Friday, December 26, 2008

Career plans

Not surprisingly, most of Curly Arrows readers are early career chemists, predominantly PhD students and Post Docs. So although subjects such as publications, H index, impact factors etc. have been beaten to death elsewhere I thought I'd do a brief post on the topic here because it is very important for your career prospects that you start thinking of these things early on. When in the past I have been presented with a pile of job applications the first things I (and others) look at are:
a) Name of applicant and of recent supervisors (to see if I know any of them)
b) Publication list
So since 95% of the time I don't know the people the applications fate is determined in the course of 1 minute based on your publication list.
It sounds unreasonable but this is how you quickly eliminate 75% of the applicants. If you make it through the first screen then people actually sit down and read your application in detail, request references etc.
So if you want to get the dream job work hard and publish lots of papers. It doesn't have to be Nature papers the main thing is that your look productive (journals with impact factor >2 are fine for a synthetic organic chemist).
Unfortunately, too many supervisors will give you dead end piece of shite projects that are destined for the bin. Check your prospective boss out. How much does he publish, in what journals, talk to former and current students in the group etc. Also worth considering is whether the group publish papers with alphabetical author lists or not. The alphabetical approach can really screw your career in a fair few countries. When you apply for grants in Denmark they generally look for first and last authorship to determine your project input but also at which journals you published in to estimate the quality/impact of the work.
Having a decent track record and publication list is going to get you through the first screening round. However, to make it to the interview good references and relevant skills will obviously be very important. So think about it and start planning your career early on. D!

Tuesday, December 16, 2008

NMR Tube Cleaner Part 2

Some time ago I had a post about the amazing NMR tube cleaner. I love this piece of equipment and use it regularly. However, as some readers pointed out some people are remarkably good at breaking these things (repeatedly!). Where I work now we have a workshop and the guys there create the most amazing gear for us including an almost unbreakable NMR tube cleaner. It's made from hard plastic and metal and isn't affected by organic solvents. So if you are fortunate enough to also have access to a workshop you may consider ordering one of these beauties. D!

Sunday, December 14, 2008

What is a liquid?

I recently had dinner with some chemists and after a bit of red wine the question "What is a liquid?" popped up. The reason the question popped up is the gas sulfur hexaflouride. I had never heard of this stuff before but allegedly you can float solid objects on top of it. Intuitively, I would say that if a ship can sail in it it's a liquid but things clearly aren't that simple. There's quite a few videos with this stuff on the web. In this particular video they float an object on some SF6 in a fish tank (I'm assuming the video is not a hoax). So what is the definition of a gas/liquid? Obviously it' a density thing. Did anyone out there pay attention when they had physical chemistry and would they care to explain it to a simple preparative chemist? Also what is the least dense liquid out there? Besides pentane (0.626 g/cm3) I can't come up with much that has a density below 0.7. D!

Wednesday, November 05, 2008

What is Click Chemistry?

2001 was a big year for K.B. Sharpless. He received the coveted Nobel Prize in Chemistry and introduced the concept Click Chemistry. I had the great pleasure of meeting him in 2001 and his lecture on Click Chemistry completely changed the way I think about chemistry.
I do not do Click Chemistry or even Click Reactions but I like the overall concept and I fulfil about half of the Click Chemistry commandments in my daily research.
Most chemists have no idea what Click Chemistry really is and think making a triazole makes you a Click Chemist. This is incorrect and many papers are published with Click Chemistry in the title even though it isn't Click Chemistry! Click Chemistry is not a specific reaction it is a concept. Here's a condensed version of rules you have to fulfil to become a Click Chemist.:
The reaction must be:
(1) modular
(2) wide in scope
(3) give very high yields
(4) generate only inoffensive byproducts
(5) stereopecific
The process must be:
(6) simple reaction conditions
(7) readily available starting materials and reagents
(8) use no solvent or a solvent that is benign or easily removed
(9) simple product isolation by non-chromatographic methods
Sharpless published an excellent paper introducing the concept
Click Chemistry: Diverse Chemical Function from a Few Good Reactions, H.C. Kolb, M.G. Finn and K.B. Sharpless, Angew. Chem. Int. Ed., 2001, 40, pp. 2004-2021.

