Crystals are a girl chemist’s best friend

My name is Anna Ahveninen. Although that surname can try to convince you otherwise, I’m half a year into my PhD at the University of Melbourne, in Australia. The broad scope of my project is the synthesis of metallosupramolecules and their characterization by X-ray crystallography. The finer details? Well, that’s taking a while to figure out.


I’ve only been at the University of Melbourne for as long as I have been working on my PhD. I moved to the Abrahams-Robson group from Monash University, where I completed my undergraduate degree with honours. Having fallen in love with transition metal chemistry — the beautiful coloured complexes and their satisfyingly sparkly crystals — and crystallography in my honours year, the transition to my current project was not a difficult one. Kickstarting it has definitely been troublesome, however. In the past six months, I have been chasing a discrete assembly without a grain of success. The last two months saw a change in my focus from discrete assemblies to coordination polymers (with the same coordination motif), and just a few short weeks ago, I finally hit the jackpot. A red, sparkling, reproducible jackpot.

Since then, I have been working away at trying to turn that result into more results, hoping that it will propagate into a project and grow, with care and love and hard work, into a thesis. The following is a sample of how I am going about that.


Mondays are pretty exciting for someone working on a crystallography project. Mondays mean that my reactions will all have had at least two extra days to crystallise! I pick up my rack of vials and carry it with a flourish over to the microscope to check for clean edges and tell-tale sparkling. Since we do not have a microscope with a camera in-built, macroscopic pictures of my sparklers will have to satisfy you (Fig. 1).

Figure 1: Vials full of sparkly crystals, ripe for the X-ray diffractometer.

Figure 1: Vials full of sparkly crystals, ripe for the X-ray diffractometer.

I set about my run-of-the-mill inorganicky business until my group’s favourite time of the day: tea time. Although we have no formal group meetings, we meet with our supervisors every day around 4 pm for tea. It gives us the opportunity to ask questions of our supervisors and bring new results to their attention, while also being a nice break and group bonding activity. The group bonding consists of doing the quiz in the Herald Sun and a game involving Fred Basset. Fred is a little tradition that goes far back enough in the Abrahams-Robson group that its origins are unclear. In this game, one of our group members describes the comic strip (Fig. 2). Our job is then to guess what Fred says in the last frame. Weirder than weird to an outsider, this tradition absolutely grows on you, and has become akin to a religious duty in our group.

Figure 2: Fred Basset in his natural habitat. Fred's home is at gocomics.

Figure 2: Fred Basset in his natural habitat. Fred’s home is at gocomics.

My afternoon comes with the pleasant surprise of overnight time on the X-ray diffractometer. One of our postdocs does all of the diffractometer time allocation to ensure that the time is divided fairly, so it always seems to spring up on me.

The X-ray diffractometer (Fig. 3) has to be my favourite instrument. I get a serious thrill when sorting through crystals on a glass slide under the microscope, picking the one I think looks the most promising, mounting it on the diffractometer, centering it and then shining some X-rays on it. The excitement builds at the initial blank frame, and a few seconds later – boom! Diffraction (Fig. 4)! As is common in science, the usual result is very little diffraction, streaky diffraction, or no diffraction at all. It’s all worth it, though, when that first frame flashes up and the spots are well-defined and single and strong and beautiful.

Figure 3: The University of Melbourne X-ray diffractometer.

Figure 3: The University of Melbourne X-ray diffractometer.

Figure 4: A frame from one of my X-ray diffraction data collections.

Figure 4: A frame from one of my X-ray diffraction data collections.



The morning begins with a coffee with my group mates, followed by the weekly inorganic chemistry seminar. This week, it is a group member’s colloquium, wherein he has chosen a field of chemistry outside his project to give a talk on. These talks are very interesting to listen to and are usually very educational, both for the speaker and the audience. The rest of the day is spent trying to make sense of my X-ray diffraction data, since I have had the misfortune to be working with high-symmetry cubic systems with a high degree of disorder.

Late in the afternoon, I stop bashing my head against the crystallography wall and take some of my amorphous and microcrystalline samples to the IR spectrometer in the teaching labs. IR spectrometry is free and easy; it helps give me an idea of whether a reaction that doesn’t want to grow nice crystals is worth pursuing.


Wednesday morning is when I would usually demonstrate for my first year class, but since there are no first year practicals running this week, I get a free morning. I spend my time marking reports from the previous experiment. I turn my attention to the lab afterward, but discover that frantic preparation for powder samples for the Australian Synchrotron from two weeks prior has left my stash of 3 mL plastic syringes precariously low. I get a reaction or two in, and am then forced to find something else to do while I wait for the chemistry store to fill my order.

Mid-afternoon, I meet with my supervisor for a long talk regarding my red, sparkling, reproducible jackpot and where we can take my project from here. An hour of musing, brainstorming and me frantically scribbling down notes later, we break for tea. My spirits are elevated and the future of chemistry is looking good.


To my annoyance, I discover that the delivery of 3 mL plastic syringes is excruciatingly slow. Crippled into inability to do my reactions, I spend part of my day backing up my lab notebook. A good method that I learnt from the postdoc in my honours year, is to take pictures of your notebook pages and create an index in Excel to correspond to compound syntheses found on particular pages.

Leafing through my notebook leads to a decision to create a spreadsheet to track the variables of reactions I have been doing. I feel more secure having it available at a glance and organised, as I swear I can feel the details slipping out of my brain. I also spend some time catching up on my journal RSS feed, which I admittedly ignore in favour of doing lab work much more often than I should.


With the delivery of my plastic syringes, I can get into some serious synthesis action. My ligand, when deprotonated, tends to oxidise easily in air. To combat this, I bubble nitrogen gas through all three layers to drive out as much air as possible before layering my ligand with a layer containing a base, a metal salt and a counter-ion (Figure 5). The third vial contains a buffer layer between the two. I run two reactions parallel, as this saves me time in the long run.

Figure 5: How metallosupramolecular chemists do air-sensitive chemistry.

Figure 5: How metallosupramolecular chemists do air-sensitive chemistry.

In case you are curious, the 3 mL syringes come in during layering. I layer my reactions in the reverse order, starting with the least dense layer. Then, I inject the buffer layer below the initial solution, and finally, the densest layer. The volume of the syringes is important since I don’t like to do more than one injection per layer: for one, the suba seal becomes compromised quicker, and for another, it is easier to mess up the layering with more than one injection. Syringes with a too-high volume are also unwieldy and tend to draw in too much gas. When layered well, the reactions can look pretty spectacular (Figure 6).

Figure 6: Either layered reactions or bottled sunrise.

Figure 6: Either layered reactions or bottled sunrise.

My day, and week, draws to a close with drinks, snacks and a game of Cards Against Humanity with my group mates. What better way to end a week of brain-intensive work than a really inappropriate game with a bunch of really awesome people? It’s evenings like these that remind you that life – and science – are awesome.

