Welcome to the 2018 #RealTimeChem week! My suggestion for this year’s theme was the most voted on Twitter and it’s now time to explain to all of you why I proposed this hashtag.
First of all, my name is Gabriele Laudadio, and I am currently pursuing my PhD at the Eindhoven University of Technology in the group of Dr. Timothy Noël. Since I was a child, I have been fascinated by chemistry and how the interaction between different molecules originated life as we know it. For this reason, as soon as I graduated high school student, I decided to go for it: I wanted to be a chemist!
From the very beginning, I realized how tough studying chemistry can be. So many different disciplines, so many different courses to attend. None of this scared me though, quite the opposite happened: the more I got into the field, the more I knew that it was worth all my time.
Learning the basics of chemistry felt like learning a new language. Atoms make up the alphabet, molecules can be used to form sentences and drawing reaction mechanisms pretty much compares to grammar: the rules are clear but there’s always an exception! The amazing thing about the chemical language? It’s universal! Chemistry can be used to communicate with any other fellow chemist around the world and to unravel the mystery of our universe.
Looking back to the last couple centuries, it’s so clear that chemistry not only serves the purposes of the chemical community, but affects society as a whole. From the understanding of microbiology to new approaches in the synthesis of bioactive compounds, from the production of polymers to the relevance of transition metal complexes in drug discovery…this list could be so long! What’s certain is that the Chemistry in all these discoveries radically changed the Life of every human being on this planet.
And that’s where the theme I suggested comes from: a reminder that Chemistry and Life are indissolubly linked together. What’s left to us chemists, scientists, and curious tweeps around the world is the task to learn the language of chemistry to interact with Nature. Have you had the chance in your career to glimpse into the bond between Chemistry and Nature? How did your research contribute to bring us one step further as society? Tell us all about it this week! This will be an awesome discussion I am certainly looking forward to!
But there’s also a second meaning for this #Chem4Life RealTimeChem week, one for all the insiders of the chemistry world. Nothing in life binds people together like common passions and interests, so this week we want to know how Chemistry impacted your own life. Which people/places/adventures changed your life as a chemist? Myself, I had the chance to meet fantastic people during my studies: many of my lab mates are among my best friends and I even had the luck to find love over chemistry books (My wife probably knew I liked her the moment I enthusiastically offered her my jealously guarded Org Chem notes during our masters ☺)
So let’s use the great platform of Twitter to talk about Life in Chemistry!
And don’t get me wrong: I know life as a chemists is not all sunshine and rainbows. There’s many challenges all of us face when devoting our time to Chemistry, both as scientists and as human beings. So don’t hold back and feel free to start any discussions on “the dark side” of chemistry as well… (what about working-life balance, funding situation, preprint papers, issues with the peer-reviewing systems, diversity in science, intercultural awareness in international labs…)
I certainly hope that this #Chem4Life will be a great opportunity for all chemists to remind ourselves of how lucky we are to work in this great field, to inspire and support each other through real-life examples and to reflect as a community on what we hope to achieve/improve in the future.
Chemistry for Life and Life in Chemistry, one for all, all for one!
Enjoy this lovely week, and don’t’ forget the hashtag! #Chem4Life.
Gabriele Laudadio received his masters degree in Organic Chemistry from the University of Pisa in 2016.
He is currently pursuing his Ph.D. in the group of Dr Timothy Noël at the Eindhoven University of Technology.
His research focuses on the application of Green Chemistry to improve Organic Chemistry methodologies,
combining continuous-flow microreactor technology with electrochemistry and photochemistry.
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.
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.
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 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.
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.
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.
Anna 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.
Hello! I am Clemens, a postdoc at the University of Cambridge, and in this #RealTimeChemInFocus blog post you will follow me, a chemist, doing some “biology” a.k.a. the dark side of the Force.
I know it’s weird. Why would a chemist venture into the world of biology in the first place? Honestly, it just happened! Organic chemistry was my first love as an undergrad, even after my final product of a 9-step carbohydrate synthesis decided to spontaneously decompose! I still try holding on to my first love by attempting to solve the Denksport problems of Dirk Trauner’s group and I still admire elegant total syntheses. However, the dark side of the Force has always been strong in me and over the course of my PhD and postdoc, I gradually moved towards chemical biology. I can’t help it; I am simply fascinated how chemistry can give answers to complex problems by probing or perturbing cellular systems. So, without further ado, this is a typical week in my life.