Tuesday, November 04, 2008

Curly Arrow - Established 18th October 2006

Curly Arrow has now been in business for two years. Things have been a bit random the last year primarily due to shifting between jobs and continents. Let's hope things will become a bit more structured in the coming year. Thanks to all bloggers for comments, endless enthusiasm and emails.
The year 2006-2007 all the top 10 visitors were from the US or UK. This year things are a bit different with Australia and Canada making an entry at 5th and 7th place and the first company (GSK) has made it on the list at 8th place. D!
From 9 November 2007 to 4th November 2008
Absolute unique visitors: 21,250 (previous year 13,369)
Total visits: 37,513 (103 Visits/Day) [previous year 34,820 (89.47 Visits/Day)]
Average time on site: 1:28 minute (previous year 1:06 minute)
The 10 most frequent visitors identifiable:
(1) Princeton University (last year: Scripps Research Institute)
(2) Scripps Research Institute (last year: University of Cambridge)
(3) Oxford University (last year: Oxford University)
(4) University of Cambridge (last year: University of California)
(5) Flinders University (last year: Princeton University)
(6) State University of New York at Buffalo (last year: Columbia University)
(7) Carleton University (last year: University of Rochester)
(8) GlaxoSmithKline (last year: Harvard University)
(9) University of California Santa Barbara (last year: Pennsylvania State University)
(10) University of California Irvine (last year: North Dakota State University)

Tuesday, October 14, 2008

The Periodic Table of Elements

One of my non-chemist friends recently introduced me to The Periodic Table of Videos. This is a very cool and informative website.
I've learned lots of stuff since I started watching these videos. Thumbs up to the University of Nottingham for this excellent initiative. D!

Monday, October 13, 2008

Cisplatin is my friend!

One of my best friends has just recovered 100% from cancer because Cisplatin rocks. Here's a bit of inorganic chemistry courtesy of Wikipedia:

Cisplatin was first described by M. Peyrone in 1845 and this year it celebrates its 30th FDA approval anniversary. D!

Monday, September 01, 2008

Anhydrous Solvents Part 2: The THF Still - Do's and Don'ts

The THF still is one of the most common reasons for serious fires at chemistry departments around the world. As solvent purification systems (SPS) become more and more common this problem will gradually disappear. However for now SPS is still pretty expensive so the THF stills will linger around for some time to come. There are many reasonable ways to construct a THF still. All you need for a basic THF still is:
  • A round bottom flask
  • A still head
  • A reflux condenser
  • An inert gas inlet and gas bubbler
  • A heating mantle
  • Sodium, benzophenone and some THF
The main reason why THF stills blow up is incompetent users. It only takes one sloppy chemists to screw things up in a big way. However, even with competent, careful chemists THF stills occasionally blow up. So what can you do to avoid the THF still disaster?
First and foremost train all users and/or limit the number of people allowed to turn it on and off. Have an on/off sheet where people record their name, time etc.
  • Get a flow-stop switch - This clever little gizmo shuts the power off if the water stops running. This will stop most accidents before they happen. Your electrician will know what to do.
  • Get a "hat" for your heating mantle (see picture) to avoid water dripping in and setting the whole thing on fire.
  • Use Teflon joints or Teflon sleeves to protect joints from fusing (see picture)
  • Don't use excessive amounts of sodium. Ideally use a sodium press to make thin sodium thread. This will give you a large surface area and ensure that you don't end up with a big fat ball of sodium when you eventually have to quench the still.
  • Never turn the inert gas off.
  • Have enough THF in the system. Always ensure that the round bottom flask (RBF) is filled sufficiently with THF to allow the still head to fill up and leave the RBF at least on third full.
  • ONLY fill the THF still with dry THF. Don't just grab any old THF bottle from the solvent cabinet. Have THF bottles specifically for the still only.
  • Don't put a stirring bar in the RBF. This will only result in a big fat ball of sodium down the track. Sodium wire is generally enough for controlled boiling. If you must add something throw some boiling chips in.
  • BE PATIENT! Don't turn the heating mantle to the max because you are in a hurry. It take 30-60 minutes to get a THF still up and running in a controlled fashion.
  • Place your heating mantle on a lab jack. When the shit hits the fan you can lower the heating mantle and stop heat transfer immediately.
I think that is enough for today. There are many things to consider and I have by no means covered everything but this should be a good start. D!

