A Sabbatical Takes an Unfortunate Turn

So it is winter in Canada. The cold hands wrap around your house and the restless fingers of cold probe to find gaps in the thermal walls of your home and psyche. In the old days, it was a time for "forting up". A time for reflection and repair. But now? Now we defy the weather and try to behave as if the weather is an inconvenience but life goes on 24/7.

So it snows again and again and I dig out the car again and again.

We have had some kind of snow every week since December and for the past month we have had about three snow storms (where accumulation is more that 15 cm) every two weeks. So the snow has built up to the point where the snow blower can no longer get the snow up over the snow banks. The school kids have missed so many days of school that a somewhat panicked school district had them go to school in a 20 cm snow storm two days ago. As a parent I am somewhat torn on one hand I need them out of the house so I can think and on the other hand I do not want them lost in a blizzard walking to school.

So, I make what accommodations I can for the weather but my sabbatical is slipping away so just like before I clean off the old Kia Rio and head out. To make a long story short, there was slush on the road, the Rio has a very light back end (unlike mine) and when the back end came loose in the slush I focused on getting the car slowed down and in control. By the time I started feeling good about control the car reached its "tipping point" and very slowly slid sideways down into the ditch.

There is a shocking disjoint when one finds yourself sitting in your car but with the gravitational orientation frame orthogonal to the visual orientation frame.

It would appear that my travelling days are over until spring. I guess it is time for some of that good old "rest and reflection".

Dealing with Limitations

It has not been a particularly productive month. At the beginning of December I was working in the drybox preparing samples when I got a call on my cell. It was not good news. A close family member had an accident at work and within a couple of weeks he succumbed to his injuries and our shocked family was trying to cope with the aftermath. That was coupled to an astounding series of winter storms that left us housebound.
What that also meant was that at a very inopportune moment in the research cycle I was forced to walk away from the bench. Christmas, as somber a Christmas as I remember, came into the mix and suddenly it was a wintry January. It wasn't that it was impossible to do research as much as it was just the wrong time to have to leave the bench work. I had an agreement with my family that in the heavy winter months my commuting to the two research universities would be kept to a minimum and only on days where the roads and the weather were clear.So, with the work incomplete, I started the writing process by organizing and reading the pile of literature related to the research.

But writing (at least the way I do it) cannot be done in a vacuum. I need some back and forth discussion with other chemists, so to take part in the research group discussions I had to dig out the Silver Bullet and head out in the early morning.
When I get to the research university I first have to check on my neglected reactions and update my observations but my limited time on site means that all I can do is watch. This reaction has gone from a corn-straw yellow to a clear cherry red for no good reason. I wish I knew what was going on in there.
Then we have discussions and debates in my temporary office (borrowed for the year from an emeritus professor who had research contacts with an Italian chemistry group, thus the prints over the chalkboard).
Head stuffed with ideas and the light declining I turn the car towards home and the rising Moon for the two hour trip back. Back to the literature and trying to write a paper on incomplete research so that when we do get the bench work done the paper will be ready to go. Not the best way to do things but the way things have turned out. Four hours of driving for seven hours on site and a chunk of that spent in the library reading the industrial chemistry literature that almost seems like it is written in a chemical language I don't know. It is as if they have their own non-systematic name for everything. Ugh.It is always good to get home. I am happy to have the freedom to focus on research during this sabbatical period but as the half-way point slips by I feel that I am way behind and I need to start working harder and smarter. This must be what students feel like.

Everyone Gotta See This

Truth, all truth.

http://www.pbs.org/kcet/wiredscience/video/82-dangerous_science.html

This is my story as well. If this were a religious evangelical meeting I would be on my feet yelling "Testify!".

I in fact have my own first edition copy of the "Golden Book of Chemistry Experiments"!

I in fact had my own "lab space" under the basement stairs in my parents house.

TESTIFY!

Research and Ghosts

So ... it's been a long time. I was pushed into a sabbatical, worked out an agreement with the family and a regional university that has me working in a nearby city, bought a broken down Kia Rio and got it working, developed an association/collaboration with a research group and started cooking up chemicals.

Research at the bench is what it always has been. Sometimes it is a visceral delight as the reagents combine into something new. More often than not the process involves taking pure, expensive starting materials and turning them into sewerage but that's the way love goes. 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 where I live and drive to an urbane and quiet small city with a wide beautiful river where I used to live. 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 chemistry relevant to some aspects of battery chemistry. I am currently up to my eyeballs in various forms of oils that refuse to form solids let alone crystals. But it's the colour changes that jazz up my day. I have discovered a chemical reaction between two white compounds 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 (so far ... Blue, green, yellow (lots of bright yellows), orange and red). 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 the Chemistry building two days ago. The water filled a room so that it was about a meter deep and the doors into the room could not be opened (genius designer had them 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 rural 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 still finished in four. I remember meeting him in the hallway of the Chemistry building the year he graduated ... 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 commit to living in the precious gift of the present. As long as I live, I will carry the memory of that last conversation. 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.

