Tuesday, May 30, 2006

Submitted - YESSSS!

After a tense hour or so this morning I was summoned to see my supervisor. He was satisfied with the HPLC trace and so, after an agonising few moments, I have finally clicked [send] and it has disappeared into the cyberspace aether, winging its way merrily to Harwood at Reading.
It is such a relief to have submitted it.

This morning I'm actually doing the Ru-catalysed hydroborations ... more on that story later, assuming no pesky undergraduates turn up for their practicals.

Monday, May 29, 2006

Bank Holiday

Bank holidays are always a bit strange in the lab. All the people who are sallaried seem to regard it as an unalienable right to take a day off, despite the fact that many of them will regularly work on Saturdays and/or Sundays out of personal choice. Most of the D.Phils were in, except those who have boyfriends/girlfriends who are in paid employment.

I was somewhat frustrated that my supervisor wasn't in, since my paper is sitting in his pigeon hole waiting for him to OK it for submission. At least it is dated 28.v and I hope he'll take the point.

I spent most of the morning thinking about rhodium catalysed hydroboration reactions and the rest of it looking for Rh(I) catalysts which seem to have been scattered around the stock system in a bizzare mixture of systematic, semi-systematic and trivial catalyst nomenclature. D's stock of catalysts are all kept in one dessicator but I'm not sure that works unless all the catalysts are kept there.

The afternoon was divided between trying another titanocene reaction, columning some old stock contaminated starting material, and brushing up my biochemistry in anticipation of teaching it to my sister next weekend.

The weather is playing some serious tricks on us, changing from blue skies to stormclouds in the space of 20 minutes and then back again. This evening has been beautifully clear. The setting sun falls on the oak opposite our house and makes it glow with a warm radiance that transforms it from an ordinary tree to a thing of beauty, and reminds me how much I like living in my house, and how blessed I am to be able to stay here for another year.

Saturday, May 27, 2006

HPLC - done!

I've finally got a set of HPLC traces that I think are good enough to show to my supervisor. There's clearly only one enantiomer of my enantioenriched product, so we'll go for >99%. I also noted that in preparing a new batch of the alcohol for this analysis that my best yield has improved from 67 to 84%!

The original date for the submission of my paper was to have been 5.iv - so it's taken nearly 2 months to sort this out but it's done now.

I spent most of the day at work. Firstly finishing the last-Friday-of-the-month clear-up that I started yesterday (including polishing my fume hood metalwork with Brasso), secondly writing up the HPLC stuff and the titanocene-mediated epoxide opening that I've worked on so far and thirdly looking at biochemistry topics to help my sister with her A2.

This evening has been spent looking at some more of the Bagley Wood mosses. I have looked at Campylopus introflexus for the first time and it is so beautiful. Bryophytes must be the most under-appreciated part of God's creation.

Friday, May 26, 2006

Highly Problematic Liquid Chromatography

is definitely the definition of HPLC.

I got in at 0610 this morning and ran the analysis properly set up and with the right eluent and ... 4 hours later: nothing - or rather something very wrong - peaks but with strange profiles!

Then I ran it again (1120-1520): no peaks at all - my sample had broadened into the baseline.

So I've given up trying for the 0.1 conditions and am running at 0.2 mL min-1.

1530 start, should be over by 1830! It had better be, since I need to be home at 1915 to meet the landlord and sign next year's lease, which is a scary commitment but nowhere near as stressful as HPLC.

I'm so pessimistic about this that I've bought a new bottle of heptane. I've now eluted nearly 2.5 L through the HPLC trying to get the ee from this reaction. That is so depressing.

Thursday, May 25, 2006

Arrrrrrgh: HPLC horror

I've decided that I really don't like HPLC. I never really considered it to be one of those exciting techniques that makes children say to their mothers at bedtime 'when I grow up, I want to be a chemist', but now it's really in my bad books.

