way it is just like measure out the ingredients (Alcohol, Molecular sieves, Dry DCM, PCC) and then bung them all together, sonicate and stir. There is barely any fussing around, just have to be careful weighing out the PCC and then you just spoon it into the stirred solution of sieves and alcohol in DCM (~0.05-.25M).

The workup is a bit of a bitch cuz you have all that nasty nasty floating around but you really just have to add some silica and some Ether and filter through some silica, wash it and then move on to column or just take it through to the next step. Pretty nice, but at the same time kinda deadly, like a portugese man of war.

Anyway, time to "Get in the Lab". Wooh! Gotta love slave labor as a PhD student. $4/hr is a totally amazing pay rate! (SARCASM!)

Feb 11, 2010

Corrosives cabinet = Clean'd

Well, it cost me some time and some lungs but after finally getting a good gas mask I was able to really get in there and clean out the corrosives cabinet. Mainly because of the stupid inventory we had to do. Anyway, the cabinet is clean but all the bottles in the cabinet are really not. They still stink of whatever the crap it was that spilt in there. I tried cleaning them off but the labels are basted in the stuff and probably need to be fully removed and replaced for there to be any improvement. (I am so not doing that btw)

The cabinet looks a hell of a lot better now though and I am pleased with the tidiness inside now. All the bottles are stacked neatly according to height and size and there should be no problems with retrieving something from that cabinet. That said, there is probably some sort of health risk by just going near the cabinet but we can't do anything about that right now really. So, today it's continuing on with the inventory, moving into the flammables and then the fridge (which also smells). WOO! More death! 

Feb 5, 2010

Why we don't like Arkivoc, an oldy but a goody.

Today my good friend Labchimp messaged me a nice little reminder of how crap some free publishers are when you don't have decent peer review.


Say hello to two new pentavalent carbon compounds. So awesome. NOT!

Feb 4, 2010

Corrosives cabinet

Well today P, MSG and me as well as our new PhD student attempted a rescue of the destroyed corrosives cabinet that we use for storing our acids. As we speak I feel I have inhaled about a litre of the brown liquid that coats every inch of that damn cabinet. The stuff is everywhere, and its all because some stupid foreign exchange student broke a goddamn bottle of bromine or something in there and didn't tell us about it. We found it cracked and leaking about 3 months after she left.

So P and MSG finally wrangled me into helping them pull the contents of the cabinet and then relabel and seal them all with parafilm. So after clearing the top shelf we decided that starting this at 3pm was probably a bad idea but we kept on and I decided to wipe out the cabinet. The paper towel was covered in a brown/orange liquid and the more I wiped it out the more there seemed to be.

So now, we have a terribly abused corrosive cabinet and its still not clean. The stuff just won't stop oozing from the pores of the cabinet. We are pretty much calling it a write-off I think. But now I feel like shit.

Jan 29, 2010

Beds in the office

I have always been a firm believer in having beds at the university somewhere. Just somewhere you can go to have a quiet comfortable nap. Like right now I am suffering from a severe food coma and need a nap so I would go have a nice lie down for 30min or so just to catch up and then be ready to go again. 

I know this has been proposed before and one company takes it to the extreme. But seriously, I get tired after lunch and would love a nap. I think there ought to be some more sleep time factored into work. Although, this blog is sending me to sleep right now. Better just to get back in the lab and clean up. Friday is so not fun, until you leave.

Jan 27, 2010

Australia Day = Awesome

So yesterday was Australia Day. Normally, I wouldn't really have anything grand planned for it but this year it was different. This year it was proposed that the back hill in my mum's house would be perfect for a slide. Couple this with a pool and you have some wet and wild fun just waiting to be had. So after searching for hours trying to find a suitable sheet of plastic for a slide we came across a giant tarp in mum's garage, some tent pegs and 2 or 3 bottles of $1 dish washing liquid. Then it was just add water (and beer). We set up a sprinkler hose down the length of the tarp, pumped some tank water through it and then it was game on.