Monday, August 25, 2008

Let's talk about TLCs Part 4 - Ninhydrin Stain

2008 was the year where I became an amino acid chemist and as a consequence the Ninhydrin Stain has become my new friend. Many of the amino acids I handle these days are not UV active but fortunately the Ninhydrin Stain is great for visualising free amines and primary amines. Most of my amines are BOC-protected but they still develop nicely with ninhydrin because the BOC group is cleaved upon treatment with the stain.
Ninhydrin Stain Recipe
100 ml container
0.2 g Ninhydrin
0.5 ml Acetic acid
100 ml n-Butanol
4.5 ml Water
After treatment with a heat gun Ninhydrin Stain tends to give brightly coloured pink to purple spots as shown above. The spots can fade rather fast so record the result immediately. In the past I have been using a Ninhydrin Stain that didn't contain water, however adding a bit of water seems to improve the result a fair bit. D!

Tuesday, August 19, 2008

How to make a primary amide - The Ley Way

Steven Ley's Group really produces some cracking results. This time they have developed a really simple method for preparing primary amides from carboxylic esters. This is very good news because this seemingly simple transformation is in fact not as simpel as one could have hoped for. In the past I have used ammonia in methanol to achieve this. The commercially available NH3 in MeOH is rather variable in quality so making it fresh by saturating methanol with ammonia using a gas cylinder is preferable. It's an annoying exercise making the solution and the actual reaction CO2R to CONH2 doesn't really work that well.So when Steven Ley comes up with a method that involves scooping solid magnesium nitride into a flask with your ester and some methanol, heating it to 80 oC for 24 hr, work up, filter, done! then that is really exciting good news to the synthetic organic chemist.
Magnesium nitride is reasonably priced, e.g. Aldrich (#415111) 10 g for less than 40 Euros. D!

Monday, August 18, 2008

Guidelines for giving a truly terrible talk

I'm giving a presentation in a month's time which reminded me of the stuff below. Unfortunately, I can't remember what web site I got this stuff from but apparentely it's from "35-mm Slides: A Manual for Technical Presentations", by Dan Pratt og Lev Ropes. Surprisingly many scientists seem to use these guidelines. Here we go:

"Strict adherence to the following time-tested guidelines will ensure that both you and your work remain obscure and will guarantee an audience of minimum size at your next talk. Continuity of effort may result in being awarded the coveted 5:00 P.M. Friday speaking time at the next national meeting." Slides:
(1) Use lots of slides. A rule of thumb is one slide for each 10 seconds of time allotted for your talk. If you don’t have enough, borrow the rest from the previous speaker, or cycle back and forth between slides.
(2) Put as much information on each slide as possible. Graphs with a dozen or so crossing lines, tables with at least 100 entries, and maps with 20 or 30 units are especially effective; but equations, particularly if they contain at least 15 terms and 20 variables, are almost as good. A high density of detailed and marginally relevant data usually prevents penetrating questions from the audience.
(3) Use small print. Anyone who has not had the foresight to either sit in the front row or bring a set of binoculars is probably not smart enough to understand your talk anyway.
(4) Use figures and tables directly from publications. They will help you accomplish goals 2 and 3 above and minimize the amount of preparation for the talk. If you haven’t published the work, use illustrations from an old publication. Only a few people in the audience will notice anyway.
(1) Don’t organize your talk in advance. It is usually best not to even think about it until your name has been announced by the session chair. Above all, don’t write the talk out, it may fall into enemy hands.
(2) Never, ever, rehearse, even briefly. Talks are best when they arise spontaneously and in random order. Leave it as an exercise for the listener to assemble your thoughts properly and make some sense out of what you say.
(3) Discuss each slide in complete detail, especially those parts irrelevant to the main points of our talk. If you suspect that there is anyone in the audience who is not asleep, return to a previous slide and discuss it again.
(4) Face the projection screen, mumble, and talk as fast as possible, especially while making important points. An alternative strategy is to speak very slowly, leave every other sentence uncompleted, and punctuate each thought with "ahhh", "unhh", or something equally informative.
(5) Wave the lights pointer around the room, or at least move the beam rapidly about the slide image in small circles. If this is done properly, it will make 50 % of the people in the front three rows (and those with binoculars) sick.
(6) Use up all of your allotted time and at least half, if not all, of the next speaker’s. This avoids foolish and annoying questions and forces the chairman to ride herd on the following speakers.
Remember, the rest of the speakers don’t have anything important to say anyway. If they had, they would have been assigned times earlier than yours. D!

Wednesday, August 13, 2008

Melting point then and now - Kofler Hotbench vs. OptiMelt

I think that most chemists will agree that doing melting point determinations sucks big time. Especially when you have been putting it off for 6 months and have to do 22 in one day (yes I learnt my lesson and it took two days). Until recently I only knew of a few ways to determine melting points. My preferred method was to get a rough melting point using a Kofler Hotbench followed by an accurate determination using a full-on old school Reichert melting point microscope. The microscope beats getting your compound into a melting point tube and watching it melt through a crappy magnifying glass. Firstly, you place your crystals between two wafer thin glass plates (very simple). Secondly, you get to see your beautiful crystals through the microscope. On one occasion I managed to have a small rainbow in my crystals which sure beats staring at a melting point tube. Nevertheless, melting point determinations suck so I have toyed with the idea of having a camera record the melting in my absence and then come back a couple of hours later and fast forwarding the movie to the melting point and recoding the numbers. Now that would be easy.
As always someone else got the idea first and where I work now melting point determinations are fully automated using an OptiMelt system. It records a little movie and prints out the numbers while you are at home watching Buffy. Amazing stuff!
So what happened to the redundant Kofler Hotbench? I found it on display in the Departments historical collection of hopelessly ancient relics. Strange to think that where I worked only two months ago this was state of the art equipment. D!

Tuesday, June 17, 2008

Farewell Australia

Goodbye and thanks for all the sunshine, chicken parmis, red wine and last but not least all the fish. Blogging will resume again sometime in July. D!

Wednesday, June 04, 2008

Japan vs. Germany: 1-0

Just a minute ago I was looking through the early view papers for Angewandte Chemie and I spotted these two papers virtually back to back. Japan wins by three days. Can you spot the difference? D!

Sunday, May 25, 2008

Vacuum Control - updated!

It took 88 cardboard boxes and 1.5 km of packing tape to get my belongings packed up and on its way in a container destined for Denmark. Hopefully, I'll see it all at the other end in 2 months time. So with that stage of the move over and done I believe it's time for a post.