Author biography

AnnaBioAnna Ahveninen was born and raised in Finland. She completed her Bachelor of Science with Honours in 2014 at Monash University, Melbourne, Australia. She is currently a PhD student under the supervision of Assoc. Prof. Brendan Abrahams at the University of Melbourne. She tweets under the handle @Lady_Beaker and blogs on Chemistry Intersection.

If you are a blogger interested in writing a guest post for #RealTimeChemInFocus, please get in touch with @RealTimeChem on Twitter.
Also don’t forget about #RealTimeChem Week 2015’s blog carnival, starting 19th October. Find out more here.

Chemistry: Lost in Translation (sort of)

I’m Jason Hoshikawa, a 2nd year PhD student in the Kitagawa Lab at Kyoto University in Kyoto, Japan.My main area of focus is polymer synthesis and heterogenous catalysis using porous coordination polymers (PCPs).

The thing about working in the sciences (and maybe the arts too) is that we generally work in a multi-cultural environment. During my undergrad and Masters in the US, I was the native surrounded by foreign students. It was a wonderful experience. Many of the members of that group were from India, specifically from around the Hyderabad area. This turned out nicely for me because Indian food is my favorite food. When I entered my first research lab as an undergrad, I was assigned to work with a woman that makes the most amazing food. She quickly learned the key to motivating me to work hard in the lab. If I worked late enough, she would bring me dinner. I miss those dinners more than you can imagine.

Kyoto University's clocktower. - Image Courtesy of Wikipedia.

Kyoto University’s clock tower – Image Courtesy of Wikipedia.

But, now, I live in Japan where I am the foreign student surrounded by natives. Aside from learning about chemistry, I’ve learned a lot about myself. This is not the first time I’ve lived in Japan, but this time it’s very different from my previous experiences.

More than the simple difference in culture between the US and Japan, the other bit of context that may be important is that the Chemistry Department at my previous university is relatively small compared to our department at Kyoto University. The change in environment was quite significant. Going from a department where everyone basically knows everyone else to a department where there are simply too many people to know hardly anyone outside one’s own research group was rather shocking.

In my research group, all of the students are assigned various jobs. Most students are assigned to manage an instrument or two, and some students, like myself, are assigned to administrative roles. I have two administrative roles, actually. Firstly, I am the lab manager. I’m responsible for the general day-to-day operation of the lab (i.e., the room where experiments are performed). I purchase all the expendables (e.g., gloves, vials, pipette tips, glassware, weigh paper, etc). In a separate (but related) administrative role, I’m also responsible for buying all of the solvents (both regular and deuterated) and common reagents (acids, bases, metal salts, etc). Basically, I buy everything except specific reagents that only one or two people would use, and instrument-specific expendables.

An average day

In our lab, we work Monday through Saturday, and the layout of my day is basically the same, unless there is something special that requires me to leave early.

My alarm is set for 07:00. The actual time that I wake up varies seasonally. I don’t have blackout curtains in my room, and Japan doesn’t observe summer time (which I’m happy about), so right now, the sun rises at around 05:00. During the summer, I wake up often before my alarm, but during the winter, I can usually sleep until my alarm wakes me up.

I like to leave my apartment at 08:45 so that I can get to the bus stop early enough to get a seat on the 09:00 bus. The trip to campus takes about 10 mins. If you’d like to see the area around where I live on the bus ride to campus, watch the video below.

I take breakfast at the bakery on campus. They have a lovely breakfast set for Â¥270, and I usually add to that a donut (Â¥151). While I eat breakfast, I like to look at twitter, reddit or Instagram, while listening to a podcast. My work day starts between 09:30 and 10:00. Everyone usually gets in during this time, and we generally think of 10:00 as the start of our workday. The first work period is 10:00 to 12:30. During this time I like to look over new ASAPs in my RSS reader, and then try to write for an hour, or look up papers. Then at 12:30 we have an hour for lunch. My hearing is not so good, so I tend to eat lunch by myself in the office rather than going to the cafeteria with everyone else. I used to go, but it’s just so noisy that I can’t really hear anyone. So, I sit at my desk and watch the PBS Newshour (@pbsnewshour) on YouTube.

After lunch is the second work period that runs from about 13:30 to 19:30. During this block of time, I like to do heavy synthetic work. I try to start reactions, end reactions, and do work up during this period. If at all possible, I try to do all synthesis related work during that six hours.

Dinner from 19:30 to 20:00. After dinner, I try to focus mainly on characterization. After 20:00, the number of students starts to decrease, and it’s easier to make reservations on the instruments. I can use them in peace and quiet.

I generally go home on one of the two busses in the 22:00-hour. Once home, I decompress by taking a shower and reading until I fall asleep. With that ideal in mind, here is reality…

An average week


I like to think of my week starting on a Saturday. The reason is because that it’s the last day of the research week. I go through and take inventory of the lab in order to figure out what I need to order. It’s not as involved as it may sound. It usually occupies the first work period. I have lists of everything so I can check through quickly, and for most things, I can stand in one spot and just look around the room while marking off my list. The solvents are easy too. I open the cabinet and count the bottles remaining.

I place the orders by writing them into the order notebooks for each of the suppliers. In Japan, representatives from manufactures and suppliers come around several times a day to collect the orders, and then they deliver them directly. Each lab manages its own finances, so as long as one isn’t buying and NMR spectrometer, there is almost no red tape.

Figure 1

Figure 1

On this particular day, I spent most of it cleaning as my workbench was a complete disaster (Figure 1). Also, I didn’t want to start any reactions because the reactions that wanted/needed to do I did not want to leave running unchecked on Sunday.


Sunday is the one day a week off that we have. I treasure those days. Getting to sleep in late, and getting to do what I want all day is a luxury I try not to squander. However, there are still practical things that must be done. As if cleaning my workbench wasn’t enough, I clean my apartment and do laundry. I also cook lunch and dinner for the next seven day period. I try to do as much pleasure reading as I can because during the rest of the week, I read mainly research related materials. It’s a nice break.


I had run out of a ligand that I need to make several of the MOFs that I use. To start the process, I perform a Suzuki-Miyaura coupling reaction. I use the reaction to couple an arylbromide with an arylboronic acid.

Figure 2

Figure 2

Figure 2 shows the progression of the reaction. In the upper left is the start of the reaction. The brown color is from the palladium(II) acetate that I’m using as the catalyst. The upper right shows the reaction mixture right before I stop the reaction. The palladium has formed palladium black over the course of the reaction. During the catalytic cycle, palladium(0) is formed, and in this oxidation state, if two palladium(0) atoms bump into each other, they can begin to form palladium nano particles, which kills the catalyst. Basically, the reaction is over. The lower right shows the result after liquid-liquid extraction. Many people try to get rid of the palladium black, but I find it too much trouble to deal with, plus I always end up with a lower yield. I prefer to just let most of it get clumped onto the magnesium sulfate that I used to dry the organic extract, and if it still persists after filtration, it will be stopped by the column when I purify by chromatography. In the lower right is the nice white powder that I obtain after purification.

