Honeydew Shaken Not Stirred

OK, I pretty much gave up on the old research blog. I flirted with Facebook for a bit and there were only so many hours in the day so I let the blog slide. That and the fact that the research took several unfortunate turns. It turned out that one of the starting materials that I used most of the summer was so decomposed and contaminated that almost everything that I did in the lab over the summer could not be published and would/will need to be repeated. The work that I started at MtA has also gone very slowly but I have done several new reactions. The most exciting part of that work was cracking open an ampule of a very reactive compound that I sealed over ten years ago and discovering that the compound is still pure ... dangerous but pure. There was a time when that compound was sold for $ 1000 per gram and now it can be bought for "only" $ 165 per gram.

I have over 100 grams of the compound and I am now actively "making friends" in the chemical world. I will not sell it but will use it to participate in the research of several groups that can use the compound.

But now winter is reaching out to touch my research. I bought a "beater" car in May to drive from Moncton to Fredericton and Sackville. I was small and grossly underpowered but it got me around and after some initial problems it has been a faithful steed.

That all changed Sunday. The weather office completely missed the fact that we had a November winter storm coming and we woke up Sunday morning to 10 cm of snow on the ground. But it wasn't the ground that was the problem. It would turn out that the Moncton municiple services were also caught napping and by church time the streets were still not cleared. I wasn't so bad in the city where the speeds are low but I was heading out McLaughlin Road to speak at a church in Dundas (about 20 - 25 minutes out on a day with good driving).

To make a long story short (or at least shorter) there is a steep hill about a third of the way to Dundas. It was packed snow and slush both up and down that hill and I could hear the slush sliding by the low slung floor of my little Kia Rio. I was pleased when I got past the hill and started up the next long slow incline. About a kilometer along there was a thick line of slush and as I drove over it the back end of the car came loose and I could feel the car swing around. I turned into the slide and got the car moving forward but unfortunately that forward direction was towards the ditch. I swung the steering wheel over and it was weirdly like the iceberg collision scene in Titanic where everything is sluggish and inevitable. In my case, the car swung around but kept sliding slowly toward the ditch and it ALMOST stopped but it had just enough momentum to push the center of mass over the edge of the road and then the car pretty much toppled sideways into the ditch!

Now, it is an extremely odd feeling to be sitting in your car while it is lying on it's side. The car was running and everything seemed fine except for the odd orthogonality of the gravitational reference system. Me? I'm fine ... a little freaked out but undamaged. So, I turn off the car and face my first problem: How do I get my weight off the seatbelt so I can unbuckle it? Clever use of leverage and ligaments allowed me to a) release the seatbelt and b) discover the seatbelt was holding me up. Now I am standing on the passenger side window (ominous cracking noise from the door) contemplating how to get out of the car. I grab the knapsack with my phone, laptop, Bible and preaching notes, crack open the driver side door and crawl up and out of the car.

So, now I am standing on the side of the road (a deserted, desolate road) in a snow storm up to my ankles in slush wearing dress shoes. But, a blessing of the age, I have a cell phone. So who do I call first? Would you believe I called the church to let them know I would not be able to speak that morning? I actually needed them to look up the phone number for a towing company too so that worked out OK. Now, at this time suddenly the road was alive with Good Samaritans. I was on the phone and a guy in a pick-up truck asked me if I wanted to use his cell phone. The next Good Samaritan in a mini-van asked me if there was anyone in the car and would I like a bottle of water. And so on ...

Finally a pick-up rolled up and it was the son of one of the members at the church I was going to speak at that morning. I got in his truck (my cold, wet feet were very thankful) and finished my phonecalls. It would be a half hour for the tow truck to show up and I was feeling a bit self conscious about how long my new friend would have to wait. That, and that fact that a solid stream of people were now stopping at the car and "investigating". Now was a crucial moment. It was clear that I was fine, the tow truck driver knew what he had to do without me and Anthony was patiently waiting with me. Well, what do you do? I said "Why don't we just head on out to Dundas and I will deliver the message like originally planned?" I mean, really, what point was there to waiting? So 15 minutes later I walk into church at exactly the point in the service where I was needed. I hooked my computer up to the LCD projector and gave the message. Just like that. Surreal.

In a weird post-script to this story. When I picked up the car the only real damage to the car was done by the tow truck driver. They checked the car over and the frame, engine, steering and suspension were all fine. There were dents to the passenger side panels front to back but that was it. The tow truck had broken the plastic over the rear bumper but apparently when I had asked them to tow the car there was an understanding that they would not be liable for any damage caused by the tow. Who knew?

A Time for a Change: Sabbatical Phase II

I have enjoyed the past four months at the bench. I would not say that I completed any individual project and therefore Phase I will blend with Phase II for at least a while. I was very pleased to find a project that appears to be new and also relevant. The fact that the starting materials could not be purchased pure and the lack of a good, in-house spectroscopic handle for the product means that everything that I did was dependant on creating and isolating crystalline compounds. In that sense the project was a failure. The work however revealed exactly what needs to be done for the project to go forward. I think I can do that over the next four months by going to UNB for two days a week to essentially work up reactions from previous weeks and set-up new reactions for the week. That will hopefully allow me to generate samples for spectroscopic analysis. The spectroscopic methods that I will hopefully will use will run the whole "spectrum" (if you will excuse the pun).