You want the Chemistry? ... You can't handle the Chemistry!

OK I guess I need to provide some detail. I was a graduate student in an inorganic fluorine chemistry research group. We were investigating Main Group compounds that had inorganic pi systems created by oxidizing electron rich molecules using Arsenic pentafluoride in liquid sulphur dioxide.

The graduate student ahead of me discovered reaction 1. S4N4 is a contact explosive prepared from one of those classic fire from God reactions that were popular in the late 19th century. So you prepare the explosive and then grind it to a fine powder (grind gently because I was in a lab in England where a small beaker of the stuff spontaneously exploded and split a lab bench from end to end). You put the fine powder and some sulphur in a vessel with lots of sulphur dioxide as solvent and then add lashings of AsF5. About a week of recrystallizations later gets you to SNSAsF6 which contains the dithianotronium cation [SNS]+ (think ONO+).

Now SNS+ is a lot of fun but I discovered rxn 2. It turns out that SNS+ does not react like ONO+. SNS+ is a propargyl-allenyl 1,3-dipole favouring reverse electron demand cycloaddition reactions with pi bonds. Thus the reaction with alkynes gives the derivatives of CAT in high yield.

The hero of this story is the 4,5-bis(trifluoromethyl)-1,3,2-dithiazolium cation. I discovered that the reduction of this cation by sodium dithionite in liquid sulphur dioxide gives the blue gas radical in reasonable yield but the reaction works the best because the products are the radical, insoluble NaAsF6 and the solvent SO2. Laborious fractional distillation of the reaction volatiles give the black liquid referred to in the previous post. And I always wondered why the preparation wasn't repeated more often.

Thanks for the interest in the chemistry.

My Small Contribution to Compounds with Pretty Colours

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. 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 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 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 fluorinated anions so that the cyclic voltametry would work better (in fact the CV never did "work"). One day, late in the afternoon, I would wash a solution of the cation into a solution of potassium iodide and to my wondering eyes the whole flask filled with a pale blue gas. In my small area 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.

It is still unique in my area of chemistry.

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 an early 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.

And that is my coloured compound story.

Chemistry Labs and Teaching

It is a truth accepted by everyone that especially in Science principles and concepts taught in lectures are best understood by the student when coupled to a laboratory experience where the student not only has a "hands-on" experience with the experiment but also must grapple with recording and analysing the lab in the context of what was taught in the course. So we believe.

The horrible truth is that for the most part the link between lecture and lab is tenuous at best. In many places the labs are so de-linked from the lectures that the lab are offered as a separate course (although perversely in such institutions the number of credit hours required to graduate is increased for science students to the amount of lab courses). It takes a student with a vast memory and a strong desire to make the link to actually benefit from the lab in the manner which was intended.

And then there are the microlab enthusiasts.

Some time in the 1990's micro scale lab procedures swept the discipline. It was everywhere and the rationales were many. Smaller amounts of reagents meant less risk and the same pedagogical goals were attained. In my opinion the same goals were attained because the intent of the lab experience was lost prior to the change to microscale and its popularity was simply the result of pragmatic lab management and prescient students falling somewhere between mind reading and "Clever Hans". We who love chemistry all remember the astonishment and glee that we knew in our synthetic labs when the procedures "worked" and gave us handfulls of product with crystals that you could kill aliens with. Conversely we also knew the hot acrid taste of crystal envy or the shame of prep-TLC inadequacy. Not possible when you have a mini centrifuge tube and the positive sign of reaction is a decrease in transparency. No, it requires bulk, it requires amounts where static cling from the vessel does not retain more of the product that you can recover.

But, it is almost over and it will be soon. We could see it coming and those of us of a certain age will remember our chemical youth with nostalgia. This story has been making the rounds (first to my eyes by a citation from Derek Lowe of "In the Pipeline" commenting on this link).

In my opinion the liabilities, poor link with pedagogical goals and cost (of teaching, maintaining and disposing) of chemistry labs will bring their demise. There will be a transition period where we will rejig our labs to run on nothing but consumer chemicals and ethanol but that as well will pass because the waste will just cost too much to deal with (because the safety officer will not see how bleach in the lab could be handled like bleach at home). The bell will also begin to toll for university research chemistry labs as well. It may take longer but it will have to happen as environmental concerns and the power of safety officers approaches an absolute level. At least some of us were around for the golden age of teaching chemistry both in learning and teaching.

"Pull out the projector Tommy we are going to watch a video of a chemistry laboratory."