Although I am not a particular fan of Monday mornings, this Monday morning is one of the toughest of the year! I just came back from an exciting week featuring the ISACS16 conference in Zurich and a 3-day music festival in Austria (Figure 1). It made me realize how similar festivals and conferences are. Long days, short nights, meeting new people and listening to some raw talent all day long.
Figure 1: A tough start to this week after a conference & festival double feature last week.
Don’t get me wrong, I enjoyed it a lot, but it took a lot of energy out of me and getting up for the obligatory Monday morning group meeting at 9 a.m. is tough. I get coffee and arrive on time, a miracle! After the meeting, which is held in the Chemistry department, I postpone my plans to go to the Cancer Research UK (CRUK) Cambridge Institute, where the biology projects of our group happen, for one day and take some time to recover. After all, I missed a lot of science in the last week, as my RSS feed and email client tell me (Figure 2). Even better, I have to analyze some exciting sequencing data, which were generated in my absence. Having multiple, diverse projects running in parallel is one of the great things about being a chemical biologist. As my computer does all the hard work, aligning millions of reads to a reference genome, all I need to do is drink coffee and use the software correctly. The latter is something I am still struggling with (Figure 2). Nevertheless, at the end of the day I get everything analyzed and the results tell me that I am all set for writing my first manuscript as a postdoc! I also managed to catch up with my emails and the RSS feed so it’s time to cycle home and get some much-needed rest!
Figure 2: Clearly, I haven’t figured out how to take screenshots on a mac…
Another morning and it is time to head to the CRUK Cambridge Institute (Figure 3), where I will spend the rest of my working week.
Figure 3: The CRUK Cambridge institute and yes, we do have the occasional sunshine here in the UK.
I am not sure how many of you fellow chemists have ever set food in a hardcore biology working environment, so let me give you a short tour. Things here are a lot cleaner and the number of fume hoods is sadly kept to a bare minimum. They are mostly used for “dangerous” phenol-chloroform extractions of nucleic acids. Being thrown into a new working environment, I always look out for things I recognize or can relate to. Lab coats are mandatory and even wearing eye protection is reinforced (Figure 4). You can also spot the occasional TLC chamber (everybody loves TLC chambers), although they are often used for a completely different purpose than analyzing your reactions.
Figure 4: Familiar sights for a chemist in a biology lab.
Once you are feeling more comfortable in the world of biology, you might even find more similarities to your familiar chemistry lab. For working with tissue cultures, we have special hoods that remind me a lot of glove boxes. Instead of using an airlock you are using ethanol to decontaminate everything before placing it inside the hood. Of course, once you put your thoroughly washed hands inside, your nose starts to itch. Another similarity to the familiar glove box; you have to keep the place spotless as contamination with evil bacteria or yeast will spoil not only your cells, but could affect the cultures of a whole lot of other people (Figure 5). This scenario is especially bothersome, when you have worked for months creating a cell line for a particular disease you’re studying, only to find it contaminated and yourself right back at the start of your project.
Unfortunately for you, I won’t culture any cells this week, so I can’t show of my recently acquired and still embarrassingly clumsy skills, but I encourage anyone who’s curious to give it a go. It is surprisingly simple to culture mammalian cells like HeLa or HEK293 and as a chemist you have enough skills in your repertoire to learn it quickly. Because you have to work carefully and be gentle with the cells, I always picture myself handling tert-BuLi, which freaks me out, but my cells seem to appreciate the gentle treatment.
The plan for the week is to continue with a project I stopped working on before my week abroad. To cut a rather long story short, we identified some potential protein targets in a screen and are now keen on validating these hits. To get an independent confirmation, we need to clone all 28 proteins of interest (P.O.I.) into a transfection vector and express them inside the cell as a tagged version, in order to confirm the interaction by Western blot. That should suffice to give you a rough idea, and the rest of my day is spent planning everything and diluting 56 primers to the right concentrations. By the time night falls, my pipetting thumb has had a good workout!