Uv-visible : the compounds are coloured and this will need to be done once we has isolated crystals of pure compounds. The spectra will show us what the pi systems in the double bonds are doing but this method is very sensitive to minor impurities if they are highly coloured. The challenge for this method is that we will need to make special cells so that samples dissolved in SO2 can be measured.

ESR (electron spin resonance) if the compounds have unpaired electrons then this method must be used to measure the environment that the unpaired electron lives in. In many ways this can be complementary to Uv-visible and both of these methods can be modelled by high level calculations.

Vibrational spectroscopy (IR; infra-red and Raman) these complementary methods are measured by dramatically different techniques but when combined gives a complete picture of all the molecular bonds in a chemical compound. IR is dead easy to measure with just about any heatlight source and a heat detector. Raman is a very different method and the main reason why Phase II will mostly occur at a different University. UNB is a two hour drive to the west from ABU while MtA is a half hour drive to the east. At MtA however they have just installed a research grade Raman instrument and it will be my job in this phase of my sabbatical to learn how to use the Raman and make some publication quality measurements with it. This will all be new work for me and I am looking forward to it.

If this sabbatical is going to generate publishable research it will happen in the next four months or not at all. So the pressure is on.

Lies, Damned Lies and Statistics

LINK: http://www.phdcomics.com/comics.php

As usual Jorge Cham has nailed the essence of the significance of the research done in most University Laboratories. In reality, if you actually do work that gets published, the paper will get read by a small group of people (no more than a 100 would be my guess). Most of them will go "Meh" and forget the work unless they are thinking of writing a review or a paper where you might review one of their manuscripts.
The university system is actually designed to train scientists not to really turn the scientific world upside down. We forget that when we continually ask professors "So when are you going to make Flubber anyway?". Still when you are hip deep in research and trying to convince yourself that the work is in someway relevant ... well it can all get a little delusional. It is good that we now have a test to get our heads back from the clouds.

A Creeping, Fitful Progress

So, I spend two hours every Monday morning and Thursday evening on the road between the M-R-D Metropolitan area and Cathedral City. I happen to like the trip but it cuts into my day and driving with tourists on the road drives me nuts.









I also happen to love Cathedral City where I grew up and went to University. The place just can't have a bad picture taken of it even with a cellphone camera in bad light. On the other hand the city has no reason to exist other than that it is a provincial capital and has a university. It means that it is a largely white collar city where no one really works for a living.











Now, the reason why I am doing this is to get some publishable research done. That means that I have to get something done that a) no one has thought of before b) if they did think of it they failed and c) succeed. Which requires creative thinking, discipline, keen observation and old-fashioned luck.

This summer my focus has been on the physical chemistry problem of what happens when a well known industrial reducing agent [which everyone uses in huge excess because it is a) typically impure b) short lived in solution and c) has the solubility of beach sand (are you still with me on this sentence, we had a digression there that was almost humanities style writing in length, I am going to have to fix that before I try to write a scientific paper ... Subject -Verb - Object, keep it simple and stay away from weird tenses ... anyhoo back to our regularly scheduled sentence)] becomes a soluble species. In my hands, it has pulled a Luther on me. When Luther was in the tight grip of the Catholic Church they were able to minimize his eccentricities. However, when he was "free" of the confines of the church he went mad (so to speak) and started chewing the furniture (check out R. C. Sproul and "The Madness of Luther"). That is what happened to my compound when I was able to get it to dissolve ... it started chewing one whatever was around (solvent, container and spectrometers).

The problem is that I need pure compounds to characterize and with this material I am already starting at 85% purity on the best commercial samples. So my only hope is the formation of crystals that I can separate from the impurities and chewed on bits of furniture.

I thought I had the problem licked when massive well formed crystals formed from one of my oils. For a week I gloried in my crystals, there they were so close, just on the other side of the glass, so close. But I needed to isolate them and that meant work-up. Then things did not go so well, the crystals survived filtration and back distillation of the solvent but the real test is when you evacuate the reaction chamber to remove the solvent so you can handle the sample in the drybox. In less than a minute, while I watched, the massive crystals lost all structural integrity and became something that looked like Playdough if Campbell Soups made a tomato soup play dough.

What I have done once I can do again. But this time the path will be much longer and technically difficult to avoid the decomposition of the solvated crystals. I still do not know why some German or Russian did not do this chemistry 50 years ago and so in my spare time I am scouring the old literature for secondary research stories to make sure that I am not re-inventing the wheel. But that is research.

It is good to be back at the bench. The glassblowing is coming back to me and I like the people I am working with. I feel blessed and I will feel even more blessed when in two weeks the science courses will be taught at ABU without my name listed as professor. Then I will know what a sabbatical feels like.