Here is how to have a blast on Aussie Day:
Crack a beer, drink half, down the slide, drink some more, down the slide again, drink, then jump in the pool. Rinse and repeat. The BBQ was fired up and some well marinated sausages and onions were fried up with plenty more beer and the party was definitely in full swing. Some rest time after eating, have a chat over beer then watching some cricket in the street out the front of the house. PERFECT AUSTRALIA DAY!

You can't ask for a better set up - public holiday on a tuesday where you are almost expected to be shady at work the next day. Lots of sun, lots of beer and tons of fun.

Any of you out there keen to share your day post it up, I'm keen for some more ideas for next year.

Jan 25, 2010

Super ASAP

Now THIS is what I call ASAP (ACIEE paper on ent-Hyperforin):

Jan 23, 2010

RBF Teaches: Lab Safety

While it really is impossible to go through all aspects of lab safety in the space of one short blog I still find that it is indeed quite necessary, especially when you lay out a number of reaction procedures initially and direct young chemists to your site for demonstrations and support on fundamentals on lab life. I also was greatly inspired by excimer and his fellows and followers at CBC who recently compiled a great topic on lab safety which ranged through various points and all of them very valid. So, for those of you who want a straightforward rundown of exactly what was covered in that blog I hope that you will find that here. Along with (hopefully) a few pointers from MSG who, IMHO, is perhaps one of the most pendantic, but also the most safe and efficient chemists I know [MSG edit: why thank you ;)]. So let's get started.