I spent my PhD in an enzyme-engineering lab, so I did my fair share of cloning and from my experience I can tell you everything starts approximately like this:
Figure 6: Every good cloning starts with a successful PCR. The tricky thing is where to go from there.
For the current task at hand it is a bit trickier. For half of our P.O.I.s we were lucky and could obtain the cDNA – that is the complementary DNA synthesized from the corresponding messenger RNA – in the form of E. coli glycerol stocks that carry a vector containing the cDNA. For these proteins, cloning is easy: isolate the plasmid from the E. coli precultures and simply amplify the cDNA with the correct primers. We use primers that have 5’ and 3’ overhangs, which allow us to subclone the amplified cDNAs into the Gateway cloning system (Figure 7, http://scienceftw.wikia.com/wiki/Gateway_cloning).
Figure 7: Step-by-step workflow of Gateway cloning.
This method is neat, because it uses a recombinase instead of restriction enzymes and the main objective is to bring your insert into the entry vector for the Gateway system. From there, you can use another recombinase and insert your cDNA into a whole bunch of different vectors that carry appropriate tags and also allows transfecting mammalian cells! Compared to 10 years ago, when I first tackled a cloning problem, this protocol is a piece of cake.
As I started the E. coli precultures from the glycerol stocks before I left yesterday, my day consists of isolating the plasmid, doing the PCR reactions, and purifying the inserts. Sounds like a walk in the park, but it takes time (a lot of pipetting again). By the end of the day, I got 12 out of 28 cDNAs ready to insert them into the entry vector. It was clearly a successful day and I leave the lab happy for my weekly basketball game!
Today, I start the cloning of the P.O.I.s we couldn’t obtain from the cDNA in the convenient E. coli glycerol stock form. This cloning is a lot trickier, as we have to prepare our own cDNA. For this, we isolate the total RNA from HeLA cells, which involves a phenol-chloroform extraction (so dangerous!) in a real hood (so happy!). Next, we use a poly dT primer that – at least in theory – is expected to hybridize with all mRNAs in the cell as they carry a complementary poly A tail. Creating an RNA-DNA duplex allows us to reverse transcribe the whole transcriptome and generate our sought-after cDNAs. In principle, we should have our P.O.I. cDNAs in there as well, however there is no easy way of determining the concentration and whether they were fully reverse transcribed in the first place. Nevertheless, we take the crude reaction as a template for some PCR reactions. Given that we are working with a complex mixture, I start a gradient PCR – which probes annealing temperatures between 50 and 70 degrees – and hope for the best. A few hours later, I load the first 48 out of 96 PCR reactions onto an agarose gel (Figure 8), and after size separation take a look at the gel under UV light! Hurray, for 4 of 6 targets we amplified something (Figure 8). I check, whether they have the right size, which they all do, and purify them. The second batch looks equally good, which means that combined with the inserts I amplified yesterday, I got 25 out of 28 constructs ready for the recombination reaction. That’s pretty awesome and I call it a day!
Figure 8: Loading of my agarose gel on the left (hoping), results on the right (celebrating).
It’s Friday! And it’s a special Friday, as we are invited to our bosses place for a British “summer” BBQ. I prepared some salmon-spinach roles yesterday night, but they really looked ugly so I didn’t dare taking a picture. With the BBQ coming up later in the afternoon, it will also be a short day in the lab, which suits me, as all I need to do is finishing the first stage of my cloning efforts.
To insert my cDNAs into the Gateway entry vector, all I need to do is mix the vector with my PCR products. I then add the recombinase enzyme that swaps the standard insert – a gene encoding for a toxic protein that prevents growth of false positives – with my cDNAs. After incubating the reaction for an hour at room temperature, I thaw some chemically competent E. coli cells, which I will use for the upcoming transformation. These bacteria are suspended in a buffer-DMSO mixture, conditions that promote plasmid uptake through the cell membrane when heated to 42 degrees Celsius for a short time (about a minute). This procedure is a bit cruel as it kills most of the bacteria; after all they don’t like the DMSO too much. However, some bacteria that took up the plasmid during the heat shock survive and they are allowed to recover at 37 degrees Celsius in a rich medium for half an hour. Next, they are pelleted by centrifugation and resuspended in 100 μL of medium. The E. coli suspension is finally spread onto LB agar plates that have the right antibiotic (kanamycin) in them, which ensures the plasmid is amplified while the bacteria happily divide. Normally, you would incubate at 37 degrees Celsius overnight, which will give you good-sized colonies; however, with the BBQ and the weekend coming up, I just place them on my bench, where they will incubate at room temperature over the weekend, delaying the growth by about two days (Figure 9).
