synthesis

Crystals are a girl chemist’s best friend

Posted on by doctorgalactic

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.

Monday

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.

 

Tuesday

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

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.

Thursday

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.

Friday

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)
		

						Posted on  by doctorgalactic		

	


	

		
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


Saturday 


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 


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.


Monday 


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.




Tuesday 


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.




Wednesday 


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!


Thursday 


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.


Friday 


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 (https://www.youtube.com/user/ChemistInJapan), and Instagram (@ChemistInJapan).







		
	
			




			
				


	

	

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

						Posted on  by doctorgalactic		

	


	

		


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:


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That was the longest day of your life.
		

						Posted on  by doctorgalactic		

	


	

		
Image


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-     

			




			
				


			

			
		

	

	

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

						Posted on  by doctorgalactic		

	


	

		


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.


Ooookay….why? 


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 www.chemistry-blog.com 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 1)
		

						Posted on  by doctorgalactic		

	


	

		


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 the trademarked compounds mentioned.


So the final instalment of Christopher Nolan’s Batman trilogy, The Dark Knight Rises, has been released bringing to an end the best trilogy since The Lord of the Rings. I promised the other week (yeah I know it was aaaaaaages ago *grovel*) that I’d write something more geek related and so here it is a little piece on some of the chemistry supporting Bruce Wayne’s one man war on the criminals of Gotham City.


Batman has always been renowned for his use of gadgets and state of the art technology, which is probably for the best because he’s a superhero without…well, the super bit. Nolan’s films have taken a grittier, more realistic take on the Dark Knight of comic book lore and that’s the version I’m going to be looking at here.


See? Look how serious Christian Bale is taking this. That’s his serious face.


This started out as a short blog post and it got away from me somewhere in the middle, so I’ll be breaking it into two parts.  This first post will concern Batman’s most obvious bit of kit: The Batsuit itself. The second will focus on his other gadgets (in that nifty belt shown below).


Like all scientists worth their salt, Fox can smell bullshit from miles away.


So….In Batman Begins we’re introduced to God Morgan Freeman as Lucius Fox, Fox is the research head (and apparently the only researcher) of the Applied Sciences Division arm of Wayne Enterprises. This basically involves watching over all the important and ultra cool aborted research projects and prototypes that Wayne Enterprises came up with over the years but never put into general use (they do this A LOT seemingly).




Fox becomes Batman’s armourer and throughout the trilogy he oversees the construction of two different Batsuit’s. The first in Batman Begins is more cumbersome than that used in the majority of The Dark Knight and The Dark Knight Rises. This second suit actually made Batman’s signature cowl more like a motorcycle helmet (on the right above). This is eminently more practical as Bruce Wayne points out to Fox in The Dark Knight: 


Bruce Wayne: I need a new suit.

Lucius Fox: Yeah, three buttons is a little ’90’s, Mr. Wayne.

Bruce Wayne: I’m not talking fashion, Mr. Fox, so much as function.

Lucius Fox: You want to be able to turn your head.

Bruce Wayne: Sure would make backing out of the driveway easier.


The latter bodysuit is made of “hardened Kevlar® plates over titanium-dipped tri-weave fibres for flexibility” and is broken into multiple pieces over the  bodysuit for greater mobility than the original neoprene “Survival suit” from Begins that was coated with Nomex® and had Kevlar® armour plates. Now there’s some materials chemistry at work here, so let’s have a little deeper look.


These are Kevlar fibers, NOT yellow candy floss.


Like a lot of modern materials, Kevlar® is a polymer. That’s right folks basically it’s a plastic like most of the military survival “smart suit” that becomes the evening wear of a certain caped crusader.


You can even follow Kevlar on twitter. How modern!


Of course, Kevlar is the trade name of the material (you could probably tell by the ®, right?). Poly-paraphenylene terephthalamide just doesn’t sound quite so catchy especially when you are in the business of actually selling stuff. Kevlar was first isolated in a workable form by Stephanie Kwolek, a polish chemist, whilst working at DuPont in 1964. It was one of those serendipitous discoveries, which only came to light when they investigated a solution that would normally have been thrown away. Instead, finding that it was “cloudy, opalescent upon stirring and of low viscosity”, they convinced those running the “spinneret” to do them a favour and discovered that the fiber that was drawn out did not break, unlike nylon (a related polyamide).