  1. Cleanliness is next to godliness in the lab - In my opinion it is vital that you have a clean area before you start work, this will prevent you accidentally bumping over glassware, spilling solutions and give you a good idea just what things are needed in the hood for the reaction to begin. [MSG edit: the best time to clean up is when you're waiting for your reaction to finish (rather than heading straight for the next free computer to play restaurant city on facebook). Clean up whatever glassware and equipment you used and any mess you've made. Then read ahead and prepare whatever pieces of glassware, reagents and equipment you need for your work up. This will help you save time (so you can go home and play restaurant city), get your experiment to run more smoothly (which means better marks), and being organised means less likely to rush and get into accidents.]
  2. Preparation is key -Before you start, before you even enter the lab, know what you are doing and know it well. It is ok to have your reaction procedure with you while you are doing the experiment but what is more important is knowing what each step means in terms of the reaction (e.g. why do you add the water slowly, to quench? so it doesn't explode in your face! That's why!). If you are planning on scaling up a reaction then remember that the bad things that can happen on a small scale can increase exponentially on large scale.
  3. Always do your MSDS - this is important to understand what you are working with and although it is on an industrial scale and a lot of the time not relevant to lab scale it still outlines the dangers of chemicals, sometimes it may be wrong or leave out important facts. [MSG edit: puuuhlease use the fumehoods!]
  4. Lab safety equipment is vital - I know it can get hot or the goggles can hurt your nose but imagine losing your eye because a piece of glassware explodes or you spill a solution of corrosive liquid on you and the only barrier is your shirt. Therefore, Labcoat, Goggles and Gloves are all VITAL! [MSG edit: Ok guys all this gear is not just for show - you've gotta be a complete idiot to think you're invulnerable coz you're not! From most important to least important, I'd say it goes goggles, enclosed shoes, gloves, labcoat. REMEMBER, you can be the safest chemist in the world, but you still need to protect yourself against accidents caused by people around you!]
  5. Check your equipment - Star cracks in RBFs are a good one to look out for (implosion from high vac is not something you want to experience). Make sure your heater stirrer is working (this will save time if it isn't and you have to rearrange your whole experiment). Blocked needles can lead to big problems (don't force a syring if it isn't moving, you will probably end up with a facefull of reagent).
  6. Know your exits, showers, eye wash stations and fire extinguishers - May sound simple but the nearest shower may save both your skin and your life, just pray it never comes to that. Make sure before you use any lab that you know where they are so that you can find them with your eyes closed...literally!
  7. Never work alone - This is one that is often not obeyed by organic chemists. It is never wise to be in a lab on your own. That other person in the lab may just be the only one capable of pulling your arse out of a really bad situation. If they aren't there and things go wrong start praying.
  8. Ask! - If you haven't done a procedure before and you are unsure, a second opinion is great to have. Whether its an experienced post-doc or even a co-worker to just watch over while you do it, it is better to have someone else there if you are not confident.
  9. Don't Rush - The expression haste makes waste is often used and seldom heard. If you are rushing an experiment to get home on time you are more likely to break something and cause yourself more time and potential danger. Take it slow and get it right and don't feel that you are too slow, there is no such thing in chemistry. [MSG edit: In fact, if you rush, stuff up the experiment (which usually happens), you then need to repeat the experiment, which ends up taking up considerably more time than if you did it slowly but properly the first time around. 'Slow and steady wins the race'.]
  10. Documentation - Although it really isn't a safety issue, taking notes and making sure every step is documented is very important. It may be that another researcher will need your notes to do the same experiment, or you might one day want to publish your procedure, or if you make a mistake, you may be able to go back and see where you went wrong. Documentation people is what makes you a scientist! [MSG edit: Despite how hard you convince yourself, you won't remember what you did in the lab the day before (or even 3 hours before). Document what you did when you have spare time, for example, while waiting for a reaction to complete or while waiting for rotary evaporation to finish.]
  11. Checklist - This can be similar to your documentation but more of a mental thing. Go back over these points - do you know what you are doing? What can go wrong? What to do if it does go wrong? Make sure you can answer these questions before you start as well as while you are doing the experiment. You might feel indestructible but believe me you are flesh and blood and both of those can be peeled away with a spill of t-BuLi.
  12. Focus - stay aware of the experiment while you are running it. If you can leave it that is fine but remember it is there and what can go wrong and don't lose your focus on what you are doing, if something is bothering you fix it before you proceed. Don't get cocky. [MSG edit: Concentrate on what you're doing. If you're focused on your job, you're much less likely to be caught napping and panicking when accidents do happen.]
I know it all sounds very dramatic, and it kind of is, but remember its your life and your body on the line every day. It may sound like a dull job but the risks are there for the next careless person to find. (We really should get paid more) Get lots of sleep, stay focussed even if it is a boring column (these can shatter in your face) and at the end of the day always be wary of liquid oxygen in your cold trap.

[MSG edit: I don't know if you kinda got my drift, but safety and experimental success (at least in the undergraduate lab where every experiment is supposed to work) are strongly correlated. If you want good marks, then you want your experiment to go well, which means that you need to be prepared, focused, ask for help when needed etc. These are precisely the same sort of things you do in order to practice lab safety, so even if you don't care about your health or your colleagues', at least do the above for the sake of your own marks!]

Jan 22, 2010

I need sleep

I am struggling with the weather here in Oz, yes I'm Aussie but I still hate going to sleep covered in sweat. I haven't found much bearing in the whole drink warm milk thing, it's summer so I don't want to be drinking warm things. I wouldn't mind testing out the whole Turkey thing, tryptamines are pretty cool but I am still a student and affording all that turkey right now just isn't possible. Which brings me to the potential for drugs, I am totally not a druggo and I really haven't done anything hardcore at all, but there is something mildly alluring about doxylamine that makes me curious on whether I could possibly synthesise it safely in the lab.... I am pretty sure the answer is I could synthesise it but would I be willing to ingest it afterwards? No, I don't think so, not with the all the other stuff that might be in there.

So I go now to delve into scifinder. Maybe that will put me to sleep, but then again, maybe not.

Jan 20, 2010

More stink


Once more I have soiled the lab. I was doing my Barton decarboxylation once again and this time decided to show someone from another group how bad t-BuSH smells. I opened up my small plastic cylinder that I use for smelly syringes and the whole lab cleared out within 30secs. Thiols are so totally awesome.