Incidentally, I love watching the condenser of the rotavap.


It’s lab clean up day! Every Tuesday morning, everyone gets together and cleans the lab. At my university, every lab is responsible for taking out the trash and the recycling. The cleaning staff are only responsible for common areas. The labs are our responsibility. This is an average load of refuse for a week (Figure 3):

Figure 3

Figure 3

The product from the previous reaction has a methyl group attach to a phenyl ring. This methyl group can be easily oxidized to a carboxylic acid. A synonymous reaction would be that of turning toluene into benzoic acid. The method I prefer is heating the starting material in a hydrothermal vessel in the presence of about 30% nitric acid (Figure 4).

Figure 4

Figure 4

This reaction makes me nervous because it heats nitric acid to 170 ℃. The product of this reaction, aside from the carboxylic acid, is a lot of nitric oxide gas. I made a video showing the opening of the vessel after the reaction.


After the ligand has been purified, it’s time to make the PCPs. The PCPs that I use are made of a mix of ligands. That means I combine more than one ligand to form the framework in the hopes of altering the pore surface functionality. I made two different PCPs on this day. One is a copper(II)-based PCP, and it’s synthesized in two steps.

In the first step, one set of ligands are combined with a copper(II) salt. This is then stirred for two days. The video below shows the mixing of reagents at the beginning of the reaction.

The other MOF is aluminium(III)-based. It’s a one step reaction that performed in a glass vial in the oven at 120 ℃. Unfortunately, that’s all I can say about those projects until they are published!


I spent most of this day performing spectroscopy. Of all the spectroscopic techniques, NMR is my favorite. I fell in love with NMR the first day I had ever heard of it.

Figure 5

Figure 5

Our NMR lab (Firgure 5) has three spectrometers, all made by JEOL. In the foreground is the 400 MHz, behind that is the 600 MHz (my workhorse), and in the back on the right side is a 500 MHz. The sample that I was measuring that day was of a polymer that I had synthesized. I was doing a full set of characterization, so I set up a whole set of experiments: 1-D 1H and 13C, COSY, HSQC and I measured relaxation t1 with a double pulse experiment.

Figure 6

Figure 6

The sample (Figrue 6) was dissolved in benzene-d6, and I was was worried that since this sample would be running for 3 or 4 days that the solvent would slowly evaporate, so I sealed it rather than using a cap.


I realized that I forgot to add the group meeting schedule to my calendar. I’m presenting on Monday of the next week. There’s two things you should know about me. First, I have a terrible memory. If my Google calendar doesn’t remind me about important things like group meetings, I will surely forget them. Of course this isn’t a fail proof system because I have to remember to put these important reminders into the calendar first!

Normally, I do it right when I get the e-mail from the boss with the schedule for the next month. Somehow, I forgot.

The second thing is, I really hate making presentations. I often wish I could pay someone to do it for me. In some ways, I think this might make me a failure as a scientist (Editor’s note: Far from it!) While I love using my computer, I hate being chained to it. That’s how I feel when I have to sit and work on a presentation, or poster, or paper. I would much rather just work in the lab. However, I realize that it doesn’t work that way. My results, success or failure, are meaningless unless I report them.

However true that may be, making presentations is still probably my least favorite thing to do in science. And so, since I forgot, I spent most of the Friday and Saturday compiling data and making figures and putting together a presentation.

Maybe next week won’t be so crazy.

Yeah, that’s what I always tell myself.

Author biography:

wLT3vNAF_400x400Jason Hoshikawa is a 2nd year PhD student working in the Kitagawa Lab at Kyoto University under Assoc. Prof. Takashi Uemura. He was born in Dallas, Texas. After working in the television and radio industry as a high-power transmitter engineer, he started his undergrad education at the University of Hawaii at Manoa, but returned to Texas to finish his BS in Chemistry (2010) and MSc in Organic Chemistry (2012) at the University of North Texas under Prof. Mohammad A Omary. After being awarded a Japanese Government Scholarship for Research Students (2013) he entered the Graduate School of Engineering at Kyoto University to complete his PhD studies.

You can follow Jason on Twitter (@ChemistInJapan), on YouTube (, and Instagram (@ChemistInJapan).

#RealTimeChem week 2014 – Tweets of the Week

Hello everyone,

First of all, thank you very much to everyone who took part in #RealTimeChem week this year. Once again it was great fun and fantastic to see such a wide variety of chemists taking part from across the globe. It’ll be interesting to see what happens in 2015!

Obviously, #RealTimeChem is a 24/7 project, so feel free to keep sharing chemistry whenever you want and engage with your fellow chemists around the world.

There were a lot of really great tweets this week as seen in this years awards. This was actually really really hard to decide on. If I had enough prizes I would have given you all one. Unfortunately, only the very best of the best can win one of this years prizes.

This years must have item for the discerning chemist.

Time to find out who has won these beauties!



Below you shall find the three winners of the “Tweets of the Week” for #RealTimeChem week 2014. These three tweeters not only produced these excellent tweets, but also many more throughout the week and I think they are all worthy winners of a #RealTimeChem Week 2014 mug. Congratulations to you all!



From Monday – this tweet from the whimsical Laura Jane (@laurajane0103) was only one of many fantastic contributions during the week. It sums up a typical day in the laboratory for many in a fun way. It’s what #RealTimeChem is all about and was a great way to start the week.



From Tuesday – this polyurethane strawberry milkshake almost looked good enough to drink! Andres Tretiakov (@Andrestrujado) shared a whole host of wacky, fantastic and exciting chemistry during the week and any one of them could have won a Platinum award, but I try not to give out more than one to any contributor!




From Wednesday – food was a big theme of #RealTimeChem week this year and I’m definitely a fan of cooking (even if I’m not that good at it). John Grimes (@jgrimesjr) shared quite a range of tweets over the week, but my favourite was this close up tweet of a delicious looking peanut butter-y product. It could also be the clouds of a gas giant! Either way I love the texture in it and I also really appreciate the humour with which the tweet was delivered, chemistry often looks better than it smells!



So there you have it. If all three winners could please send me a DM on twitter with their address as soon as possible and I’ll get that prize out to you.

Once again thank you to everyone who took part in #RealTimeChem week 2014. I hope you had fun, learned something new and found some new connections in the chemistry world.

mischief managed

-Doctor Galactic & The Lab Coat Cowboy-

Thoughts on recent RealTimeChem developments (with a poll!)

Hello everybody!

Yes I am still alive, I know I’ve been a little quieter over the past month or so than I said I would be, but life and that holiday that used to be all about the birth of Jesus Christ intervened. Some large changes are coming my way in the form of a new job (I’m moving from my academic life as a “lab monkey” into publishing as an editor) and that’s involving a change of scenery too (from smelly old London to Cambridge).