Reels and reels of Kevlar


This generated a whole series of new polymers known as Aramids (a portmanteau of “aromatic polyamide”) – a class of heat-resistant and high strength synthetic fibers. Kevlar was introduced as a product in 1971 and has found widespread use, although most famously as a material in bullet proof vests. Other uses include – as a cryogenic material for superconducting magnets, sports equipment, tires, basketball shoes, audio speakers, tennis racket strings, frying pans (as a substitute for Teflon®), ropes, cables, smart-phone cases, brake pads…I could go on, suffice to say it is a versatile material and there have been 8 different grades used for different purposes.


Of course despite its versatility the use of Kevlar that people generally remember is still in “bullet proof” (or ballistic) vests because of the wonderful P.R. job that Hollywood has done. For instance, it saved Doc Brown (eblow) in Back to the Future, which is a good or bad thing depending on how you felt about those two sequels (I love them for the record!)


Great Scott! Kevlar saved my life! Does this mean I’m really Batman?


The first all Kevlar vest was introduced in 1975, by American Body Armor. It was called the K-15, and unsurprisingly consisted of 15 layers of Kevlar and steel shock plates over the heart. The material continues to be used today, despite many other bullet resistant materials having been developed, in part because by comparison it’s quite cheap. Kevlar stays strong down to even cryogenic temperatures (e.g. even in liquid nitrogen at −196 °C), whilst it starts to lose its strength slowly above about 160°C over a prolonged period of time.


This is part of a polymer chain of “Kevlar”, obviously it takes a LOT more of these for form a massive strand. In Bold is a monomer unit. Imagination time!


The reason Kevlar is such a useful material to Batman is due to this  remarkable strength, protecting from knives, bullets and physcial smackdowns. The fibers are about five times stronger than steel on a pound-for-pound comparison. The chains of the polymer are ordered in parallel lines where the benzene rings stack to give a symmetric and highly ordered structure (much like silk) with man inter-chain bonds due to the interaction of the carbonyl and NH groups along the chain (see figure above). Further to this there are aromatic stacking interactions between adjacent strands. These interactions are exceptionally important in giving the material its high tensile strength.


Nylon type chain on the left has little to hinder a cis type amide formation, whereas the hinderance of the bulky aromatic rings makes cis unlikely in Kevlar.


In nylon, the chains are generally more able to twist from a trans (opposite side in Latin) to cis (same side in Latin) peptide geometry. This has the result of royally messing up the nice fiber that we want. Kevlar is different. The cis– conformation is just far too sterically (or spatially) hindered i.e. the hydrogens on the rigid aromatic groups interfere with each other. As such Kevlar remains almost always in the trans– conformation, hence the beautiful fibers.


I’ve borrowed this one from wiki as chem draw was being less than helpful in finishing this blog post…


Kevlar is synthesised in solution from the monomers 1,4-phenylene-diamine (1,4- diaminobenzene) and terephthaloyl chloride (1,4-benzenedicarbonyl chloride) in a condensation reaction. The reaction yields two equivalents of hydrochloric acid as a by product. 1,4-phenylene-diamine is a precursor to many aramid plastics and fibers, which exploit the monomers difunctionality allowing the molecules to be strung together. Kevlar is of the simplest AABB type (i.e. it goes one monomer then the other).


The solvent used in the reaction was originally the highly co-ordinating hexamethylphosphoramide (HMPA), which isn’t as toxic as many make out, but it does have a pesky habit of being rather carcinogenic….


One of these two solvents is not very nice…hint: it’s the one on the left


Generally now, the polymerisation is conducted in a solution of N-methyl-pyrrolidone and calcium chloride. It should be noted that salts and other impurities, such as calcium with can interrupt the hydrogen bonding interactions of the chains and care has to be taken in production to make sure the polymer is as free from these as possible


Once the reaction is complete the brand spanking new polymer is filtered, washed and dissolved in concentrated sulfuric acid (I miss sulphur) and is finally extruded through spinnerets. The string of polymer (or filament) is passed through a narrow passage and goes through the wet spin process where it is coagulated in sulfuric acid.  The filament can take different paths; it can be formed into a fine yarn, washed and dried which is wound into spools (see picture!) or it can form filament pulp, spun-laced sheets, paper and obviously Batsuits.


The cowl (in both instances) used by Batman in all of Nolan’s movies, is also made of a Kevlar polymer, reinforced with graphite or carbon-fiber. You could write a whole blog just on this, so I won’t go into detail here. Suffice to say that carbon-fiber-reinforced polymer or carbon-fiber-reinforced plastic is an extremely strong and light fiber-reinforced polymer, although it’s apparently no match for an old man with a mallet…


He’s not SIR Michael Caine for nothing you know.


And it’s not much good against this guy either…


I am Bane. Hear me roar….And stare weirdly and shit.