Rotary evaporators are great and we use them all the time but solvents have a bad tendency to bump and splash resulting in a mess. One way to partly control the mess is the use of a splash guard but it is still a pain. Chemists in industry generally don't have these bumping issues because they can afford a vacuum controller. These are great little gadgets where you punch the vacuum you would like to achieve in and hit go. On the more fancy systems even this is unnecessary as a clever little vapour pressure sensing device regulates the pressure ensuring the perfect distillation. However, these things are expensive and high maintenance so universities don't normally have them. Recently, a good friend that works at one of Australia's top institutions introduced me to a simple piece of glassware that essentially replaces the fancy vacuum controller at a very low cost (see picture left). The principle is very simple. The tap has two setting one allows passage through a wide glass tube and the other through a capillary tube. When you start the rotary evaporator you have the wide tube open and when the distillation starts you switch to the capillary tube. The capillary tube basically ensures that the current vacuum is maintained and stops it from going further down. Too easy! In addition the solvent recovery is dramatically improve saving the planet and importantly also your pump. All specifications for the gadget can be found in this paper:
Prevent the Loss of Volatile Solvents in Rotary Evaporators with a Simple Device, Daan van Leusen, Journal of Chemical Education, 1994, 71 (1), pp. 54-55. D!
One of the regular readers just emailed me a picture with a similar set-up to mine that does the same trick (See comments and picture right). The main difference is that this alternative set-up doesn't allow you to turn the vacuum off by turning the tap. Were I work we have a house vacuum system that requires a lot of tap turning so the set-up above is nice as this simplifies turning the vacuum off. However, if you are using a diaphragm pump this alternative is perfect and presumably also significantly cheaper to produce. D!

Friday, May 02, 2008

The Robots are Coming

Posting on Curly Arrow is already a very erratic affair and things will not be improving for a while. There is less than two months til the big move back to Denmark. I'm experiencing total organisational chaos and trying desperately to obtain some results in the lab before it is too late. So please be patient.
I'm sure that the following paper from Journal of Medicinal Chemistry is great (I haven't read it). The title is certainly great.
Designing Active Template Molecules by Combining Computational De Novo Design and Human Chemist's Expertise
Eric-Wubbo Lameijer, Reynier A. Tromp, Ronald F. Spanjersberg, Johannes Brussee, and Adriaan P. IJzerman
J. Med. Chem., 2007, 50, 1925-1932

Wednesday, April 09, 2008

The Invisible Phase Boundary

All organic chemists have experienced it. Your reaction is done and your transfer it to a separatory funnel with an aqueous and an organic phase. You do your shaky, shaky bit and the phases separate but it is impossible to tell where the phase boundary is. The problem is most commonly encountered when very dark phases are obtained but it can also occur with perfectly clear phases (see picture). The solution to this problem is very simple. Simply tip a clean NMR tube cap into the separatory funnel and observe as it settles on top of the bottom phase. Problem solved. D!