I have spent most of the day running the HPLC of my asymmetric compound. I had 2 sets of conditions separating the racemate, one with a flow of 0.2 mL min-1 and the other with 0.1
The 0.1 is slighlty better but takes a lot longer. What I hadn't realised was how much longer my single enantiomer would take to elute compared to the racemate. I think I have a hand-wavy argument for why this is, but it doesn't include the words 'theoretical plates' so it's probably wrong.

The long and the short of it is that due to 3 mistakes in a row I still don't have the ee of my compound. I'm going to get up super early and try and get in and get it running before 8am. That way I might actually have the answer by lunchtime. From what I've seen today, it's looking good with only one peak in the asymmetric product implying >99% ee.

Tomorrow's the day - it just has to be.

The suspense is unbearable

No posts since Tuesday because I've been frantically busy. I've made the enantioenriched ketone and am now running the HPLC analysis.

I haven't been this tense about work for a long time: I've edited the text of my paper all ready to insert the data, print it and give it to my supervisor. There's still another 2h to go, though.

Update to follow later ...

Tuesday, May 23, 2006

Nothing to demonstrate

Junior demonstrating is one of those things that D.Phil. chemists are ambivalent about.

On the one hand, it is a really boring experience where you get to watch a bunch of incompetent and inept undergraduates make a complete hash of really easy experiments, break countless items of glassware and if you're unlucky, injure themselves in the process. Most of the time it is about as exciting as watching paint dry and it usually turns out that your demonstrating slot coincides with the day that you have the most other stuff that really needs to be done now.

On the other hand it pays. In fact it pays rather well: about £70 per day (usually 4-6 hours with 45 minute lunchbreak). Pay is something that no grad student (especially if it looks like he'll over-run) can afford to turn down. It's much better than tutoring since there's no preparation, no non-contact time marking, and you can usually take an entertaining book to read (I've been taking PG Wodehouse this term (see:Wodehouse: the non-Jeeves stories)

Just occasionally, though, there will be a really, really good day where nobody turns up! Since experiments have to be started by 1130 (in order that they have a reasonable chance of finishing them) if no one has turned up by then the demonstrators can leave, but they still get paid (they can be called back to sign someone off if required).

Today has turned out to be one of those glorious days! So it's back to the lab for all the column chromatography anyone could wish for. There had to be a downside, didn't there?

Monday, May 22, 2006

Monday in the lab

Quite the most exciting thing today was the HPLC trace (see previous post), but I've also managed to make another target (a bicyclo epoxide) for a test reaction. I've even characterised the epoxide and launched the test reaction to run overnight. Slick or what? It makes a real difference getting in before 0830 - I seem to get so much more done in the mornings.

The HPLC's not looking quite so promising. I'm making the enantioenriched to test in comparison, but I'm still looking for that elusive better separation. Oh well.

We had a group meeting this afternoon during which I struggled to stay awake. Sitting in a warm darkened room straight after lunch, listening to a talk your not particularly interested in is not a recipe for staying awake!

I've felt quite tired all day but that might be due to having woken up at 0510 coupled with the fact that I have increased the distance of my morning run. I'm not sure how far it is exactly, but I think it's now a little over 2 miles (so about 3.5K) up and down a very big hill! For someone who generally avoids physical exertion I think I'm doing OK. It does seem to improve my mood, so perhaps all the people who talk about endorphins and serotonin levels being boosted by exercise are actually right.

HPLC - success!!!!!!!!

Finally, I've managed to resolve the enantiomers of my racemate by HPLC.

Quite long retention times (~100 minutes), but you can drive at least a medium sized saloon (if not quite a bus) between the peaks!

Very happy indeed.

Bagley was fun!

I got down there at about 6.20pm and had an hour and a half of very exciting, though at times quite damp, fieldwork. It was very tranquil - I met one guy out walking his dog about 30 seconds after entering the woodland and then no one else for the rest of the time.

I walked around the edge of the section I was recording and then made my way across it a couple of times. The map that has been made available to me is somewhat out of date, and some of the paths that are marked as minor have become major thoroughfares for (I guess) landrovers whilst other apparently once major tracks have been abandoned and become overgrown.