Research and Ghosts

So ... it's been a long time. Research at the bench is what it always has been. Sometimes it is a visceral delight as the reagents cook up into something new. Sometimes it is a grind to get through routine housekeeping necessary to keep a lab working. Sometimes bench research erodes the soul with countless small stumbling blocks that can stop a research program in its tracks. I have known them all in the last month or so.

The car has worked well. The driving has been fine since the trip from home to here is in my opinion a great little drive. The weather has been "tourist weather" (hot and sunny). So I leave the unplanned garish squat of a community by an unloved river and drive to an urbane and quiet small city with a wide beautiful river. Why did I ever leave here?

Ghosts.

The research has gone pretty much as I expected. Slow and at times frustrating. I was fortunate to stumble into a discovery that will allow me to look at some interesting and relevant chemical aspects of battery chemistry. I am currently up to my eyeballs in various forms of oils that refuse to form solids. It's the colour changes that jazz up my day. I have discovered a chemical reaction between two compound that have been known for decades and one of which is an industrial reagent. Not only that the reaction features the combination of two white crystalline solids with a secret solvent and I get the brightest most interesting colours and colour changes. If I can determine what the chemical species are that are responsible for the colour changes I may just get into the inorganic textbooks after all. It looks like I will be spending the balance of my sabbatical doing ESR and Raman and hopefully X-ray crystallography. Why did I ever leave here?

Ghosts.

We had a water main break in the the basement of our Chemistry building two days ago. The water filled a room so that the water was about a meter deep and the doors into the room could not be opened (genius designer had then all swing INTO the room). Not only that the only access to a shut-off valve was behind a wall in the room filled with water. Needless to say the lower floor (which includes the chemical storeroom) was inundated and they had to turn off the electricity to the whole building. We suddenly discovered that the fumehoods have an important role in making it possible to breathe the air and we all bolted for the nearest exit like a bad Mexican burrito.

That meant that yesterday I ended up in the Engineering Library doing some long delayed literature work. After a long day of somewhat fruitful reading I headed out of the library and wandered around looking for a bathroom.

Ghosts.

In a random corner of a random corridor I ran into this picture ...

And this picture had this small detail ...

Kevin was a friend, a good friend. We went to school together, we worked together and we enjoyed each others company. He was bright and devoted to sports. We were both raised in a community where feelings were mostly repressed but I knew him as a sensitive and curious brother. We sort of drifted apart in University I went into science and he went into engineering but it was a measure of his ability that in a program where the "four year degree" took everyone five years to complete ... he finished in four. I remember meeting him in the hallway of the Chemistry building ... we walked by each other and simultaneously turned and realized who the other person was. For fifteen minutes it was like old times ... but time had moved on and Kevin was anxious for work so he had decided to go into the Armed Forces. We talked about wives and babies and then the tide took us apart.

About a year later we heard that Kevin and some other students were down in a hole in British Columbia learning how to wire explosives. One of those can't ever happen accidents happened and some people died including Kevin. I went to his funeral where a doddering old pastor who didn't know him said some stuff that had no meaning to a young wife and daughter. We all cried at the outright wrongness of his early death. And then our lives moved on.

So here I am in this random corner of a random building crying again. That is why I left this place ... there are too many ghosts that can bubble up from my past and rob the precious moment of the present from me while I remember old wounds, words or loves. I have gotta go home and kiss my family and live in the precious gift of the present.

As long as I live, I will carry the memory of that last conversation with me. It is precious to me and, in reality, symbolized all the friends left behind while I was off chasing electrons. Rest in peace brother ... you are not forgotten.

A link to an appropriate piece of music for my mood.

Dealing With Unstable Compounds: Part 5

Well, this series was not intended to be a current file but a nostalgic recollection of events when I wore a younger mans clothes ... then this happened.

About ten years ago I had an undergraduate student make up a batch of S3N3Cl3 (trithiazyl trichloride, about 10 grams in three separate sealed glass tubes). My intention at the time was that I would use the compound in a simple synthetic sequence that I helped discover.

S3N3Cl3 + 3 AgAsF6 --> 3 AgCl (s) + SNAsF6
8 SNAsF6 + S8 --> 8 SNSAsF6

This was the summer that I was going to bring the plan to fruition and I started the process by getting the sample tubes out of the old storage lockers. In my research group air sensitive compounds such as S3N3Cl3 were stored in sealed glass tubes, wrapped in paper towel and then packed in sturdy cardboard tubes.

Now, these glass tubes were placed in a blue plastic case and moved from ABU to UNB in my car and then kept in my office while I considered when and how I should do some chemistry with them. Late last week I got a call from a graduate student (in the research group that I am now working with) and he said that there had been an explosion in my office. I arrived about 10 minutes later and the top two floors of the chemistry building smelled strongly of sulphur-chlorides (a distinctive smell somewhere between skunk (thiols: LINK) and chlorine. The office itself was filled with a choking fume to the point where I could not enter the office while still winded from running up the stairs. Once we got the windows open and the ventilation fans working this is what I found:


It would appear that over the years a significant amount of the S3N3Cl3 had decomposed.