I’m still very interested and committed to #RealTimeChem which seems to be in constant use in the chemistry twitterverse, which is frankly fantastic. Particularly intriguing is the situation brewing with the masked chemist @SeeArrOh on his blog Just Like Cooking where #RealTimeChem has been used as a call to arms to investigate a recent Fe-S catalysis reaction in the literature. This has created some excellent discussions and more importantly attempted repetition of the results, which have not been turning out great so far. I suggest if your interested to keep an eye on See Arr Oh’s twitter feed and blog.

SeeArrOh - who probably isn't a dog in real life. Although wouldn't that be AWESOME? A dog doing chemistry? What would Chemistry Cat say?

SeeArrOh – who probably isn’t a dog in real life. Although wouldn’t that be AWESOME? A dog doing chemistry? What would Chemistry Cat say?

I think this is great. This is what #RealTimeChem is there for, to be used by the chemistry community to report on chemistry being done right here and now. Science in general needs to have greater transparency so that we don’t appear to be a bunch of sentient robots, plugged into computers performing boring laboratory reactions and the general evil bidding of “the man”.

Hell there, so I'm told you're a chemist?

Hell there, so I’m told you’re a chemist?

There are all sorts of interesting tweets being made so check it out under the #RealTimeChem hastag or follow selected highlights on @RealTimeChem (I’m trying to keep up I swear!). Alternately, if you are looking for more twitter related fun you might want to check out the hashtag #OverlyHonestMethods which is also shining a light into the dark corners of REAL laboratory life with scientists of all kinds playing on the idea that some parts of their experimental methods probably wouldn’t get past peer review!

Yeah you know that product is going in that dirty water any second now, but you certainly aren't going to put THAT in your experimental section!

Yeah you know that product is going in that dirty water any second now, but you certainly aren’t going to put THAT in your experimental section!

My final point for today is to discuss the future of #RealTimeChem. I’ve made in known via twitter that at some point this year I’d like to run another event. The last one went down rather well, but many didn’t get the chance to participant so next time around the format is going to be stretched into a week. Yes folks in 2013 there will be this:

RealTimeChemWeek copyYep that’s 7 days (I know some of you work weekends) where every chemist in the world (on twitter) is encouraged to tweet about their life in chemistry for a week. You won’t have to do the whole week unless you really want to, but it you a bigger window to join in with everybody else essentially.

So when will it be? Well, I think I will leave that up to the community! Below you shall find a poll, where you can vote for the month that you would like #RealTimeChemWeek to happen. You shall note it starts from April, largely because there will need to be some preparation time for it.

So vote away and if you have any suggestions, comments or questions please leave a comment or get in touch with me via twitter.

Oh and happy New Year!

-Doctor Galactic & The Lab Coat Cowboy-

24 favourite tweets from 24 hours of Real-Time Chemistry.

The above banner was by @squidring on twitter. Check out her art here. Multi-talented! 

Chemistry was tweeted in real-time on the 7th November. It seems from feedback I’ve received that it was enjoyed. Obviously there is some room for improvement, so please, if you were disappointed don’t hesitate to tell me what you’d like to see in the next RealTimeChem event. As promised I’ve written this post in order to showcase my observations of the day and my favourite-ist tweets and pictures from the day.

It’s been a reeeeeeeally difficult task, as there was a LOT of excellent #RealTimeChem, so if you don’t see yourself mentioned here, I apologise and still think you were wonderful. All tweets and your time were appreciated.

In keeping with the theme of the event here are 24 of my favourite tweets:

Read More

That was the longest day of your life.


So it is all over! RealTimeChem day has come and gone on Twitter and what a day! There was so much chemistry going on that I pretty much broke my twitter account and I scarcely know where to begin when it comes to summing it all up!

I’d like to thank everybody that got involved in tweeting about their daily life as a chemist, no matter how small the contribution. You all helped to make it a engaging and all round fun day. There are some tweeters who deserve some special gratitude and I’ll highlight those in the next blog post, which I’ll hopefully have done on Monday.

Additionally, I’ll be posting up some of my favourite tweets and pictures from the day once I’ve had time to process all of the awesomeness that occurred.

While #RealTimeChem day is over, the hash tag is still there for use whenever you feel like informing the everyone what you are up to in your personal chemistry world. I think its important in this modern age of social media in particular that chemistry continues to engage with the masses and chemists are able to pass on their knowledge, enthusiasm and general love of their subject onto others in an entertaining way.

Moreover, as a chemist myself it’s really great to see what other chemists in all areas of the profession are doing daily. To see what sticky mess a reaction has made. To see what instruments are being used. To see what articles are being written or read. Even to see how dirty all those fume hoods really are!

Hopefully you enjoyed RealTimeChem Day and it has helped you to feel a part of a substantial community united by our desire for scientific discovery (and twitter!). It’s certainly inspired me.

There will most likely be further RealTimeChem events in the future, but for now…

Mischief managed. 

-Doctor Galactic & The Lab Coat Cowboy-     

Today is #RealTimeChem day

This is it!

This is #RealTimeChem day! Thank you to everybody who is planning to join in, I’m excited and looking forward to seeing all the wonderful chemistry you are up to. I hope that you all have a fun and informative time. Comment, laugh, discuss or be amazed at what the Chemistry community does in the average day.

In addition, Happy Birthday to Marie Curie!

Below I’m going to post all of the RealTimeChem posters I made during the run up for your viewing pleasure:

I’ll be tweeting as @doctor_galactic from my laboratory and re-tweeting #RealTimeChem via @RealTimeChem. It’s going to be a busy day balancing lab work and twitter duties!

However, this day isn’t about me, it’s about you and your chemistry. Let’s show the world what it means to us and by extension to them too.

-Doctor Galactic & The Lab Coat Cowboy-

RealTimeChem Day – All you need to know for the big day.

Hello everyone!

It is now just a week until #RealTimeChem hopefully takes over twitter. The response so far has been pretty enthusiastic and I’m looking forward to all the chemistry that’s going to be on show for the world to see!

Seeing as there isn’t long to go and a few people have been asking for more detail, I have produced an FAQ section so that you everyone knows the how, when, who, what and why of #RealTimeChem day.

So…what is RealTimeChem Day?

Real Time Chemistry day is a twitter based event where chemists from all over the world will be tweeting about their daily lives in chemistry… in real time.


Chemistry often gets short shrift when it comes to media exposure and that’s a bit sad. So Real Time Chem Day will be a day to celebrate chemistry and give the world an insight into the kinds of work and the science that we do as chemists every day. It will also hopefully help to connect the chemistry community and spark intriguing discussions and it’s just pretty darn fun to see what other chemists are up to!

Interesting! …When is it?