Anyway, as promised, here are the pics of the setup. Its very simple. Large RBF, condenser, hot plate, oil bath, 240W lamp and retort stand. Argon feed in the top (i usually replace this line after the experiment as there is always some thiol stench in it, plus I vac the argon line to purge the system.) as well as the syringe with the acid chloride in it.

Voila, decarboxylating in progress.

Jan 19, 2010

Wooo free stuff

MSG, Thujone, P and I found ourselves jostling with a number of other fellow scientists in a biology lab that was closing down yesterday. All of us trying to find the best free stuff in their unfortunate lab. We came back with a mighty haul. After frantically scrambling over each other to get at the goodies (constantly wary of the Sodium azide jar complete with cracked lid) we raked in a large number of chemicals that were either in new packets, running low in our lab, or were known to cost a pretty penny.

Unfortunately, we missed out on the small Uranium sample that was up for grabs by mere seconds (this remains a sore point with Thujone). However, a number of cadmium compounds, some silver nitrate, a fresh 2.5L bottle of chloroform among other things, made up well over $2,000 worth of chemicals. The best part of all of it is that the lab was (as I mentioned previously) a biological one and I feel quite satisfied knowing I made them pay through the nose for once. And they provided me with a new 300W lamp for the lab which should be good for some of my photo-initiated reactions.

Take that Biology!

Jan 15, 2010

I hate patents

I have been slaving over these incomprehensible peices of crud for days. I seriously hate them with a violent passion. Nothing is ever straight forward and the crappy USPTO puts their patents up as quicktime images for crying out loud. Major fail. This means going to freepatentsonline.com and finding it there because SciFinder just links to the god awful USPTO website. Give me PDF or give me death. At least it isn't in Chinese [1].

Meanwhile, in the lab I have been synthesising more starting materials. On monday/tuesday I will be repeating the Barton decarboxylation so hopefully I will remember to bring my camera. Everything here is back in full swing. Even W is in the lab now and then, turning his pump on as well as the argon. It's good he enjoys a bit of time away from his calculations. I know I would. Those things are damn hard to understand.

The talk of the office is also hilarious, a co-worker was recently found to have been using her full name as a password. It was by chance that we found out, someone asked randomly if she did that and her suspect reply was enough to warrant an investigation which led to the discovery of the fact. Subsequently the password was changed after many hours of laughter at their expense.

Soon to come are some interesting experiments, we hope. A number of reactions that require a bit of technique and some clever thinking will hopefully be posted. Not by me cuz that's not my style, but hopefully MSG or Thujone will have a nice treat for you guys out there. I will be looking at posting some more RBF teaches soon which will hopefully help the undergrads out a bit as well as the tutors who teach them.

[1] and I finally get it translated only to find it isn't what I was after in the first place. Hooray for the little wanker who thought he was really smart by obscuring patents. I hope you are really proud of yourself. One giant clap for you buddy.

Jan 12, 2010

Can you have Mi Goreng with SOUP?

As you know, instant noodles are an essential part of grad students' diets. One particular favourite of ours is Indomie's Mi Goreng. Not only does it taste absolutely awesome, but it is unbelievably cheap, costing about $0.30 AUD per packet.

Mi goreng is malaysian for fried noodles. This makes it different from many other instant noodle brands in that you simply mix the seasoning and the flavour sachets with the moist but drained noodles. Unfortunately, SOME people in our group prefer to eat these awesome noodles in soup.

So if you've had these noodles before, it's time to settle this issue once and for all:


Hands up

Ok, so I have been thinking lately that a number of journals are becoming more electrosavvy and as such are including a nice little picture in the table of contents. And, while its not for lack of trying, a lot of our fellow researchers are struggling to produce a nice picture that truly represents the experiment and captures the reader's attention.