8 S3N3Cl3 (s) --> 3 S8 (s) + 12 Cl2 (g) + 12 N2 (g)

That kind of decomposition lead to a build-up of pressure in the glass tubes and it is possible that in moving the tubes microcracks in the tubes started to propagate to the point where the glass tubes failed in a spectacular manner. It is true that it is unfortunate that the explosion occurred at all but my oh my, I might have been stunned if I had have been in the office when the tubes exploded and I might have been in worse shape if they had have exploded in my car during transport. There is also the point that I had a tube of S4N4 in the same case (see below). I think that all in all I was lucky.

It all reminded me of 25 years ago when the senior graduate student in the research group that I had joined had a disagreement with me over the nature of my glass tube seal off. I favoured a secure heavy glass seal-off while he favoured a more fragile "elf's cap" seal-off. His comment was that if for any reason the pressure was to build up in the glass tube it would fail at a low pressure. I guess he was right.

I am unaware of any published account of an explosion resulting from S3N3Cl3 decomposition in sealed tubes with time (or for that matter even heat). Makes me wonder about all the other Main group chemists out there that might have similar tubes of similar vintage.

Back From the Land of the Bluenosers

So I take a used car that I have owned for three weeks down the student conference and the wucka-wucka-wucka noise just gets louder the further I get from home. And the weather just gets worse and worse (heavy rain and wind). So I'm driving along singing "Nearer My God to Thee" as I drive through some awful weather and I do not have a clue what I will do if the car breaks down. But I get to the land of the Bluenosers and the student conference. The attendance numbers were pretty good with over a 100 students attending but my focus as a judge were the oral presentations. I was expected to take notes on all the 15 minute long student presentations and be ready to assess them in six categories with first , second and third prizes in each. The Powerpoint presentations are all pretty good but they keep coming every 15 minutes from 9 AM until 4 PM. To my eyes the biggest problem is trying to determine what work was done by the student and what work was "group work". The end of the conference and of course there would have to be a 2 hour meeting for an interprovincial / interuniversity organization that I am on the executive. Then and only then me and the car beat it home.

So I go to the car dealership and complain bitterly about the car and we work out a deal to get the car fixed and since I have to go to Cathedral City they lend me a car. It was this stylish number with an air scoop and and big wing on the back. And all that on a 2004 Rio that has a top highway speed of 120 km/hr. Oh, it's a headturner, everyone watches me drive by like I am some sort of idiot from the backwoods. At least it was free I keep telling myself. It got me there and back and that was all I needed.

Cathedral City is really looking better now that spring has finally made an appearance and the leaves are filling out. Kind of surprising considering it was just three weeks ago I made the first run. But now with the National Conference starting this weekend it has got to be about the research.

So I am pushing together a presentation on the calculations that we have been doing. On one end of things the fact that we can do the study using simple calculations means that I can participate without access to any fancy cop equipment like they have on CSI but to me it seems like a sterile non-chemistry project. I guess you have to ride the horse that brought you. I will make my presentation and after the seminar the job will have to be to get the paper written and submitted. This first paper of my sabbatical probably does not deserve publication in the first rank journals but we think it will get into one of the second rank journals. It really doesn't matter since no one actually read s the journals any more and for the most part all journals are deposited with the majour online search engines so that any search of the journals online will result with a hit.


This first project is really quite simple. All first year students are taught about Born-Haber cycles to use to evaluate the thermodynamic aspects of chemical reactions. Our group was part of a new simplified calculation of a key component of the cycle called the lattice energy(essentially the force that holds a solid together). It was in fact my academic grandfather Neil Bartlett that had the insight first and then my academic father developed it with a British chemist so that the calculations were more general. It fell to me to find a way to use the calculations on an experimental problem and it worked out pretty good. Our calculations both explained what the pat term of reactivity that we observed in out system and also were predictive concerning what reactions would or would not work. But first, I have to get this presentation out of the way, so as much as I have been tortured by Powerpoint presentations in recent days here I am putting one together. I am trying to tell myself that I need to keep the slides simple, use colour sparingly and cut as much out as possible.

These Made Me Laugh

Brilliant contribution from the chemistry blog Everyday Scientist at :

http://blog.everydayscientist.com/

It seems that the creators of the Demotivators posters have posted a program for creating your own poster. Some of these are excellent.

Chemistry and Cars

So a week later and back in Cathedral City for more discussions and beginning the assembly of the presentation. But the whole process is mired in discussions about the significance of certain seemingly small differences in patterns of reactivity. That means that while research discussions are important and necessary they sometimes really slow down progress on what needs to get done immediately.

And then there is the car. The big gamble that I took on this sabbatical is that I went out on a limb and bought a five year old car driven by a little old lady. It was clear that I was going to have to make a lot of trips to Cathedral City so I had to make a choice between rental cars every time I needed a car and a purchase. I bought a five year old car with 64,000 km on it. Worked fine for two weeks and then it went past 66,666 kms.