The area I was looking at was a mixture of birch, norway spruce (with beautiful carpets of old pine needles and moss), mixed oak/beech and also some more open heath-like areas, which promise to become quite overgrown with bracken as the year progresses (at present the new crosiers are just beginning to unfurl).

I made 15 stops for collections, collecting 1 or 2 spp at each site, so I've now got about 20 species to identify! I made a start on Sunday afternoon, looking at just three of them. One was Mnium hornum, which is a very common woodland moss, but it's been a while and I wanted to make sure. Another I managed to ascribe to the genus Bryum but Smith's keys stated explicitly that I couldn't get further than that without having the spore capsules - so that one will need to be re-visited at some point in the future. The third one I looked at (only briefly) was really difficult. The leaves were about 2 mm in length, very narrow and also highly incurved, making microscopic examination quite difficult. I'll have to look at that one again.

I hope to work on these over the next 10 days and then head back to Bagley sometime during the weekend after next. I didn't manage to do any sketching (at one point when it started to rain heavily I considered pausing under a tree and having a go, but the rain eased very quickly and I was back to the mosses). I did take some photos, however, of what I believe to have been Polytrichum commune - there were huge stands of it bearing immature capsules which were very striking. The light wasn't good and I used my camera's automatic metering and flash - but I'm hopeful.

A bonus was meeting some deer. They were in shaddow and too far away to be certain, but I think they were probably fallow deer, rather than muntjak but I'm not sure.

Saturday, May 20, 2006

Anticipating some botanising later ...

I'm writing this post in odd moments between doing lab stuff - it's Saturday afternoon, so I don't have to be working all the time :o)

I'm meant to be doing a survey of the bryophytes in Bagley Wood (a large area of woodland to the southwest of Oxford owned by St. John's College) . That is to say that I was encouraged to embark on this project, obtained permission, did a bit and then ignored it for a long time. After finishing in the lab today I hope to get down there for the first time in ages. I've noticed that my permit is up for renewal in November and in order to have it renewed I think I'll need to be able to produce some data!

Bagley is quite an interesting place. It's mentioned by Arnold in The Scholar Gypsy:

In autumn, on the skirts of Bagley Wood—
Where most the gypsies by the turf-edged way
Pitch their smoked tents, and every bush you see
With scarlet patches tagged and shreds of grey

(I like Arnold's work, but don't think I understand very much of it!)

For a long time the Oxford Forestry Professorship was associated with St. John's and in consequence the whole wood is a massive collection of forestry experiments. Every 100 yards or so, the trees change completely! An ideal situation for high bryodiversity and therefore a lot of fun for a bryologist. I would be happy to describe myself as an amateur pteridologist, since I can identify a good chunk of the British fern flora, however the title of 'amateur bryologist' can't really be applied to me, since I'm still at a very basic level with my mosses. I am able to execute the survey, though, with the help of some good keys. I use mainly Watson, but also have Smith on hand for a more detailed desciption of species, especially those that are only sparsely described (and in smaller type too) in Watson. I also have ex-Library copies of the 3-volume Atlas of British Bryophytes (my best value book buy ever @ £3 total!).

Doing a full transect-method/ quadrant weilding survey is beyond my expertise and time available, and previous records are constituted by a checklist, so that is what I'm going to aim for. I've divided the wood up into areas and am hoping to produce a checklist of species for each area (and perhaps sub-divide each area to smaller sectors), so as to produce an overall checklist for the whole wood with some element of distribution data. Today I hope to do a first sweep of an area I haven't looked at before. Each area will need several visits because mosses are small enough to be easily missed, plus some species will be more identifiable (e.g. bearing capsules) at different times of the year.

I'm also taking my camera and sketchbook. I haven't done any photography or sketching for ages and I'd like to get back into it at some point. I'd also like to work on my watercolour technique, but I think that will have to wait until after I've written-up my D.Phil.

All in all, I'm quite excited about going today, which is good since my enthusiasm for the whole project has been low for so long. Of course the fieldwork will need to be backed up by a lot of microscope work tomorrow in order to get identifications of all the specimens I collect today. The temptation is always to start as soon as you get them home, but I think an hour of the Calvin biography that I'm reading followed by an early night is much more in order. Perhaps I could fit in an hour first thing tomorrow before church.