Moving on to another material mentioned by Fox, in the build of the Batsuit Nomex® is a fire-resistant polymer also devised and marketed by DuPont and is closely related to Kevlar by being an aramid type polymer. In the case of Nomex it is a meta-aramid, derived from the condensation reaction of monomers, m-phenylenediamine and isophthaloyl chloride.


This is Nomex. You will notice that it simply doesn’t stack as nicely or as straightly as Kevlar. This makes it considerably weaker.


Nomex simplycannot align itself as well as the straighter chain of Kevlar, so the filament formed and has poorer strength properties. However, it does have excellent thermal, chemical, and radiation resistance. So you can thank Nomex for helping Batman survive when the Scarecrow lights him on fire in Batman Begins: click here for clip.


It may also have aided Val Kilmer’s Batman from being turned to dust in Batman Forever though, so…swings and roundabouts really.


Sir Not-Apearing-In-This-Blog-Post


The properties of Nomex also make it the perfect protective material for race-car drivers – Batman is also one of these at times, having no respect for the rules of the road naturally.


Racing is quite dangerous. Nomex has helped save many lives. As many as Kevlar has certainly.


Nomex will burn when you hold a flame to it, but it near immediate stops as soon as the heat source is removed, it is inherently flame retardant. Its thick woven structure is (like Kevlar) a very poor heat conductor, allowing you to…say jump out of a window and roll in the rain like a boss.


There be Neoprene in them there pectorals.


The other polymer mentioned is the much simpler, Neoprene  (another DuPont material unsurprisingly – this is turning into a DuPont advert). It is a much older, but extremely versatile synthetic rubber that was originally developed as a substitute for natural rubber with better oil-resistant properties. Its other properties include:


    

  • Resistance against degradation from sun, ozone and weather
    • 

  • Retains strength over over a wide temperature range
    • 

  • Physically tough
    • 

  • Fire Resistant burning inherently
    • 

  • Outstanding resistance to damage resulting from flexing and twisting
    • 



This is the polymer known as neoprene. Where n is a huge number.


The chemical name for neoprene is polychloroprene as shown below. The reaction is initiated via free-radicals, with the monomer being 2-chlorobutadiene. It generally carried out in an aqueous emulsion and has been conducting using a wide range of emulsifying agents such as alkyl sulfonates.


Titanium alloy rods. Make your own joke about rods.


Titanium is apparently also used from The Dark Knight onwards as a coating for the polymer fibers. You’ll find this metal on that chemistry thing known as the periodic table,filed under the symbol Ti and possessing an atomic number of 22. It has a relatively low density, is silver in appearance and is a strong, lustrous and corrosion-resistant metal of the transition series.


It was discovered in by William Gregor from Cornwall, UK in 1791. It is so named for the Titans of Ancient Greek mythology a comment on its strength. It’s pretty common in a range of minerals, and titanium dioxide is the metals most commonly used compound being used in the manufacture of white pigments (you even eat the stuff all the time, creepy yes?). Another compound worth mentioning is titanium tetrachloride (TiCl4) which is a component of smoke screens, but more on that in part 2.


How much do you want to bet there is some titanium in there somewhere?


Titanium’s versatility as a material and its use to the Dark Knight is all due to its ability to form alloys with a large number of other elements. Strong lightweight alloys of titanium have found uses in aeronautics (jet engines, missiles, spacecraft and flying Bat vehicles), industrial processes (chemicals and petro-chemicals, desalination plants, pulp, and paper), dental instruments and fillings, sports equipment, mobile phone parts, and many other applications.


They even made Lt. Dan’s “magic legs” out of titanium.


I’m smiling due to the power of material chemistry….honest.


So by dipping the tri-weave fibers of the suit in titanium, in a high-tech and admittedly unknown process the Batsuit is given some limited amount of the most useful properties of titanium – in particular it has the  highest strength-to-weight ratio of any metal on the periodic table, which is pretty useful when fighting crime one imagines.


Add this to the already sterling properties of Kevlar, Nomex and Neoprene and you have something that makes a wet suit look like the equivalent of swimming with Jaws naked.


Yes. It’s “Hollywood Science” time! *jazz hands*


The last thing to mention is that whole “memory cloth” stuff that Batman uses for his cape in the Nolan universe…I’m pretty sure that is Hollywood hokum I’m afraid. There have been some attempts at making self-healing memory materials, but none of this is quite as spectacularly useful as what Lucius Fox invented.


Yeah. I totally believe this.


Truth.


That’s all for now folks. Come back for Part 2 in a couple of weeks to learn about the chemistry behind some of Batman’s gadgets.


Update: Part 2 can be found here.


 


-Doctor Galactic-