And started to fall apart. Getting the beast fixed has cost me precious time that I did not have and the front end is still making a speed dependant wukka-wukka-wukka noise. That means more time, more money and more distraction. This has got to end soon.

Anyway this weekend I have to go to a student conference as a judge which means I will have to pay attention to about thirty 15 minute powerpoint presentations. I hope to find some time to work on my own presentation with weekend.

Getting Started

Spent a day in Cathedral City trying to sort out some details of what I might be able to do on my sabbatical. There is a tension between trying to do something that I would like to do and something that is helpful to the research group that I am joining. It is clear that the lab will be busy this summer which will be good for developing a research culture but will also strain resources and restrict availability of materials and equipment. Dr. J says that there will be room at the bench for me (what I want to do) as long as writing papers is the number one priority (what I need to do). I am still entangled with The University in the Wildwood but that is quickly resolving. The focus right now is "combat literature reading" to get myself back into some level of research literature engagement for preparation of the paper at Winterpeg later this month.

The drive back and forth was peaceful and this morning the River was so high it was close to the bank edge but so quiet and peaceful that it looked still even though it was ripping along. The trees are just starting to bud, the farmers are working the higher sandy fields that have drained in the hope that the spring flood has crested. I miss the cycle of planting with hope, working with determination and harvesting with joy (the best way to mark time). Another day and a lifetime ago.

This must be what a student feels like.

Dealing With Unstable Compounds: Part 4

http://en.wikipedia.org/wiki/Thiazyl

This stuff was a hoot. The synthesis was something out of alchemy and gave a wicked smelling residue from the filtered reaction mixture that had at least four different crystalline compounds in it. Pasteur separation of the products and repeated recrystallisation gave a binary mixture of sulphur and S4N4. This is where it becomes interesting. S4N4 is a contact explosive and the sulphur moderates the explosiveness (remove the sulphur and it becomes treacherously unstable). My first research job as an undergraduate was to recrystallize S4N4 until "it crackles when you grind it" (that was what I was told). Not a lie. The crackling was the result of tiny explosions between the mortar and the pestle and indicated that the S4N4 was pure enough to use. Later I would go to work at a lab in Durham England where an amazing chemist from Czechoslovakia prepared very pure S4N4 and purified it further by sublimation. One night a small beaker of the stuff just spontaneously exploded and destroyed a lab bench (one end was wrecked and the bench was split its entire length. What was ominous was that the explosion occurred without any initiation. That was new and we all started to find ways to do our chemistry without S4N4. When I taught this section in my inorganic chemistry courses I would bring in some S4N4 crystals and grind them before the students and then tap the powder and get a small bang like a gunpowder cap. Then the students could smell the sulphur containing decomposition products in the air above the mortar. That was until I had a larger class and used more crystals than usual. I was using my large, very expensive agate mortar and pestle and the explosion was a bit more exciting than usual. The explosion jumped the pestle out of my hand and it shot across the classroom leaving my hand numb and the mortar itself was split in two. Best ... classroom .... demo ... ever.

Dealing With Unstable Compounds: Part 3

Ah yes, metal azides. Most excellent and unpredictable explosions.

My first job in a research group was to act as the “hands” for a graduate student that had been preparing a new Tellurium azide. He had prepared a small amount (about 50 mg) in a Monel can and was in the drybox working up the reaction when it exploded in the bottom of the can. Unfortunately, the metal can served to focus the explosion and neatly sheared off the ends of two of his fingers thus creating a job opening for me. My first job was to repeat the chemistry that the graduate student had been doing. They said that it would be safer because I would do it in a glass vessel so the explosions would not be as extreme (the bursting pressure of a well made glass vessel was about 10 atmosheres according the group elders). Thankfully the grad student was so close to completion that they decided he would not need the reaction to graduate and I was moved over to the sulphur-nitrogen work.

Dealing With Unstable Compounds: Part 2

Preparing the post below brought up some great old memories. There was a point in my research career that I really, really wanted to get into phosphaalkene and phosphaalkyne chemistry. The problem was that the entry compound was tris(trimethyl silyl)phosphine [P(TMS)3] which one could buy at that time for $100 per gram. The only option was to make it. The best preparation was refined by Manfred Regitz and his glorious mitarbeiters in Germany. Get this the reaction involved taking pyrophoric white phosphorus (horrifyingly toxic) and heating it in explosively sensitive thf to reflux while slowly dropping liquid Na/K alloy (the liquid metal reduction fire from God) from a pressure equalized dropping funnel (PEDF) all under a dynamic bed of Argon. Once the addition of Na/K was complete you then opened a second PEDF that contained lashing of trimethyl silyl chloride. After the screaming and weeping you then fractionally distill the product to collect the P(TMS)3. I had to hire a post-doc for the one task of developing this reaction in our lab. I later learned that Regitz was so concerned about th potential for disaster in this preparation that he actually had a concrete bunker built in the chemistry department parking lot where his students could do the reaction and if something happened they wouldn't take the chemistry department building out. I had a hard time convincing my post-doc to wear safety glasses.