Figure 9: My prize after a week of cloning! Grow E. coli, grow!
All there’s left to do: Head home, get the ugly salmon-spinach roles out of the fridge, cycle to my bosses place and enjoy a burger and some beer at the BBQ. Obviously, rain begins to fall as soon as the BBQ starts, but hey, that’s life in the UK after all.
Figure 10: A proper British “Summer” BBQ in the rain.
Clemens Mayer is a postdoc, working at the University of Cambridge under the supervision of Prof. Shankar Balasubramanian. He was born in Graz, where he completed his undergrad in 2008. Subsequently, he moved to Zurich to pursue his Ph.D. in the field of enzyme engineering. In 2014 he joined the University of Cambridge, where he is currently investigating the role of RNA structures in biological processes. Passions include coffee, basketball, the accumulation of useless knowledge, being a geek, and dreading the English summer.
If you are interested in writing a guest post for #RealTimeChemInFocus, please get in touch with @RealTimeChem on Twitter.
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 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.
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 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):
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).
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.
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.
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.
Jason 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.
In this world there are two kind of postdocs: some are hired for a specific project and are focused on that, others are jolly helping here and there. I am, ladies and gentleman, a jolly.
I’m Vittorio Saggiomo, a postdoc in the BioNanoTechnology group at the University of Wageningen (in the sunny, sunny Netherlands). As a jolly, I’m working on PDMS microfluidics chips, coacervate micelles and (quite a lot) of devices with chemical sensors for soil, animal food, and recently, malaria vectors.
As I tend to swear a lot, in this blogpost I’ve censored myself changing the word f*ck with frak (Doctor Galactic: I’m partial to frell myself).
Fig 1. Example of the research going on in my university…
Monday starts like all my Mondays: the alarm clock buzzing on my night table, me thinking that it’s Sunday morning and relaxing a little bit more in the bed. Between 10 and 15 minutes later I finally realize that it’s not Sunday and I have to rush to the university. Welcome, first frak of the week.
Our building is probably the only laboratory in the whole of the Netherlands that is uphill (here it’s called “the mountain”) and when I’m late I try to bike as fast as I can. Entering the corridor of the building is like finishing the marathon, with coworkers cheering me up and giving me water. In a chaos of people screaming my name I finally enter my office with only 30/45 minutes of delay. Then I usually need 10/15 minutes to recover from the high speed biking uphill, and to get my heartbeat on a human level and to try to breath again.
Turn on my computer, 20/30 unread email, 10/15 “frak I completely forgot about this” and “oh for frak’s sake” and finally I’m in the lab, my acetone smelling kingdom.
I devote the first two days of the week on synthesis. We are trying to control the core of the coacervate micelle (very huge 100 nm micelles with a soft core of chocolate (ok, maybe not chocolate, but still a soft core) for incorporating and releasing drugs on command (hopefully our command). I put a couple of reactions on the notes of Metallica and/or AC/DC.
I spend the rest of the day supervising (or trying my best to) two master students.
Tuesday is purification day. I love column chromatography, I find it extremely zen and relaxing. And it gives me an awesome excuse not to do anything else -“come on dude, I cannot stop my column, I’ll come to you later”-. TLC, rotavap, NMR, and then i can choose between: “fraking hell, why you don’t want to work?”, “what the frak are you?”, “for frak sake, who on earth is doing a 2 h proton NMR?”.
Then I try not to get mad at one master student because he believes that his column didn’t work because the size of the capillaries is wrong. Between a colloquium and a coworker that MUST show you at least 10 youtube videos the day passes quite easily. Tuesday after work is also squash night with my boss. Perfect for stress reliever and for legs related injuries.