It’s on the 7th November 2012 and lasts for the whole 24 hours.

Who can take part?

Anybody in the world who works in the field we call “chemistry”. As long as you are tweeting about part of your everyday life that involves doing chemistry then it counts – lab work, journal reading, writing papers, teaching, demonstrating, field work, instrumental work etc.

This is an all inclusive event no matter what branch of chemistry that you partake in (including biochemistry! Geochemistry! Astrochemistry! Crystallography!) or what level of chemistry you are currently at (High school! Undergraduate! Postgraduate! Industrial! Person in shed!).

Please though only join in if you can spare the time. I understand that you’re all busy people – work commitments and getting our chemistry done must take priority.

What do I have to do to join in? What should I tweet?

To join in you simply have to tweet about your day in your particular field of chemistry using the hashtag #RealTimeChem to show that it is part of the event.

As for what you tweet, well that is entirely at your discretion so long as it’s got some link to doing chemistry. In my case, I will be tweeting about actual chemistry I am performing in the laboratory.

All things that happen on the day can be tweeted, good or bad. I’m sure the former shall outweigh the latter, but we should be giving everyone an accurate view of what happens.

Incidentally, pictures of your day (such as great looking experiments) are most welcome. Obviously, only take pictures of things you are allowed to show, we understand some chemistry must be shrouded in secrecy.

Please feel free to engage with other #RealTimeChem tweeters and start a conversation. This is a day for chemists to unite and enjoy what they do.

How much do I have to tweet?

As much or as little as you want to, even if it is just one tweet. So long as it includes the hashtag #RealTimeChem it’ll count.

So just feel free to randomly tweet your chemistry as you go along, this day is for you to share what you do with the rest of the world.

How can I follow the event?

Search for the hashtag #RealTimeChem on twitter or follow @RealTimeChem for highlights. I’ll be keeping an eye on twitter all day and re-tweeting every #RealTimeChem tweet I can (or as many as twitter will allow!) and commenting on the fabulous things you are doing.

Who invented #RealTimeChem?

Certainly not me. However, I have been participating for a while on an off in doing some #RealTimeChem tweets. I believe that the inventor was @azmanam who was trying to determine what was in Lemishine and happened to tweet his results using, and @JessTheChemist produced a storify page to follow all the RealTimeChem that happened. Since then it has caught on a many others have joined in to tweet their chemical reactions in real time using the same hash tag.

I think we all agreed that tweeting about laboratory chemistry was such fun that it would be nice to have a #RealTimeChem day to celebrate, and here we are!

Why is #RealTimeChem day on 7th November?

This is the birthday of Marie Curie, the first woman to win the Nobel Prize and the only to win it in two separate fields, chemistry and physics.

If you want to do something extra fantastic on the day please feel free to donate to Marie Curie Cancer Care.

Who is running #RealTimeChem?

Mainly the same person who runs this blog, “Doctor Galactic and The Lab Coat Cowboy” who can be found under the name @doctor_galactic on twitter and also @RealTimeChem. I’m a post doctoral researcher in the UK, who is just coming to the end of his contract. For me this is possibly one last hurrah before looking toward chemistry pastures new.

In addition to the @RealTimeChem feed, @JessTheChemist will be continuing to update her storify page and will be showing #RealTimeChem tweets in their Chemistry twitterverse box.

Anyone else who wants to post anything about #RealTimeChem on their blog or anywhere else is most welcome to so long as they refer back to @RealTimeChem somewhere.

Can I help to promote #RealTimeChem day?

Sure thing, just retweet any information you want regarding the event and mention it to your chemistry friends on twitter. Even mention it to your chemistry friends outside of twitter. The more chemists we get to tweet, the more chemistry we get to enjoy!

There are a couple of posters that have been uploaded on @RealTimeChem with some more to come this week. So feel free to use these as you will or make your own!

What’s with the “24” theme?

It felt particularly relevant to the nature of the day. We are all Jack Bauer on #RealTimeChem Day, we just do chemistry.

I want to do something really spectacular, can I?

Yes, so long as you are safe. All the normal rules of chemistry apply, including the use of PPE (Personal Protective Equipment). We don’t want anybody to get hurt doing something on #RealTimeChem day.

I don’t want to tweet but I want to watch, can I?

Of course! If you don’t want to tweet you can still watch the rest of us on twitter. The best bet is to follow @RealTimeChem which will be re-tweeting as many highlights as possible.

What will happen afterwards?

I plan to sift through the tweets and make a series of blog posts highlighting my favourites here on this blog. The real point of the day is to have some fun and get chemistry out there for the world to see, so that will hopefully be its own reward.

Will there be future #RealTimeChem days?  

Everyday can be #RealTimeChem day if you so choose it. The hashtag is there to use whenever you are doing any chemistry. If the event itself is popular enough, then most certainly we’ll try to organise another full day in the future. I would like to make it an annual event and perhaps expand it to cover a whole week. The possibilities are endless.

Any other questions? Then drop me a line in the comments box on here or via twitter @RealTimeChem.

Enjoy the day, I’m looking forward to it!



-Doctor Galactic and The Lab Coat Cowboy-

The Chemistry of the Dark Knight (Part 2)

Disclaimer: Obviously, I don’t own BatmanTM or any of the other stuff discussed in this blog post. This is just for fun, so Warner Brothers and DC, please don’t sue. The same goes for all the owners of any trademarked compounds mentioned or any other intellectual property, especially you George.

Second disclaimer: Many of the compound mentioned in this blog post are extremely dangerous. I do not endorse the use of any of this stuff. Batman is a fictional crime fighter, so don’t go getting any ideas.

From this point onwards, there be potential spoilers for The Dark Knight trilogy. You’ve been warned.

Welcome to the second part of my look at some of the chemistry at work in the adventures of the intrepid Dark Knight. In the previous part, I got somewhat wrapped up in the materials used to make the Batsuit. This time I’ll be focusing on his gadgets (and a few other bits and bobs I just randomly threw in).

“I’m Batman”

The Dark Knight Rises…and Rides and Flies and Glides and….

Just imagine that line in a husky voice and if you’re the kind of geek I think you are then you’re probably getting tingles. He’s not the hero we need, but the hero we deserve…or something like that. He’s not a superpowered alien from across the cosmos, he’s just your average orphan-billionaire-genius-playboy  turned crime-fighting vigilante. Without superpowers Batman relies on other things and Batman wouldn’t be Batman if he didn’t have his trusty utility belt, filled to the brim with all manner of useful gadgets to help him battle the scum of Gotham City.

So the question is:

Where does he get What Chemistry is invovled in all of those wonderful toys…?”

Even the Joker asked this (kind of). Look. He’s relaxing with a martini in anticipation.

I’ve generally been focusing on Christopher Nolan’s version of Batman, being that his is the most “gritty and realistic” (not to mention recent) version of the character on film thus far. Even though there have been some changes over the years, certain elements of Batman’s arsenal have stayed the same.