Anyway the product was air sensitive and would spontaneously catch fire in air and if it came in contact with anything such as cloth or tissue a fire would quickly occur. Needless to say we handled it with the greatest of care.

One day I decided to go to a conference. It was my habit to call back to my lab at dinner time to get caught up on what was going on in my research group. On this one day I was in a phone booth and I called the lab to have my post-doc answer the phone and say the words all supervisors dread ...

"Oh Professor H. it's good that you called ... the firemen have just left."

It turns out that, despite a strict cleaning protocol concerning the glassware used in the P(TMS)3 preparation, a PEDF with a teeny tiny speck of Na/K had somehow made it into our huge rubbermaid ethanol/KOH bath. Hilarity ensued as the teeny tiny speck of Na/K set fire to the ethanol and we immediately had a huge serving of glassware flambe. The column of fire roared up to the ceiling and my post-doc and a graduate student (net cost to me per year ~ $ 46,000) wasted three CO2 fire extinguishers trying to put the fire out. No luck. By now the sides of the rubbermaid container was starting to melt and the contents drip out onto the floor in a scene reminiscent of the movie "Volcano". It was my undergraduate summer student (net cost to me per year ~ $ 0) who understood the situation and found a dry powder fire extinguisher and put out the fire in seconds.

Yes, the fire was out but now every surface in the lab was contaminated with the powder and we would be weeks cleaning the lab. I have no doubt that there are surfaces in that lab that are still contaminated.

The Clock Resets to 505 Days

As of today, Tuesday, April 17, 2007
There are 0 days left in the lecture schedule, only the exams remain.

AND

There are 505 days until the next day that I have to lecture here again (the first day of classes in the fall semester 2008).

Teach us to number our days that we may apply our hearts unto wisdom Psalm 90 : 12

Where will Professor Honeydew go on sabbatical you ask?

May 2007 Preparation for conference presentation on research at National Chemistry Conference of the Chemical Institute of Canada in Winnipeg.

May – August 2007 Travel to the Chemistry Department of UNB (at the invitation of Professor P.) to initiate a new study on the unusual equilibrium between the cations in the reaction of SNS+ with alkenes.




September – December 2007 Travel to the Chemistry Department of MtAU (at the invitation of Professor B.) to work on a project involving low valent phosphides from tris(trimethylsilyl)phosphine



January – May 2008 Manuscript preparation and submission (at home in Moncton) on the two projects listed above and preparation of conference presentations for both projects in May 2008 at National Chemistry Conference of the Chemical Institute of Canada in Edmonton

June – July 2008 Travel to the Chemistry Department of Dalhousie University (at the invitation of Professor B.) to investigate reactive strained rings incorporating phosphorus.




August 2008 Vacation and preparation for the fall semester 2008

There are other projects I am thinking about including:

Learning how to make DSC measurements on air-sensitive compounds.
Conducting a survey of the first year chemistry courses in our region.
Initiating a project with Professor C. at SMU just for the fun of it.

Sabbatical Stories: Part 1

They say that I am going on sabbatical.

I have taught at this university for eleven years. In that time I have pretty much done what I could. There was teaching that had to be done. I did it as best I could. There were committees that needed participation. I did it as best as I could (indeed, for two years I functioned as Associate Dean just to attend meetings for the Dean). Then there was research. I came to this university at the point of a clean break from my research. At that time I had three research projects near completion and two papers submitted to journals. There just wasn't the time or opportunity to get the projects completed or the trivial experimental work done that would have gotten the papers published. I moved from a full functioning chemistry department with over 20 faculty members to a university where there were 17 faculty. I brought more equipment with me from my research than the university could afford to purchase. Each year I see more pieces of my research equipment break and wear out. Necessary losses all.

When I resigned from a tenured faculty position with a research group at Memorial University in 1996 I understood that I would be coming to an institution that did not have a Chemistry department, did not offer a Chemistry major or minor and in fact had no plans to do so. It is called sacrifice because it hurts.

In 1996 I was hired with TJ to start the Science department here with a degree in Biology. In 1998 we added AB to faculty to support the Biology degree. Under the leadership of TJ we initiated a Biopsychology degree in 1999. It was ironic (somewhat) that after fashioning a degree around our in-house expertise that the following year T left to go to Dordt College citing personal reasons and financial pressures. A subsequent attempt to create a Environmental Studies degree here was lost on the rocks of internal politics and the Science program started to drift. We then hired and lost a faculty member due to concerns over the completion of his doctorate and moving his family to Moncton. We hired ZY in 2001 to replace TJ and then we lost AB two years later (who returned to his deeper and truer love of international development with Food for the Hungry). Our subsequent hire of PH brought our complement of Biology faculty back to two but we continue to bow to the pressures of the moment as P. completes her doctorate.

What this has meant is that we have a regular Biology degree that is respected and accepted by our regional sister Universities. I would argue however that we have not made it uniquely ours or indeed uniquely Christian ... yet.