Friday, April 04, 2008

Dry Column Vacuum Chromatography (DCVC) - revisited

I get a lot of questions about Dry Column Vacuum Chromatography (DCVC) so I believe it is time for another post on the topic. DCVC is really taking off and the paper now has >70 journal citations.
Firstly, let me reiterate that like most things in life DCVC is best learnt by doing. Some of the questions I get are very detailed and specific and I can't provide clear cut answers. With experience you'll have an idea what to do and you'll improvise along the way and get it right.
Q&A session with the true believers:
(1) ...did you know that your paper had the"honor" of being "html-ed" by Rhodium....
- I didn't know that. I guess that everyone is purifying their illicit drugs in the garden shed using DCVC these days.
(2) ...searching for a good source for the silica gel, right now it is about 4-5 times more expensive than our flash gel source...
- That is a huge difference. You have a very sweet deal on flash silica. In my case it costs about 40 % more but considering how little you use compared to flash it works out as a big saving. If you find a cheap source of DCVC silica please let us know.
3) ...In the comments, you mentioned that you have done DCVC with 50-100 mg, and I was wondering what size of fritted funnel (frit diameter) you would use for that. Just calculating the size using the approximate amount of silica gel gives me something ridiculously small...
- The smallest sinter I use has a diameter of 1 cm. I have run 20 mg columns with 5 ml fractions on this column with no problems. Smaller than that would be impractical.
(4) ...Also, just to help me chose the size [Column] if I'd get one or two funnels made, what diameter(s) would you use for say 500 mg to 5 g?...
- I currently have the following four columns: 1, 4, 6 and 8 cm. My favourite (that I use 80% of the time) is 4 cm. It's a good size to work with and it's good for 20 ml fractions. I'll do anything from 100 mg and up to 5 grams or more (depending on the separation) on that column. For your requirements I'd say get a 4 and 6 cm column.
(5) ...frit porosities - the notation 1 - 4 is what is used in Europe, here in the US they have C, M and F, which actually don't directly correspond to the 1-4 sizes. "3" is a size where there is no direct equivalent, which is too bad because it seems ideal also to have in a flash column. The actual numbers are below, and I was a bit surprised because it seems that the P3 should clog up with time when using the Merck 15111 silica gel with its size range of 15-40 micron.
American standards - (Kimble & Corning, ASTM) nominal pore size, in microns, Medium 10-15 µm, Fine 4-5.5 µm
European standards - (Robu & Schott, ISO 4793) nominal pore size, in microns, P3 (P40) 16-40 µm, P4 (P16) 10-16 µm
- I had no idea about all this. Why on earth can't we just standardise these things. Anyway, thank you very much. I have always wondered exactly what the pore sizes represented.
(6) ...What is a least polar couple of spots with delta Rf 0.05 (often called "eight", "8") which you would separate via DCVC?...
- I only do DCVC. If it fails the next stop is prep. HPLC. Fortunately it still hasn't failed. As with all normal phase chromatography super non-polar compounds separation sucks. That said I have often columned stuff (not super non-polar) that appears to be one compound by TLC and managed to get two compounds of the column. Behold the power of slow step gradient elution. I have achieved truly mind boggling separations over only 20 fractions. The worst column ever occurred 1.5 years ago. I kept getting a fair bit of each diastereoisomer clean but it took 5 columns to get it fully separated. Still it was easily done in one day by using the same column 5 times and only collecting 30 fractions per column.
(7) Do you always start from heptane even for very polar mixtures?
- Yes! It gets the stuff off the Celite on to the silica and wets the column so that it runs well. Generally I do 4 x hexane, heptane or pet. ether first.
(8) ...can I use toluene/ethyl acetate, chloroform/ethyl acetate or chloroform/methanol mixtures successfully?...
- Yes! You can even use really low boiling solvents such as acetone, dichloromethane, ether etc. but due to evaporation it is easier to work with higher boiling solvents. Where I work now hexane and heptane has been replaced with 40-60 petroleum spirit which I use for my columns without too much difficulty. Remember to have the pump exhaust in the fume hood, especially with the low boiling solvents.
(9) ...Does it work substantially better [with Celite] than preadsorbtion on silica gel?...
-Yes! Celite is easier to handle and it doesn't affect resolution.
(10) ...Does this trick with Celite work even if a sample is only sparingly soluble in an eluent?...
- It doesn't matter what your eluent is. Dissolve your compound in something polar that is easy to get rid of, for example ethyl acetate or methanol. Add Celite, concentrate in vacuo and load it on the column. Ensure that you have removed all solvent prior to loading. A lot of say methanol in the Celite will compromise resolution.
I hope that helps. If you are new to this area please read the previous post and check out the following paper (a copy can be supplied upon request):
Dry Column Vacuum Chromatography, D.S. Pedersen and C. Rosenbohm, Synthesis, 2001, pp. 2431-2434.
Let me know if you have more comment, suggestions or questions. D!