Wednesday is PDMS and devices day. Since I came in this lab I have fallen in love with PDMS, an extremely nice polymer for making microfluidics chips, stamps for microcontact printing and bouncing balls. I spend most of the day playing around with PDMS, using different crosslinkers, checking the swelling and the stability, pressure and so on. We are currently applying for a patent on a discovery we made last year and now are waiting to publish it. Usually on a Wednesday I also discuss a little bit with the boss. It happens more or less randomly, but most of the time it is on Wednesday. My boss’ office is between my lab and my office and when I walk from one place to the other I can clearly hear someone screaming my name.
The discussion goes often like this (I’m currently working on many different projects and I’m extremely picky on which new project I can accept):
Boss: Maybe we can do this…
The discussion can go on for hours. The first that lowers his eyes loses.
When I’m finally back in the lab I can start soldering wires, checking resistances and programming Arduino and Raspberry Pi. It’s not chemistry but it’s quite entertaining.
Thursday is terminator day. The day of the machines. Now NMR, now fluorimeter, now AFM. The synthesis of new sensor would be useless without some in-depth characterization. In this day the amount of fraks climbs to the top. Swearing at a random machine is one of my favorite hobbies. When Skynet finally takes control of the world I will be one of the first to be murdered (or enslaved). The time lost in understanding why a machine is not properly working is way more than the time used for the real analysis. Today is also a day of squash with my colleagues. Time for shoulder related injuries.
Friday is group meeting day. I usually clean a little bit in the lab, write down the stuff I did in the week and program what I’ll do the following week. The group meeting starts after lunch and no one knows when it will end, but usually we finish very, very late. Beer, alcohol and junk food are more than welcome during the discussions. BBQ in summer time. We also use 10 minutes of our time collectively swearing at a random referee number 3.
….and from my side, that’s all folks. Feel free to contact me for info, news, fun or just for swearing together.
Dr. Vittorio Saggiomo is a post doc, working at the University of Wageningen under Professor Aldrick Velders. He was born in Naples (Italy) where earning an M.Sc in Organic Chemistry in 2007. He then moved to Kiel (Germany) pursuing a Ph.D. working on Dynamic Combinatorial Chemistry. In 2010 he moved to Groningen for his first post doc in the field of Systems Chemistry, before heading to Wageningen. Find about more about him at: www.vsaggiomo.com/
Hello! My name is Laura Jane, and I’m a PhD candidate hailing from Stellenbosch, South Africa, here to show you what a week in my #RealTimeChem life entails!
One of the things our group is working on is a class of molecules called dithiadiazolyls (see this paper for more). Dithiadiazolyls (or DTDAs) are sulphur- and nitrogen-containing heterocycles that exist as neutral radicals. (It is interesting to note that the SOMO, in which the unpaired electron resides, is nodal at the carbon of the DTDA ring, so it is possible to alter the nature of the R-group without significantly altering the nature of the DTDA ring.) Thiazyl radicals have been investigated as potential building blocks for the design of molecular materials with interesting and desirable physical properties, such as conductivity and magnetism. Their magnetic and electrical conducting properties relate directly to their solid state structure. Unfortunately, many DTDAs tend to diamerise in the solid state, which results in spin pairing and, consequently, loss of any magnetic or conductive properties. We therefore look into ways to override this diamerisation and direct the structure of these materials in the solid state. My project involves the use of porphyrins as supramolecular scaffolds to create novel materials.
Monday morning starts like any other, with a cup of tea and `n Ouma beskuit while I read the news, then a breakfast of fresh fruit while I check up on what’s new in the Chemistry world. After checking my email, it’s off to my supervisor’s office, to discuss my plans for the week, but more importantly – to discuss our group’s plans regarding data backups (and storing data off-campus), spurred on by the previous day’s fire at one of our neighbouring buildings. Today ended up being an office day, not a lab day. First, backing up my data. While that’s running (my laptop tends to crash if you try giving it two things to do at once), I head off on a library run. When I return, it’s time to go play catch-up by going through some data from the last two weeks that I collected, but didn’t process, as I had fallen ill.