Going to chemistry conferences these days is kind of painful in an obscure way. It used to be that my friends would cheerfully greet me at the conference mixers, extract my complimentary beverage coupons (in exchange for a ginger ale ... my standard conversion). At some point someone would pointedly ask if I felt that I had made the right decision in 1996 and I would give my usual answer that this university was a better fit for me as a whole package (person, teacher and scientist) than anywhere else in Canada and my friends would all nod sagely. This year however I got the question "So how is it that you have been there for ten years and you haven't been able to get a chemistry degree started yet?" Wow, that was a hard punch right in my privately painful teacher/scientist region. I have been asking myself the same question ever since.

We have got to get a solid Biology degree that is uniquely Christian and uniquely ours before we can build towards me (if we ever do ... I may have to resign myself to academically living as a service lecturer until I retire). I am not a biologist but what would a uniquely Christian / Uniquely Biology degree look like? I can think of some unifying themes and in discussion with some of my colleagues came up with these possibilities:

A] Under the Christian concept of Stewardship Towards God's Creation: a biology degree with a strong emphasis on Ecology or Environmental Studies where Christian Stewardship is a theme in all the courses taught. We have this marvelous, forested property that is under utilized.

B] Under the Christian concept of Education: an intimate link between the Biology and Education degrees offered here with an intentional focus on education of the Community and post-graduate Science education of the teaching professional. We already have a vigorous education degree with a professor that has a Science degree.

C] Under the Christian concept of Healing : we craft a degree program and offer courses specifically designed to aid students in entry to the medical sciences (medicine, pharmacy, dentistry perhaps even veterinary schools). We could build on the recent successful admission of one of our graduates to medical school.

If there has been a lack of leadership ... it was my failure. If there has been a problem with retention ... it was my failure. If there was a lack of collegiality that would have kept faculty here ... that was my failure as well. I have never failed at anything that I truly cared about and I am not used to it now ... I am not accepting it now. Perhaps "success" or "failure" was never the point. Perhaps it was about obedience.

I offered what credit I had as a research professor and a colleague in the local universities to give the nascent Science program here some respect in the region. Was that enough? Was that all?

The fact that I even address these questions means that I need to make a change. No one is indispensable and when one gets to the point where they feel indispensable it is time to change or move on. I am 45 and can offer another university 20 years of service. I am now at the extreme outside edge of being able to move to another university, another couple of years and I could not expect any kind of horizontal move. Perhaps I am deluded in even thinking that it would be possible now.

They say that I am going on sabbatical.

I have stuff that I have to do.
I have stuff that I have to think about.
I have changes that I need to make.

In 20 days I teach my last class of the semester.
At the end of that lecture there will be 505 days before I teach here again.

When I pray, when I lift my eyes up, when I close my eyes and feel the air I feel the need ... the potential ... the necessity for change. It would appear that this university will offer me that most wonderful of opportunities to just allow myself to think.

I wonder what I will think about.

Research Ideas: Part 1

About 11 years ago the best research idea that I ever had came from a post-doc. We were discussing the best approach to a four membered ring and he suggested a room temperature route that flew in the face of the standard medieval "heat it until something reacts" route. There was some shouting and I will admit to some childish name-calling. We finally reached an agreement that he would first try the medieval route and if there was any remaining sample of a key intermediate he could give his route a shot. My way worked ... his way worked better.




It just so happened that later that year I organized a symposium in this area at a national chemistry conference where my big news would be this low temperature route. I took a couple of minutes to sketch out the full story and abjectly gave the post-doc all the credit for the break-through. The response was crazy. I had post-docs buying me drinks and faculty slapping me on the back and laughing about how it was the funniest research seminar they ever attended. My real benefit however was the response of the post-doc. The credit for the breakthrough was really trivial in terms of my academic career but that room was full of the post-doc's potential employers, paper referees and future colleagues. Since then he has shamed me by including me in his success (which has been considerable)and giving me credit for everything from the part in his hair to the colour of his Keck clips. It cost me nothing really but the benefit has been huge.

We say that chemistry is a meritocracy where the beauty of the idea supersedes all other aspects of our behaviour. That may be a limited truth. I have been to conferences where I was on the "inside" and valued by my colleagues. I have also been to conferences where I was a ghost. Polanyi says "we know more than we can tell" and research is like that. There is more to research than the idea and the glory ... there are the intangibles such as relationship and continuity of progress that just don't get measured. My post-doc taught me that lesson, I was fortunate to have been listening that day.

