chemical education

Disease-Focused Pharmaceutical Posters from the Njardarson Group

Jon Njardarson at the University of Arizona is well known for his group’s Top200 Drugs Posters. They chronicle the structure of the top 200 pharmaceutical drugs by both US retail sales and US prescriptions.

Now, his group has changed focus slightly. The group takes a disease category, like the nervous system, and lists all small-molecule drugs that have been approved for this category. They are listed in chronological order. This is a really neat twist to a nice series of posters out of the Njardarson group. There are about a dozen or so of these posters, and they are made freely available on the group’s website.

NervousSystemDrugs

By September 17, 2013 7 comments chemical education

The Underground Map of the Elements

My son loves trains. So I came up with a train related twist to an inspection of the periodic table. We sat and cut up a copy of the table and then rearranged each element as a ‘station’ on an underground rail system. Each line represents a characteristic shared by the elements on that line. map 1.4

After (quite) a few drafts, and more time than I care to admit, we ended up with this.

It was constructed with the help of Metro Map Creator (no way I could have done it without this neat web app). If anyone fancies building some more lines I’ll happily send you the saved file (share using a creative commons attribution, non-commercial, share a like license) .

Let me know if you spot any errors.

Edit:

Thanks to Shaun, Max, IanMitch, YulLabrat and Stu (alway handy to have a Nature Chemistry editor check your work)  for spotting some mistakes. All corrected now.

Now on version 1.4. New line added, to show elements that were discovered via synthesis and then found in nature.

By August 27, 2013 36 comments chemical education, fun

Happy Berzelius Day

Jöns_Jacob_Berzelius
Today, August 20th, marks the birthday of Swedish chemist Jöns Jacob Berzelius (1779–1848).

I decided to write this post because, frankly, I knew nothing about Berzelius. He seems to be something of an “unsung hero”, despite his important contributions to science. I thought I’d take the opportunity to collect some key facts about this visionary chemist’s life.

The late 18th and early 19th centuries were formative years for modern chemistry. The names of many of the pioneers of that age – such as Lavoisier, Dalton, Avogadro, Volta and Faraday – live on in the minds of scientists to this day (mostly, perhaps, in the form of the units we use). Berzelius lived through much of this revolutionary (in more ways than one) period, and many of his discoveries and innovations have underpinned chemistry for centuries since.

Berzelius trained as a medical doctor, and found himself fascinated by the work of Volta and the latter’s invention of voltaic piles. Berzelius incorporated electricity into his medical research, investigating the effect of direct current on unwell patients. It turned out that giving his patients electric shocks did not improve their condition, but this result didn’t abate Berzelius’ scientific curiosity.

He was living in the golden (or should that be cupro-zinc?) age of electrochemistry. Berzelius was a systematic experimenter, able to collect and collate vast quantities of data and extract trends and conclusions in his analysis. His examination of the electrochemistry of metal salts led him to his theory of “dualism”. This theory proposed that all atoms bore a charge – positive or negative – and that compounds were formed by the neutralisation of opposite charges. This offered an early analogy to ionic bonding. However, the theory of dualism fell out of favour towards the end of Berzelius’ life, as its inability to accommodate new discoveries, including the developing field of organic chemistry, became clear.

It was around the time of Berzelius’ studies on dualism that John Dalton published his New System of Chemical Philosophy (1808), which introduced his development of atomic theory – that elements were made up of indestructible and indivisible atoms, which were identical for a given element. Dalton also published a table of a handful of atomic weights and associated atomic symbols.

Dalton_atomic_symbols

Unfortunately, Dalton’s determinations were limited in terms of accuracy, and the majority of known elements were omitted. Berzelius systematically examined all of the elements known at the time, and published 43 atomic weights which have proven remarkably accurate (considering the pioneering nature of the work) when compared to modern values.

As he used so many elements and compounds, Berzelius began to find the chemical notation of the time to be cumbersome. Chemicals were typically represented by pseudo-alchemical symbols, making the construction and parsing of chemical formulae difficult and error-prone.

Berzelius changed all this, and, in a short paper, introduced the basis of the chemical notation we use to this day. He substituted the alchemical symbols for letters: C, Cu, O, etc. The proportion of atoms in a compound was denoted by superscript numbers: CO2. Nowadays, of course, we denote the proportions with subscripts, but in all other respects Berzelius’ notation has stood the test of time remarkably well.

progression_of_formula

Berzelius also discovered four elements: cerium, selenium, silicon and thorium, and in addition introduced several terms to the chemical lexicon – although their meanings have changed since: allotrope, polymer, catalysis and isomer.

