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!

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.:

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The reaction must be:
(1) modular
(2) wide in scope
(3) give very high yields
(4) generate only inoffensive byproducts
(5) stereopecific
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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
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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.
D!

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!

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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)

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!

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!

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!

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.

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Ninhydrin Stain Recipe

100 ml container

0.2 g Ninhydrin

0.5 ml Acetic acid

100 ml n-Butanol

4.5 ml Water

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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!

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!

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.
Presentation:
(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!

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!