On Tuesday afternoons I have to demonstrate (“demi”) for an undergraduate practical session. First though, marking a stack of my class’s lab reports (nothing like leaving your marking to the last moment!). By the time that is finally done, there’s only an hour or two to spend in the lab, so I catch up on the always-fun tasks such as cleaning the never-ending pile of dirty glassware, sweeping the floor, taking inventory and so on. After a quick lunch at my desk while I catch up with what’s happening on Twitter, I haul myself and my giant stack of books across the road and around the block to one of the other Chemistry buildings for my demi duty. (The Department of Chemistry and Polymer Science at SU is spread over five buildings). This semester I’m involved in second year Inorganic Chemistry, a fun course to demi for as the pracs involve fundamental concepts and lots of pretty colours! Today’s practical involves introducing the students to the concept of qualitative analysis. South Africa has a very diverse population and consequently has 11 official languages – so language policy is a very important topic. While SU has traditionally been an Afrikaans university, undergraduate programs are now mostly bilingual (with postgraduate programs typically run only in English), so it’s quite a challenge constantly switching between the two languages when explaining to the students if your brain isn’t fully engaged.
Wednesday arrives and it’s time to hit the lab for some DTDA synthesis! DTDAs are very moisture sensitive, so it’s all about the Schlenk line. I work in a tiny little synthesis lab, where currently only myself and a MSc student are working in the fume hoods. Today it’s just step one of the DTDA synthesis, first creating LiHMDS in situ (it arrives in an unusable state when purchased as-is), then – no, wait, load shedding has kicked in again. Luckily, our building can get power from back-up generators (otherwise it’s 2.5 hours without power each time), but it’s still a minute of standing around in the dark waiting for electricity to return. Once the lights are back on and the stirrer plate is working again, it’s on adding the desired aromatic nitrile to form a silylated amidine. While those reactions are stirring away until completed, I turn my attention to my DTDA – metalloporphyrin complexations. These tend to take (what seems like) forever to form diffraction-quality crystals, so there are normally lots of these running in the background. Because of the moisture-sensitive nature of the DTDA radicals, I tend to set up these crystallizations in skinny Schlenk tubes rather than crystallization vials – it turns out that old-school test tube racks are perfect for holding these flasks when there’s only so much room to clamp flasks in your fume hood!
Thursday brings step two, condensation of the silylated amidine with SCl2 to form a dithiadiazolylium chloride salt. SCl2 is another reagent that we have to synthesise ourselves (from powdered sulphur and chlorine gas), and smells just about as lovely as you can guess, so luckily I don’t have many lab-mates to irritate! Once the product has formed, it’s time to filter and wash it – inertly of course. After drying in vacuo, the dithiadiazolylium chloride salt is obtained as a yellow powder. Halfway through the day, there’s a short break from the lab for group meeting. Typically, our group meetings involve one student presenting their current research and another presenting a paper in a relevant field. This week, however, was something a little bit different as our group was hosting Prof. Wais Hosseini (University of Strasbourg), who was given the opportunity to discuss some of his group’s work in molecular tectonics.
The last thing to do for Friday is reduce the dithiadiazolylium chloride salt to the dithiadiazolyl radical. There are several ways to do this, but my favourite is a solid-state reduction using triphenylantimony. (Zinc-Copper couple in THF is another option.) If the reaction is successful, a drastic colour change from yellow to purple is observed. Purification is then achieved by means of sublimation to get shiny dark purple crystals, all ready to meet up with some porphyrins next week.
Finally, the week comes to an end and it’s time to enjoy the late afternoon sun with a glass of cold Sauvignon Blanc on the lawns of a wine farm just up the road! Life in Stellenbosch isn’t all too bad!
Laura van Laeren is a PhD candidate at Stellenbosch University in South Africa. She is currently investigating novel thiazyl radical – metalloporphyrin complexes under the supervision of Prof Delia Haynes and Dr Katherine de Villiers. Her passions include the written word, scientific education and the Cape Winelands.
G’day! Welcome to the inaugural #RealTimeChemInFocus post, where I aim to give you a bit of an insight into the world of a radical chemist. Radical in the sense that I work with free radicals (molecules or atoms with an unpaired electron), not my political/social leanings. Read on for an introduction to our work on respiratory disease and atmospheric pollutants as I walk you through a typical week in the life of an organic chemistry PhD student.
The WHO estimates that roughly 7 million deaths per year are caused by exposure to air pollution. It is now well known that living in highly polluted areas makes you more susceptible to maladies such as respiratory disease, allergy, asthma and even death. My PhD aims to work out the underlying chemical processes, or chemical entities, responsible for these biological effects. Using a bottom-up approach, we expose simple biomolecules to pollutant gases and see what kind of havoc they wreak.