A Pale Blue Gas: Part 2

The product of the reaction was a radical, traditionally an unstable, reactive family of compounds with only a fleeting existence. In this case the heterocycle was stabilized by extensive pi delocalization and the carbon atoms were shielded and electronically changed by attachment to electronegative, kinetically stable CF3 groups. This also meant that the melting point of 12 degrees C resulted in a liquid with a significant vapour pressure at room temperature. This resulted in the blue gas.
I remember when I did the melting point. I had laboriously prepared the cation salt and reduced with huge excess of sodium dithionite and then fractionally distilled the volatile products three times to remove solvent and bi-products (which I would discover later to be the result of facile photolysis reactions). Then when I had grams of pure dark green black liquid I froze it and slowly warmed the solid in a Dewar until I reached the melting point. What i was not ready for was the high volatility of the solid near its melting point and soon I had huge shiny blue-black crystals growing perpendicular from the side of the flask. They were altogether some of the most beautiful things that I had ever seen. I would spend a whole year of my life preparing and characterizing this compound. The last problem to fall was the precipitation of the photolytic impurities using a method I had stumbled across in a 1908 JACS paper written by Speed Marvel in which he noted that he had precipitated polysulphide impurities with a catalytic addition of amine. I found a whisper of triethyl amine did the trick just fine.

I had pretty much photolysed the last best sample that I had in a heroic attempt to determine the vapour pressure of the liquid and solid when the word came down from Jack that a picture of the blue gas was needed the next day for an important conference in Europe. In one day I pushed a new preparation through and did the reduction and fractional distillation of the bits and scraps of material that I had available. In the meantime I took a virgin Pyrex flask and attached a new rotoflow tap and sealed off the neck to make a collection tube. I knew that the very process of placing the carefully prepared liquid in the flask and exposing it to light would destroy the compound but it needed to be done. The sample prepared the photographer was a somewhat eccentric natural light purist and he insisted that on a cold day we take the flask outside. I kept the flask warm inside my shirt with the sample tube exposed so that the liquid would remain in the tube and the flask would be filled with the blue gas. Then when the photographer said he was ready I whipped the flask out, clamped it and the picture was taken. If you look closely you can see two things. The neck connecting the valve to the flask got cold quickly and the liquid started to condense and there is a reflection of the UNB Biology Building on the surface of the flask. Thus the only picture of the blue gas was done. There would be no more.

Dealing With Unstable Compounds: Part 1

When I was a graduate student I was doing a demonstration of the generation of Cl2 from a reaction mixture containing potassium permanganate and HCl for an inorganic chemistry lab. I had set out the equipment and reagents beforehand and when it came time to do the demo I did not re-check. It would appear that someone had taken the concentrated HCl and replaced it with concentrated H2SO4 without mentioning it to me. What I remember is doing the demonstration and not getting any chlorine so I told the students to move on while I worked on the demonstration. This will now sound overly mystical but while I was holding the apparatus puzzling at the appearance a voice said “Put it away”. I was holding it at arms length, towards the back of a fumehood when it exploded, shredding the cuffs of my labcoat, spraying me with a mixture of concentrated acid and permanganate and (in a delightful escalation of events) breaking open several winchesters of waste organic solvent that a research group had decided to store in the teaching lab fumehood. The solvents caught fire. I was focussed on my face and immediately turned to a sink and began to hose my upper body with cold water. There was a point when I had two graduate students, Mike and Daniel at my back trying to put out the fire with fire extinguishers while I yelled that I needed to keep the cold water flowing on me. When they finally dragged me out of the lab the permanganate in my hair combined with the cold water to produce a ghastly effect for the assembled students and faculty as I was escorted past the evacuated building. I called my wife of six months from the hospital and for the first (but not the last) time started the conversation with "First of all I want you to know that I am alright". In the post accident analysis, the professor in charge of the course (who I privately suspect of accidently making the acid switch) just said “Well, it will make the students very safety conscious and the lab needed a good cleaning anyway”. All because I did not re-check the reagents before doing the demo. Remember, it was only stupid if you did not learn from it.



A selection on Mn chemistry from Cotton and Wilkinson, "Advanced Inorganic Chemistry, 5th Ed."

A Pale Blue Gas: Part 1

It was the summer of 1984. I was in the first year of my graduate work and I was cleaning up a project initiated by a previous graduate student. Greg was remarkable. He had a gift for being able to prepare and isolate important compounds by accident. Halogen facilitated oxidation of group IV and V compounds? He discovered it by realizing that he had incorrectly added elemental halogen to a reaction. The cycloaddition of SNS+ to pi bonds? Discovered while he was trying to find a good solvent for SNSAsF6 and he tried acetonitrile and was unable to recover his solute. I had come along at the end of his run and picked up the SNS+ reactions with pi bonds and had started with alkynes. I had prepared a variety of compounds using the SNS+ / alkyne reaction and they had worked well. My supervisor Jack decided that I should go to England to learn how to do cyclic voltametry in liquid sulphur dioxide. That brought me into the sphere of Arthur a fragile, dedicated chemist of the collegial old school. It was in Durham that I was trying to do anion exchange reactions to get rid of the AsF6- anions so that the cyclic voltametry would work better (in fact it never did "work"). One day, late in the afternoon, I would wash a solution of CAT into a solution of potassium iodide and to my wondering eyes the whole flask filled with a pale blue gas. I knew all that had come before me and I knew that I had discovered something new. I was seeing something important for the first time and it was important and new not only for me but for my whole discipline. My real research career had begun.