In the past there have been some really funny ones and I have no problem with, graphical abstracts that display the general reaction detailed within the paper, but to me something is really lacking. There is no pizzaz, no wow factor, no HOLY SH!T to the whole graphical abstract. I myself have struggled to produce a half decent picture for the intended use. So I feel that it is time someone steps up to the challenge and in doing so show the organic synthesis community how it's done. There may even be a business in it guys, design jobs are few and far between now and someone with a knowledge of both synthesis and graphic design may just find a niche market.

I have to admit though I have seen these graphical abstracts improving, combining pictures taken with cameras and some nice graphics are becoming more prevalent and some of the biochem papers have some nice rendered images but there must be something out there that can better this:

Also, if you can find any good ones guys let me know and I will post them up!

This one is so cool, even if it is biology! Super Macrocycles

And here is one that isn't the least bit confusing.... (Sarcasm much?)

 Now this one is getting there. I looked at it for more than a second so it caught my interest even though I don't really care about the topic.

Jan 11, 2010

Microwave Chemistry

I just thought I would put down a few lines on some microwave chemistry and hopefully gain some outside views as well. This all comes from a paper that my old boss recently published in Aust. J. Chem. regarding some pretty neat synthesis of quinolones and napthyridones by using microwave irradiation to replace the original FVT (flash vacuum thermolysis) methods.

As an undergrad I spent my honours year pounding on the CEM Discover microwave unit and I am so glad I did. The reactions I did in the microwave (when they worked) were so fast and I did so many more reactions in so little time that it really didn't seem fair on the other poor undergrads, like MSG, who had to do the good organic stuff in the fume hood. I kind of regret it too as I didn't really learn all that much in terms of lab technique among other things. However, I still love to use the microwave as much as I can, which is rarely now :(.

The use of the microwave for reactions such as simple esterification of carboxylic acids is a good example of MAOS (microwave assissted organic synthesis). The reaction takes no time at all and workup is no problem. But sometimes you just can't get the results you want from microwave reactions either. For example, some researchers in the past use trusty old kitchen microwaves for their MAOS and unfortunately this made replication of their experiments quite difficult in other labs. The generation of hotspots in the rotating microwave ovens is virtually limited in units like the CEM but at the same time the CEM is prone to generating a lot of heat in a short amount of time and you can really nuke a reaction and expensive materials if you aren't careful.

Another interesting part of the CEM discover microwave is the nitrogen inlet valve for "power cooling" the concept behind this being that if you cool the reaction while irradiating it you can put more microwave energy (in effect a greater vibration of the molecules in the reaction chamber) into the reaction and therefore speed the reaction up. However, in my experience the heat of the reaction was required to have the reaction proceed. Anyway, I am keen to have any outside input made as to how anyone else uses the microwave for reactions as this was deemed to be "the way of the future" in organic chemistry but we are yet to see the full implement of microwave reactions in our lab and I sure haven't been reading all that many journals with MAOS included.

Jan 7, 2010

Bringing back the stink

So today I am completing the final step in my nice little Barton decarboxylation. For any of you familiar with the reaction it is quite nifty and basically serves as a relatively straightforward method to remove carboxylic acid function from a compound. A quick search of our favourite cheat site OCP will show you that there are a couple of methods of performing the reaction either via a stannane or via the pyrithione. In both cases however a considerably stinky reaction ensues and if you are not careful (as I am often not) you could easily end up being the most hated member of your group.

I personally use the pyrithione method as I am really not fond of tin and the materials are quite cheap. However, in the reaction, which I will post a quite procedure for after the post ( I like to babble first), the when the radical of the pyrithione is formed the use of t-BuSH as a trapping reagent often causes quite a few groans from the rest of the lab. What's worse is that one time I was working up a courageous large scale reaction (>4g), which required a seperatory funnel and I inadvertently shook it too hard and ended up cracking the funnel on the fume hood door and spilling the contents all over myself. Needless to say I stripped off the lab coat but the smelly damage was done. I had to catch the bus home and I think I attracted a few admirers on the way. (By that I mean they followed me home waving flaming brands and tried to offer me a pitchfork, which I didn't need so I declined).