The week begins with an outline of the research tasks ahead and, like most, this is one dominated by organic synthesis. For us, this is purely a means to an end. Each peptide we wish to study is carefully designed with respect to amino acid sequence and composition. As we work on gram scale, it is typically more cost effective to synthesise these peptides in-house. That means grunt work and grunt work means coffee, lots and lots of coffee.1
Past me had the foresight to prepare the compound I needed before end of year closure. Present me lacked memory of events before end of year closure.
Synthesising each peptide involves protection of the amino acids, a coupling reaction, followed by extraction/washing and purification. Building up larger peptides, such as tri- or tetra-peptides, also involves deprotection and another coupling/work-up. To work efficiently, I often do two or three reactions simultaneously. Each reaction uses the same solvent, reagents and work-up procedure so this saves a lot of time.
A fairly epic prank by Aaron’s group members, who replaced all of the posters in the building the morning of his talk – this is one of about four different versions
The end of the week brings a busy day. Friday means more coffee (#FilterFriday!), our department’s organic chemistry seminar and, today, our group meeting and a couple of radical reactions. These experiments are the true focus of my PhD – new, original research, delving into the effects atmospheric pollutants may have on our body. That means its time to take those peptides prepared earlier in the week and treat them with some ‘pollution’, today it will be nitrogen dioxide (NO2•).
Every time you drive your car you are emitting not only carbon dioxide but also nitrogen oxides (collectively referred to as NOx gases) such as NO2•. This is one of the most abundant radicals in our atmosphere and has been implicated in respiratory disease, being toxic by inhalation. Once upon a time we obtained gas cylinders of pure nitrogen dioxide. As Australia does not produce it locally, they were shipped from overseas but sadly the freight costs are exorbitant and it can be surprisingly difficult to convince a ship captain to receive a cylinder of toxic NO2• gas. Tyranny of distance strikes again. We now produce our own nitrogen dioxide in the lab.
While chemistry is famous for beautiful colours, the field of organic chemistry is typically characterised by white solids, colourless oils and clear solutions. Peptide chemistry doubly so. My favourite chemical reaction, for reasons now obvious, is the classic reaction between copper and concentrated nitric acid. Nitric acid is slowly dripped over solid copper metal (such as the copper penny above), producing a brown noxious gas – our pollutant, nitrogen dioxide. The copper is converted from Cu0 to Cu2+, forming a gorgeous, bright blue solution of copper nitrate. Meanwhile, the nitrogen dioxide passes through a drying tube and is condensed as a liquid which allows us to react a known quantity with our peptides.
Once we have treated our peptides with this simulated pollution, we go through a painstaking process of identifying each product that is formed. This involves repeated HPLC purifications and characterisation with analytical techniques including HRMS, MS/MS, multi-dimensional NMR and, when I’m lucky, X-ray crystallography. Our results so far show that nitrogen dioxide and ozone are a destructive force, modifying residues or cleaving peptide chains. For a nice article on our latest research check out “Nitrogen dioxide and ozone: a sinister synergy”viaChemistry World or the accompanying paper published in Organic and Biomolecular Chemistry.
Over the last few years I have taken great pleasure in becoming a part of the online chemistry community. In particular, the burgeoning #RealTimeChem community is extremely welcoming, friendly and engaging. Whether it’s talking about the latest Nature paper, whingeing about that guy who just lined up 6 hours worth of samples on the NMR queue or asking for tips about how to get that postdoc you’ve always wanted – there’s something for chemists of all kinds. A PhD can sometimes be quite a solitary experience and I love having the opportunity to engage with passionate, creative and ambitious people from all around the globe. Get on there, #RealTimeChem and tweet me some time.
1 Thankfully, I live in Melbourne, Australia’s coffee mecca (sorry Sydney), surrounded by multiple coffee roasters.
Luke Gamon is in the final year of his PhD in chemistry at The University of Melbourne, Australia. Under the supervision of A/Prof Uta Wille, he is currently investigating the effects of pollution on biological molecules. Passions include coffee, baking sourdough, photography, sci-comm and board games.