Tuesday, March 25, 2008

Let's talk about TLCs Part 3 - Phosphomolybdic Acid (PMA) Stain

PMA Stain is a highly versatile general stain for developing TLC plates. The stain is easily prepared by dissolving 10 wt. % phosphomolybdic acid in ethanol. More PMA can be used however as stains go PMA is relatively expensive.
TLCs developed with PMA stain upon heating give green/dark green/dark blue spots on a yellow/green background (see picture).
Phosphomolydic acid (PMA) Stain Recipe
100 ml container
100 ml Ethanol
10 g Phosphomolybdic acid, H3[P(Mo3O10)4] · xH2O
Alternatively, you can go for the more expensive solution and buy ready made PMA stain from Aldrich (see picture). Where I've worked in the past we simply poured some of the ready made stuff into a jar and use it for our TLC plates. At the end of the day we poured it back into the Aldrich flask and rinsed with some ethanol. Using this method the stain lasts for a very long time. I never had any problems storing the stain at room temperature despite Aldrich's recommendation to refrigerate.
See under Vanilin Stain for general staining guidelines. D!

Thursday, March 20, 2008

100% Edible

Finally, I'm returning to normal. I'm back at the University working at full force and I've got the energy to do a bit of blogging again. Let's start with a nice and easy post. One of the new people at the University turned up with the following Fluka product the other day. Pretty sweet and good quality chocolates too. Apparently, Fluka is a Swiss based company and once a year (around Christmas I believe) they give their customers a truck load of these containers.One of the guys in the lab immediately grabbed the phone and gave Fluka Australia a call to hear if they stocked this item too. Unfortunately, this appears to be a Switzerland only bonus. The product also isn't listed in their catalogues.
Also my "great" idea of introducing Google adds on Curly Arrow was short lived. A lot of the adds where completely irrelevant to this blog so it's all been deleted again. D!

Friday, February 29, 2008

Open Access Journals - Beilstein Journal of Organic Chemistry

It's amazing how unpredictable life is. Only four months after I started my job in biotech I'm heading back to academia. Not that there was anything wrong with the job but I've been given an opportunity to return to Denmark (which always has been the long term plan) so I'm going with the flow. I recently had a post on open access journals and was moaning a fair bit about how we don't have any decent chemistry open access journals yet. Well I was wrong. A colleague alerted my attention to Beilstein Journal of Organic Chemistry (BJOC). This is the best attempt I've seen yet. They are publishing a reasonable number of papers, the quality of the material is good, the journal gets indexed by all the important organisations and it is absolutely free. The impact factor is still low (ISI WoK: 0.35) but this should improve with time. So check it out.
The past year I've been involved in setting two labs up and whilst searching for information on equipment etc. I've been quite pleased with the Google adds people have on their web sites. I found a fair bit of the stuff I needed this way so I've decided to give it a go here at Curly Arrow. So sometime in the very near future adds will start appearing on Curly Arrow that should be useful to people interested in purchasing lab equipment. D!

Friday, February 15, 2008

Catalytic Hydrogenation - now fire free

In my experience you should not do synthetic organic chemistry if:
(A) You are drunk (or the following day when you have a hang over)
(B) You are in a hurry
Recently, I violated Commandment B and decided to put a large scale catalytic hydrogenation on really, really fast. Bad idea!
Now hopefully most of you realise that the addition of palladium on charcoal (or charcoal alone) to organic solvents can result in instant bonfire. Unfortunately the chemists hand is often right above the flask as the catalyst gets added and some very nasty burns can result. Even worse the whole thing may take off and you'll frantically be looking for a fire extinguisher (Always know where the fire extinguisher is. You will need it one day).
There is an easy way to avoid this problem. If you first remove all atmospheric air inside your flask there will be no fire. In other words what you have to do is flush the flask with nitrogen or argon. I normally hook my flask up in such a way that I can evacuate it with a pump and fill it with nitrogen. I've shown one of my recent setups on the picture. You can obviously connect things in many different ways depending on what equipment you have available.
I normally evacuate the flask and fill it with nitrogen at least three times. Only then do I proceed to add my catalyst. After addition I repeat the evacuate the flask procedure but this time I flush the flask with hydrogen and at the end I attach a big fat balloon with hydrogen gas and stir the reaction mixture vigorously.
The other day when I was in a big hurry I decided to skip the flushing with nitrogen step (for the first time ever) and as a consequence I had my first Pd on charcoal fire. I was very lucky and didn't burn myself because the weighing paper was shielding my hand. The drama was quickly over as I had my lab book handy and sealed the flask with it. The hydrogenation worked fine and I made it in time to the pub. However, next time I think I'll skip the first pint with the boys and flush that flask as I normally do. D!