That’s still less belts than worn by your average Final Fantasy character.

As such, some of the gadgets discussed below naturally overlap with other versions of the Batman and there are all kinds of wacky things that I could cover from the past, but that we don’t have time for.

On the plus side, there won’t be room to talk about any of the ridiculous “gadgets” in Batman & Robin; the less said about that film the better.

I said no Arnie. Objection overruled!

So let’s start with the basics….


Bats we all know you aren’t gonna use that thing. Put it away.

Probably the single most iconic Batman gadget is fairly boring in Christopher Nolan’s universe (so we’ll skip right along). Having originally been more like their namesake, the boomerang, they’ve tended toward being more shuriken-like recently (which is more in keeping with Batman’s ninja like fighting style).

In other films, the batarang has been remote (Batman Returns) and sonar controlled (Batman Forever), whilst the comics and other interpretations of the character have included explosive, cryogenic and electrically charged variants.

Making Batarangs the Nolan way. Like. You know, realistically.

So Nolan’s batarang is basically a modern shuriken, which are these days mostly made of lightweight stainless steel and are commercially available (apparently) in Europe and parts of America. I should point out that unless you are a trained ninja or…you know, Batman, you should leave those well alone.

Throughout the Dark Knight Trilogy, Batman has used Batarangs to smash windows, knock out lights or act as distraction; however despite being like shuriken we don’t actually see him use these for offensive purposes. Similar smaller projectiles are used against Bane’s henchmen in The Dark Knight Rises (more on those later), but a traditional batarang is never used for preventing criminals escaping (this makes me a little sad inside).

So is there chemistry involved in them? …A little.

A blog post of mine wouldn’t be complete without a picture of some generic metal rods would it? If you didn’t come up with a joke about rods the first time, nows your chance.

Stainless steel is quite a well known alloy of iron, carbon and chromium (where chromium content is greater than 10.5%). It gets the name “stainless” because unlike normal steel it rusts far less being much more resistant to oxidation (i.e. the formation of iron oxide) and corrosion.

I said chromium…Not chrome. Blooming Google taking over the world….

Anyway….so why include chromium (symbol Cr, Atomic number 24)? Well, when exposed to oxygen in the air, chromium very rapidly reacts to form a layer of chromium (III) oxide (Cr2O3) upon its surface. The layer is invisible to the human eye, being only several atoms thick and therefore translucent so the metal beneath stays all nice and shiny.

This oxide layer is impervious to water and air and passive towards oxidizing acids such as nitric or hydrochloric. Thanks to this layer anything beneath is protected, which is why chrome-plated items are useful and even fashionable.

Oooh shiny AND weird.

Inclusion of chromium in stainless steel essentially adds these useful property to the alloy. This “passivation” is also seen when other reactive metals are used, such as aluminium.

So no worries about those Batarangs going rusty, eh Brucey?

You know…making these is hard. I think I’ll just use other stuff. A lot.

Smoke pellets

So batarangs are pretty boring. You’re probably snoozing comfortably now, so best to wake you up with a bang. A little background first though.

So Henri Ducard….

Everyone loves Liam Neeson.

Also known as….*big spoiler alert*…

Qui-Gon Jinn….I mean Ra’s Al Ghul… teaches Bruce in Batman Begins about being a Jedi Knight…sorry!… ninja assassin and the powerful tools of “theatricality and deception”. As part of this he tells Bruce that the League of Shadows employ explosive powders for means of distraction. Bruce then throws some non-descript black powder on the floor and viola instant smoke bomb.

I doubt Batmans smoke balls are quite so….happy.

Batman most likely crafts this black powder into smoke balls, which are little hollow spheres made of clay or cardboard, that are filled with a series of chemicals that when mixed and ignited produce a large volume of smoke for between 10 -15 seconds.

These are pretty easy to make at home, especially for the “goddamn Batman”. However I do not advocate this to you kids (and grown-up kids) out there and would prefer it if no badness ensued.

See? I don’t even make the rules.

One type of smoke bomb is made by mixing KNO3 (potassium nitrate, sometimes called saltpeter), sodium bicarbonate (baking soda to moderate the heat of the reaction) and sugar (usually sucrose or dextrin from ping-pong balls) with some light heating to give a gum with a peanut-butter-like consistency. You pour this into a bit of foil or a mould (shape and size are variable – you could make them Bat shaped!) and let it set, then peel the thing out.

The smoke bomb can be lit directly (not that I’d recommend it) or via a fuse, stand well back and its smoke screen time. The chemical equation for the reaction process as follows is

10 KNO3 + C12H22O11 → 5 K2CO3 + 7 CO2 + 11H2O + 5N2.

That generates quite a lot of gas!

Batman making a speedy get away in the excellent Arkham City video game.

You might have noticed that Batman’s smoke bombs are generally ignited by impact rather than him pulling out a lighter. For ignition of the smoke bomb on impact, a very tiny amount (~0.08 mg) of Silver fulminate (AgCNO) can be used as an ignition source. It’s the stuff used in Christmas Crackers and Bang Snaps to give that characteristic supersonic shockwave “crack” that you hear.

Silver fulminate: Anyone who knows their chemistry knows that doesn’t look like a nice, happy compound.

Silver fulminate has very little practical value because it is so extremely sensitive to impact to impact, heat, pressure and even electricity. In fact, the more of the compound that you aggregate the more sensitive it becomes, storing anything larger than a few milligrams is actually impossible as the compound will basically self-detonate under its own weight.

In the case of bang snaps, the tiniest amount of silver fulminate is mixed with gravel, which acts as a buffer to the high-explosive detonation, which means they can’t produce physical damage, even if discharged directly against the skin. The shell of the smoke bomb would likely contain a few of these devices, or alternatively a huge bunch of match heads, which will happily ignite (seeing as they contain phosphorus or phosphorus sesquisulfide).

This engraving at the Royal Institution showing ECH, between geologist William Smith and chemist William Allen.

Edward Charles Howard was the first person to discover “fulminating silver” along with a large variety of other fulminates, which are all explosives. After many injuries (unsurprisingly), he went on to studying meteorites and eventually got involved in the sugar industry which ultimately caused his death. In 1816 he suffered fatal heat stroke from visiting the oven of the sugar refinery that he owned. This NOT being the DC or Marvel universe, he sadly didn’t turn into “sugar man”.

Bat-bombs (& other explosives)

Bat bombs!

Aside from smoke bombs, Batman quite clearly has a few other types in his arsenal. In Batman Begins he blows up a wall in Arkham Asylum to escape from SWAT and get Rachael Dawes back to the Batcave.

Much to the surprise of these gormless idiots.

So what’s in these little guys to make them blow up a whole wall? They are impact grenades of some kind and probably not all that dissimilar from your standard frag grenade (a nasty invention).