But seeing as though this is a chemistry blog and I feel like the few readers we have so far read this blog for some form of enlightenment I will share with you the procedure I follow. It is broken up into parts you need to prepare.


50mL RBF, inert atmosphere 

To a suspension of dry carboxylic acid (R-COOH, 2g) in anhydrous DCM (10mL) at room temperature is slowly added oxalyl chloride (1.5eq). The suspension is left to stir for ~30min until solution turns clear. The solvent is removed in vacuo ~40tor is usually good then 0tor for another 10min to ensure everything is evaporated. The white solid is then purged with inert atmosphere and anhydrous benzene (10mL) is added.


250mL RBF, reflux condenser, inert atmosphere

In a 250mL RBF is added ~1-1.1eq of dry and recrystalised 2-mercaptopyridine N-oxide sodium salt (you can use the non-salted version but I find the salt works better, this is also known as Omadine and apparently can be found in anti-dandruff shampoo). To this salt is also added ~2eq (~2mL) t-BuSH (the stink factor), 30mL of benzene and a catalytic amount of DMAP. The omadine should be shielded from light until you are ready to perform the reaction. Once you have your acid chloride solution prepared you can begin to reflux the solution and then irradiate with 250W tungsten light a short time before you begin to add the acid chloride.

Addition of acid chloride is a personal preference. In some instances when you have this under inert atmosphere it is probably a good idea to have a sulphuric acid bubbler attached to the system to prevent the stink from entering your argon lines. Also, I add the acid chloride via a syringe  in the top of the condenser and try to drip the solution into the soup without getting it on the sides of the condenser. Another method would be to use a dropping funnel but who really wants to clean up all that stinky glassware at the end of it all.

Anyway, dropwise addition of the acid chloride - you don't want to add it too fast or the formation of gas can cause a stink explosion- over about 20min. Follow this with a further 1hr irradiated reflux.

Cool the solution in an ice water bath and quench the stink with 10-15mL calcium hypochlorite sat. soln. added in portions to the vigourously stirring soup. Then extract the solution with 25mL ether and wash with 3x25mL water. Back extract the water with a further 25mL ether and dry the combined extracts with MgSO4. Run the decarboxylated product down a column and voila. You have made a mess a  lot of stink and some decarboxylated product. YAY!

Jan 5, 2010

Welcome 2010

Well it is definitely the new year, I know this because the boss is back and everything is in full flow again. The lab is humming with the dulcet sounds of high-vac pumps and the clink of clean glassware. Yesterday P, MSG and I (I mostly watched) decided that the THF still had looked like s#!t long enough and we should give it a clean.

What a mission that whole ordeal was, so much benzophenone and sodium crud settled at the bottom. We didn't know whether it would all react when we were adding some EtOH to quench it. We added it slowly but we weren't sure whether after adding small bits at a time, if there was a layer of crud covering a chunk of sodium, we would end up with a lot of EtOH and the sodium finally being exposed to the crud and the whole still going up in a giant bubbling ball of crud. We got lucky I spose but after we decided it was all quenched the crud was all clumped together making it nigh on impossible to simply tip it out into a waste bottle. After a lot of poking (with our patented lab-chopstick) P finally got the crud out and we could wash out the rest.

So that was fun, but now I find that to start up my reactions again I need to distill all my solvents (I say found out but deep down I knew). If there is one thing that makes me reluctant to get in the lab its the fact that I have to take around 2 hours just to set up for the reaction. Mind you this is large scale here and the solvents are definitely not the nicest. I have to distill t-butyl thiol and benzene and if they don't kill me then the rest of the guys in the lab will for the smell that always comes from it regardless of how careful I am. The tiniest drop inadvertently spilt anywhere causes an immediate reaction with someone else in the lab.

So here I go back to the lab, hope that my liver, which took a beating over the holidays, doesn't give up the ghost.