Thursday, February 07, 2008

Recycling Silica Gel

Insert usual excuse for infrequent posting here: .....
I recently received the following email regarding recycling of silica gel:
"In the past we used to regenerate SiGel with fuming nitric acid, much as you do here (refers to previous post - D!) .Place the coloured, used SiGel (which of course must be uncoated and completely dry) in a large beaker. Approximately a third full. Place it inthe fume cupboard and pour in the nitric acid so the SiGel is completely moistened. If necessary, stir it. After a possible initial fuming has stopped, heat it on a steam bath for 10 minutes - leave it overnight. Next day, fill up with water, stir and let it settle. Wash 3 more times. At this point, it should be colourless, if not, repeat with more nitric acid. Then wash with satd. sodium bicarbonate until neutral and filter on a Buchner funnel. Wash with water, methanol and acetone and let it suck completely dry. Finally, activate by heating it in an oven overnight at 100-120 C.This way, it is as good as new for most purposes."
This may be of use to some chemists working at institutions where money is very scarce. However, considering the amount of time and large volumes of solvent required to do this I think it can be classified as historically interesting but not practically useful to most of us.
Nevertheless thank you for the email. I have wondered exactly how you would go about recycling your silica gel.
Speaking of silica gel and techniques that are disappearing from the chemists hood check one of the most recent posts at In the Pipeline out. Derek seems to think that TLCs are on their way out as LC-MS is becoming more and more common. I believe that it will take several decades before Derek's predictions come true (especially in academia) but he does have some very good points. D!

Thursday, January 03, 2008

How to clean your sintered funnel

Lately when I have been cleaning my sintered funnels people have stopped and asked me what I was doing. To my surprise many chemists don't seem to know how to take a nasty, dirty sintered funnel and making it nice, white and shining again in about 15 minutes.
These days I'm doing lots of old school chemistry that involves heating the crap out of the components using for example conc. sulfuric acid as the solvent. Needless to say things are polymerising and decomposing left, right and centre and when you filter it through your nice white sinter it ends up looking nasty (see picture above). The stuff doesn't go anywhere with acetone, water, 2M sodium hydroxide or hydrochloric acid etc. so what should you do? Before I proceed please note that if you attempt any of the following you must:
(1) Wear a closed lab coat, safety glasses and plastic gloves
(2) Conduct the cleaning in a fume hood with the sash down at all times
(3) Ensure that all the glassware is clean and doesn't contain residual organic material such as acetone
Please take the above advice seriously. People have had nasty accidents doing the following because they weren't careful.
There are two common ways to get your sinter clean:
(1) Conc. nitric acid, or
(2) Conc. sulfuric acid and hydrogen peroxide
Nitric acid is the easy solution and more often than not it does the trick. However, occasionally it is necessary to use more vigorous conditions. I have never had a sinter that didn't become white after treatment with conc. sulfuric acid and hydrogen peroxide and this is generally the method that I use because I know it works every time.
(1) Fit the funnel to a Büchner flask attached to a vacuum that you can control easily
(2) Add a small amount of conc. sulfuric acid so that it covers the surface of the sinter
(3) Add a dash of hydrogen peroxide and stand back. Things get pretty hot, bubbly and exciting at this point (See picture above).

(4) When the ingredients have been cooking away for a minute or so apply a very gentle vacuum briefly. This should be sufficient to suck the sinter dry (See picture above),
(5) Allow the cocktail to settle down and cool off and clean all the equipment with lots of water taking care not to pour the contents all over yourself. Your sinter will now look like this.
Too easy but please do be careful guys. D!