A grenade rather simplistically consists of an outer shell, usually made of steel, containing an explosive and a fuse for ignition purposes that has a short burning time. The explosive is generally something called “Composition B”.

Composition B consists of a mixture of about 60% RDX and 40% TNT with 1% added paraffin wax. That’s not just shits and giggles.

This is chemistry at the scary end of the pool. RDX (left) and TNT (right).

RDX is somewhat less well known to the average person than TNT, probably thanks to the ubiquitous use of the latter throughout Looney Tunes cartoons.

The Legendary Wile. E. Coyote. He probably blows up shortly after this.

RDX stands for Research Department Explosive (how original!), it is a nitroamine that’s been used to blow stuff up the world over since its first usage in the Second World War. It’s actually more powerful than TNT and was discovered in 1898 by German chemist Georg Friedrich Henning. It was manufactured, by nitrating hexamine nitrate (hexamethylenetetramine nitrate) with concentrated nitric acid. This is something I’d not recommend doing if you fancy going home with all of your limbs attached.

RDX is also known as cyclonite, hexogen (particularly in Germany), and T4. Its chemical name is cyclotrimethylenetrinitramine is rather a mouthful and slightly boring.

In pure form, RDX is a white, crystalline solid that is actually pretty stable to store at room temperature. You’d probably not give it a second look if it were sitting on your desk, but it is considered one of the most powerful and brisant (i.e. rapid shock wave building) military grade explosives available.

TNT is an abbreviation of 2,4,6-trinitrotoluene. It’s a yellow coloured solid and is pretty much the best known explosive in the world (as previously mentioned). It does have other uses in chemical synthesis, such as making charge transfer salts, but I doubt Batman has the time to be doing that. It was first prepared in 1863 by yet another German chemist Julius Wilbrand and looks pretty innocuous.

This is TNT. Not your breakfast cereal.


Its great value is that it’s pretty insensitive to shock and friction, which means it isn’t going to accidently blow Batman up, when he’s attempting something cool.

TNT is certainly more stable than this fiery little shock sensitive compound below:

I don’t like to be touched.

Nitroglycerin. I’m not going to talk about this very much, but it’s worth a read, particularly as it’s bad (but somewhat deserved) reputation, hides the fact that it’s now being used to treat heart conditions and prostate cancer. Oh and it was one of Alfred Nobel’s crowning achievements. Yes. THAT Alfred Nobel

 Going back to TNT, it easily melts at 80 °C (or 176 °F for you Americans out there, and 353 Kelvin for you Chemistry snobs), without detonating so it can be poured safely and combined with other explosives like RDX. It’s water insoluble so can be used on those boring rainy days.

Note that TNT is NOT found in dynamite, which is an absorbent mixture soaked in our friend above, nitroglycerin, and then compressed into a cylinder and wrapped in paper. In addition, TNT is poisonous, and causes the skin to become irritated and turn a bright yellow-orange colour. Munition workers who handled TNT during the First World War acquired the nickname “canary girls” due to their handling of the substance. Again, this did not result in any superpowers.

You hear that Sinestro? Yellow isn’t a superpower.

Batman uses further explosives in The Dark Knight in the form of sticky bombs which he shoots from a rather fabulous looking gun.

Doesn’t that look all high-tech and futuristic?

One can assume that the explosive here are actually working on the same principal but with timers. The sticky substance looks pretty translucent and thus could be a a simple adhesive, which is another potentially massive chemistry blog post in itself. It could also be a future, (i.e. better) version of the US militaries “hilarious” sticky foam.

What the substance certainly doesn’t appear to be is that Hollywood staple, the traditional, well known plastic explosive  C4 (which IS used by villians in the Dark Knight Trilogy).

C4 is what Keanu and Sandra are worried about. That’s a totally different film.

C4 – is another composition (namly Composition C, the fourth one in that series) which contains 91% RDX and aplasticiser such as diethylhexyl sebacate (about 5%) and a binder, which is usually polyisobutylene (about 2%).C4 however, is an off-white solid with a texture similar to modelling clay and not at all like the stuff Batman shoots out of his fancy Bat-gun.

That grey stuff is C4.

Incapacitating agents

There’s a scene in the Dark Knight Rises where Batman takes out a few of Banes henchmen with what can only be described as Bat-Darts.

Bat-darts! They look very darty!

One assumes that these darts are tipped with some form of incapacitating agent, one that is non-lethal, in keeping with Batman’s no-kill ethos (with exception of the Al Ghul family, it would seem.)

This is actually harder than it seems. Films/TV/comics/books are full of awful pseudoscience (or rather “artistic license”), most is forgiveable.

Instant sedation in TV/film is usually achieved, by use of a tranquillizer dart. A pointed projectile is shot, thrown, or blown at from a distance, usually into the neck or the arse (for laughs). A sedative is either on the dart tip or contained in an syringe attached to the dart.

This generally puts  the target to sleep near instantly. Of course…

Jeff Goldblum everybody.

In large part because the same dose doesn’t work on everyone (we aren’t all the same shape and size) and sedatives work differently on different people (we all have slightly different body chemistry). Drugs are far more complex than the movies give them credit for. Below for instance is a selection of common tranquillizers and sedatives.

A fine range of compounds each with strong pharmacological properties. Smell the chemistry.

All of the above are highly potent compounds, for example, Etorphine is 1,000-3,000 times more potent than morphine and is therefore only used to sedate large animals such as elephants….


If you search for “surprised elephant” on google. You get a picture of Lionel Richie. I kid you not. “Hello, is it me you’re looking for?” No Lionel. It really isn’t.

Anyway, etorphine will kill human beings (even Mr. Richie) and is therefore sold only to vets along with the antidote for humans diprenorphine. Just in case.

In fact, pretty much all of the above will kill a human if the correct dosage isn’t used and that’s not something the Dark Knight can be trying to gauge in the middle of a fight.

So tranquillizers are out. Surely there are other agents though right? Well, not many that have been applied to military type uses, such as knocking out your enemies. In fact, there are a grand total of four. One of which, has an unknown structure because the Russians don’t like to share such things.

I have no idea what you mean…

One of these agents is the fantastically named Agent 15 (aka BZ, which you can tell was weaponised by the US Army in the 1960s right?) causes nervous system effects, including and not limited to stupor, mumbling, blurred vision, irrational fear, elevated blood pressure, confusion, panoramic illusions and hallucinations and regressive ‘phantom behaviours’ such as plucking hair and undressing without provocation.

Agent 15’s response is always. “No comment”.

Its related to atropine, and other deliriants and is dispersed as an aerosolized solid (primarily for inhalation) or as agent dissolved in one or more solvents for ingestion or absorption via a needle puncture like how our Bat friend would do.

You know the more you hear about this the more it sounds like something a certain Doctor Crane used in Batman Begins.

The Scarecrow.