Berzelius’ systematic identification of the chemistry of minerals, along with his many other discoveries, earned him the Royal Society’s Copley Medal in 1836, jointly with Francis Kiernan.

Berzelius’ legacy was doubtless cemented by his publication of numerous widely-translated textbooks. It is interesting to consider that these textbooks may have educated some of the big names of the next generation: Mendeleev, Clausius, Helmholtz, Joule, Bunsen, perhaps even Darwin. Whether or not they did, it is doubtless that they, in common with generations of chemists since, owe much to the discoveries of Berzelius and his contemporaries.

So, today let’s remember Berzelius, one of the “Fathers of Modern Chemistry”.

A bit of trivia:

Berzelius is the academic great-great-great-great-great-great-grandfather of Prof Martyn Poliakoff, of University of Nottingham and Periodic Table of Videos. Small world?

Like many chemists, Berzelius has a piece of glassware bearing his name. A tall and thin glass beaker is otherwise known as a Berzelius beaker.

 

Sources/further reading: http://www.chemheritage.org/discover/online-resources/chemistry-in-history/themes/electrochemistry/berzelius.aspx

http://www.nndb.com/people/051/000094766/

http://pubs.acs.org/subscribe/archive/tcaw/13/i12/pdf/1204chronicles.pdf

Periodic Table of Videos – Berzelius

For a review on Berzelius’ techniques and involvement with atomic weights, see W. MacNevin, J. Chem. Educ.195431, 207. (paywall)

All images are public domain.

Writing an Online Organic Chemistry Quiz

Lately, I’ve been very interested in using my university’s Learning Management System (we use Moodle, others use Blackboard or something else) to administer quizzes to my students, but as an organic chemist, I’ve been hesitant to do so. Primarily because I don’t want to ask a bunch of multiple choice questions. That’s not what my exam will be. Most of my exam answers will be structure based, so any LMS-administered quiz would need to accept structure-based answers.

NOT what my exam questions will look like...

NOT what my exam questions will look like…

I know some publishers have platforms for just this, but our university doesn’t subscribe to the service. So in some respects, I’m admittedly reinventing the wheel here.

At first I thought the LMS would be able to grade my students’ work if they type in the IUPAC name for each structure. But many of the structures have IUPAC names which can be rather large and/or outside of the scope of IUPAC nomenclature my students learn. And our ChemDraw license does not include the structure-to-name feature. So I needed something else.

I thought SMILES would be a good choice. SMILES is a condensed version of the structure, almost human readable, and ChemDraw can copy a structure directly in SMILES format. Perfect! I like the human readable aspect, as students can glance through their SMILES to check for some potential errors.

So I wrote up a pilot quiz with tutorial videos. I coded the correct SMILES into the grader – as well as some of the common errors for feedback purposes – and released it to my students. For testing purposes, I also had them upload a .jpg version of the structure so I could check it visually myself if there were any discrepancies. I’m glad I did.

The first thing I noticed when looking at the responses is that most of the students got most of the tutorial questions incorrect! I didn’t understand why. All they had to do was follow along bond for bond with my tutorial video and get the correct answer. When I checked their .jpg structures, all of the structures appeared to be correct! What is going on?

After some testing of my own, I came to a disappointing conclusion: ChemDraw gives different SMILES for the same structure depending on the order in which you draw the bonds. If you start from the left side, you get one SMILES, from the right you get a different SMILES. Start in the middle, and you get a third SMILES still. Don’t believe me? Watch this, and try it yourself:

I’ve let the ChemDraw people know, and they said they’d pass my comments along to developers. I understand that all of these are valid SMILES, but I feel that one structure should give the same SMILES from ChemDraw, regardless of how the molecule happened to be drawn. So now, I’m going to use InChI Key for my grading system. It’s not human readable, but at least the same structure seems to give the same InChI Key regardless of how the structure is drawn.

I still haven’t figured out a convenient way to code arrow-pushing mechanisms or multi-step synthesis answers using this method. If anyone has any suggestions, let me know! It needs to be something unambiguous that the students can use and the non-chemistry quiz grading software can interpret the answer.

By August 19, 2013 18 comments chem 2.0, chemical education