Friday, May 19, 2006

Windows vista

I've just read that the new Windows release (Vista) that is due for Jan 2007, has minimum hardware specs that include 15GB of HD space!

What on earth are they doing with all that?

Windows has long been known for being untidily written, but that's just plain rediculous when compared to a bootable Linux release like Knoppix, where a whole OS and program suite fits snugly on a 650MB CD.

I dread to think how much space Office will require once it is Vista-ised - 40GB seems not unlikely!

Kinetics of free radical chain reactions

I've been thinking a lot about the kinetics of my radical reactions this morning. Even modelling the initation is tricky, since my method uses the slow addition of initiator via syringe pump, which gives rise to a differential equation that I don't know how to solve:

d[In]/dt = k1(t) - kd[In] where k1 is the rate of addition and kd the rate of decomposition.

The thing that has become overwhelmingly apparent is that my abilities in the solution of differential equations (which were never very extensive) have diffused away over the last six years, and trying to skim through the big maths for physical scientists books doesn't seem to be much help.

Given that I also add the chain carrier and the electrophile via syringe pump, I think that this is going to be a nightmare of analysis. It is interesting that the kinetics texts never seem to treat chain reactions in any depth. Maybe it is too hard a problem.

Not going to be beaten yet, though.

Progress?

Another day in the lab draws to a close and I'm looking forward to heading home to eat, read and play the piano.

I'm not really sure if I've made any progress today.

The HPLC seems to be playing up and giving me weird step-like plots of random wanderings up and down the scale. I don't think my compound eluted at all, despite having previously shown a retention times of 10-40 minutes. Not sure what I'm doing wrong.

My efforts to crack dicyclopentadiene directly into my reaction yesterday seemed to have worked to some extent - I think 40% of my tosylacetylene underwent Diels-Alder (by NMR) but I think I'll try a bigger scale cracking/distillation of cyclopentadiene tomorrow, to be sure I've got some good stuff.

I found some more of the alkyne in the freezer but it looked really scummy, though recrystallisation from EtOAc/pentane produced a fine crop of fluffy yellow crystals. Waited all day for the NMR to come back because our fast 200 MHz machine is down. Again.

I've tidied my desk - at least I managed that.

I've also been thinking about kinetics of free-radical chain reactions. Last time I thought about this seriously I think I concluded that it was a very hard mathematical problem. My supervisor also thought it was a waste of time. I think, though, some theoretical analyses would look well in my thesis, so I'm adding it to my 'things to do in my copious free time'.

Platensimycin

In today's Nature (2006, Vol 441, Issue 18, p 358) there is a report of a novel antibiotic with activity against MRSA and vancomycin-resistant enterococci.

However, as far as I can see, it's a real monster of a structure to synthesise, with two quaternary stereocentres and a polycylic core with no handles for stereocontrol.

Thursday, May 18, 2006

Wodehouse: the non-Jeeves stories

I've long been a fan of P. G. Wodehouse, but my main exposure has always been the Jeeves and Wooster stories. Recently, though, I've been exploring his other novels and have found them to be brilliantly funny.

What is so admirable in his writing is the effortless way that the scene descriptions unfold with the maximum gentle release of suspense for comic effect, and the little throw-away clauses tacked on to the main sentences that communicate so much.

I'm currently reading the Lord Emsworth short stories, which are just the right length to be read over a lunchtime break.

Definitely worth reading!

First post

I've thought about starting a blog for a while, but haven't got round to it through lack of time. I still don't have the time, but hey - sometimes you've just got to get on with things ...

FYI "Ferntastic" is a contraction of "ferns are fantastic".

If you're in any doubt, then see http://www.nhm.ac.uk/hosted_sites/bps/ and be convinced.

Mosses are cool too.

Botany is sadly just a hobby - I'm an organic chemist by training. I expect some of the trials and tribulations of chemistry will become a feature here too.

Better go and check my reaction.