If Batman is having trouble getting the mix right he’d just be better off slipping the bad guys some LSD in a club or something?

Lucius Fox: You planning on gassing yourself again, Mr Wayne?
Bruce Wayne: Well, you know how it is, Mr Fox. You’re out at night, looking for kicks, someone’s passing around the weaponized hallucinogens.

See? Bruce is down with the kids.

Cold fusion generator

This thing just shouts, “IMPRESSIVE SCIENCE INSIDE” doesn’t it?

Okay, I’m wrapping things up now with a bit of a non-gadget.

If there is a part of The Dark Knight Rises that I don’t particularly like, it’s the whole idea that Bruce Wayne built an entire fusion (I’m assuming it’s a cold one here) generator and then proceeds to just do nothing with it…except leave it there so that Bane can use it for his own nefarious purposes. This is despite Bruce knowing that the device could be used as a bomb. That’s remarkably irresponsible of our Mr. Wayne and Lucius Fox didn’t exactly pull the plug either.

He’s Batman though, so I’m sure he has a perfectly good excuse.

Bruce and Lucius having a good laugh about how they could totally destroy the world with that thing in the basement.

Fusion is quite complicated but it’s simply put, its the process by which two or more atomic nuclei are fused together to form a new heavier nucleus. For example:

Matter is not conserved in this process and is instead converted into energy. It’s difficult to achieve and above all maintain, it requires huge pressures and extremely high temperatures, the kind you find in stars.

Fusing like a boss.

I’m not a physicist (or even a physical chemist) so I’m not really doing the topic a great service here (but click here to find a slightly better take on the subject) and it’s not really a gadget so to speak, but I wanted to include it as a tribute to the late Martin Fleischmann, who sadly passed away this year.

Martin Fleischmann – co-“inventor” of cold fusion.

Fleischmann is rather infamous for his pronouncement in1989 with Stanley Pons that they had cracked “Cold Fusion” – the ability to perform a fusion reaction without the need for star level temperatures. The apparently produced excess heat in a reaction that they believed could only be explained by a nuclear process, it was a small tabletop experiment that involved the electrolysis of D2O a palladium (Pd) electrode.

This got people all excited for a little while. Many other scientists called “bullshit” and that’s what it turned out to be as nobody could replicate the results. Pons and Fleischman later discovered flaws in their method and experimental errors that destroyed the whole idea. So within the space of a year cold fusion was dead.

My current Post doc boss has told me a few great stories about the man when he was at the University of Southampton; such as the occasion that he burst into a tutorial to proclaiming that he had “solved” the cold fusion problem and promptly started writing it up on the board much to the surprise of the students!

Wrapping up

So thanks for making it this far and reading my rather rambling blogs about Batman. I hope that you enjoyed reading them as much as I did writing them. Feel free to drop me a comments/complaints or any suggestions for future chemistry in film/TV blog ideas you might have.

I also apologise if I didn’t go over your favourite Batman gadget, but I think you’ll agree this blog post is pretty epically long already!

Look at this crazy stuff!

Just don’t ask me to explain the Bat-Shark Repellent okay? Nobody knows how that stuff works.

Go bother Adam West, okay?

Bat’s all folks!

-Doctor Galactic-

Trip the light fantastic.

Alert! Alert! Shameless plug for my own chemistry contained within!

I would be totally missing an opportunity if I didn’t blog about some chemistry that is very close to my heart, so here’s a little ode to my PhD work. My thesis a.k.a the bane of my life for three whole months that consumed every single waking hour, until my brain felt like it had been pulverised into the ground…*ahem*  …what was I saying?

Oh yes, my thesis was entitled “The Double [3+2] Photocycloaddition reaction“.

I’m sure some of you will have quickly beaten a retreat when you noticed the prefix “photo-” in that there sentence. Photo-chemistry is an oft maligned area of research because it can be quite a fickle mistress, that behaves in unusual ways compared to your standard thermal chemistry (those high energy states just love to do crazy shit!). There are also the many practical considerations you have to account for: purity of reagents, solvent selection, direct or sensitized irradiation (do you need a sensitizer?), the specialist equipment, quantum yield measurements (which are a pain in the behind I can tell you) and the hazards of high energy UV radiation.

Of course, none of this should put you off, because what you can do with photo-chemistry is pretty darn marvelous. You see, one of synthetic organic chemistry’s greatest challenges is to create step-efficient routes toward compounds with high molecular complexity (i.e. to make something complex as possible in as few a steps possible). Therefore, reactions which provide more than one bond in a single step are of significant importance (see the Diels-Alder reaction).

In my own work we reported an intriguing case of a double [3+2] photocycloaddition reaction that resulted in the formation of a complex cis, cis, cis, trans-[5, 5, 5, 5] fenestrane derivative  from a simple aromatic acetal as shown in scheme 1.

Scheme 1 An example depicting the photochemical  reactions of arenyl-diene photosubstrate, including the double [3+2] photocycloaddition reaction.

During this transformation, four carbon-carbon bonds, five new rings and seven potentially new stereocenters are created in an essentially one-pot process using only UV light (at 254 nm). Here’s an X-ray crystall structure of it, because X-ray crystal structures always make your chemistry 100% more legit:

You can’t dispute this little beauty.

The reaction actually occurs in a sequential manner from the linear meta photocycloadduct (for a detailed review of the meta photocycloaddition reaction click here or here), via a secondary [3+2] addition of the alkene across the cyclopropane of the adduct. In addition, an angular meta photocycloadduct also produced in the initial addition step, undergoes an alternative fragmentation-translocation photoreaction to afford an angular triquinane compound. Scheme 2 gives a little idea of mechanistic stuff.

Scheme 2: A mechanistic summary of the reactions involved in the irradiation of the linear meta photocycloadduct.

We also produced a series of other fenestranes (including my favourite nitrogen containing variant) through the same method which can be found in our follow-up paper in JOC. I think we really only scratched the surface of this chemistry, but due to a set of unfortunate circumstances which I’d rather not recollect, the work has had to cease for the time being. I’d like to go back to it some day because it’s quite a unique area.

Fenestranes are quite rare in nature and their synthetic utility is pretty much untapped, but they’ve got bags of potential as possible agrochemicals, chiral auxiliaries, scaffolds, pharmaceuticals and materials. They compare favorably to the steroid class of compound in that they are both conformationally rigid and chemically robust. The real problem with them is the are hard to make (although not using our method)

A selection of naturally occurring fenestranes. Pretty aren’t they?

Penifulvin A shown above actually has notable insecticidal properties, whereas asperaculin was only recently isolated, but being a fungal metabolite it may also prove useful. Laurenene unfortunately is totally useless, but it certainly looks the part!

If you really wanted to see all the nonsense I got up to in my PhD, I have just discovered that you can buy my thesis on Amazon…which feels a bit weird. It’s still pretty cool that you can even buy a kindle version!

The Lab Coat Cowboy