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Chemical drawings in Wikipedia

29 January 2013 - Quality control

azilsartan medoxomil.PNGWikipedia has a great layout and comes with lots of tools (table making, mathematical equations) to help out with layouts. The layout for many thousands of Wikipedia articles is standardized.

This wonderful system breaks down when it comes to chemical drawings on the organic chemistry pages. No page looks the same and techniques used vary. For example the aldol reaction page containes plain .gif images in basic gif quality, the Buchwald-Hartwig amination has .png images and the aryne page adopts a tif format. In Nicolaou Taxol total synthesis it is .svg.

A vector based format such as svg would help a lot but although you can upload a svg the image is still rendered as an .svg.png. Same goes for the .tiff format. Even if you agree on a style guideline, for example that of the ACS or IUPAC the look will not yet be consistent. First of all there is the level of anti-aliasing (removing the stair-step appearance) applied to the export image by the graphical editor. And then there is image size. A trick to improve perceived image quality is to upload a very large image have it rendered at reduced size. But what size?.

A review of chemical editors can be found at In it Gunda notes that anti-aliasing is a novel feature in many editors. Good news. As it happens one of them, ChemSketch, is also available as freeware so we can put it to the test. Yes there is an anti-aliasing option but curiously only within the editor. In all exports (to tif, gif, png) it is lacking. Luckily Gunda offers a work-around: use a screen-capture such as the simple Windows 7 image snapping tool.
In other aspects ChemSketch is great. Example novel synthesis Azilsartan medoxomil (DOI)

Travor Laird complains loudly

21 January 2013 - Publishing

And he should be. Laird is editor of the journal Organic Process Research & Development and in his editorial (DOI) he complains that too many articles are titled something like 'Scale-Up of the Synthesis of an XYZ Antagonist' (5 articles in fact are titled that way in the current issue). How about something more descriptive?. Complaint number two: article summaries that pose as article summaries but in fact are not, advertisements at the most. Even more complaints: keywords like 'efficient' or 'green' are not always substantiated.
This blog cannot agree more. And it is not just OPRD. Lets have a brief look at what the other journals have to offer in terms of ineffective titles and irrelevant summaries.
From Angewandte Chemie the title The Effect of an Active Guest on the Spin Crossover Phenomenon (DOI) - what is the effect? and from the abstract A new strategy for regulating spin crossover (SCO) properties by the control of an active guest molecule is proposed - Yeah? just what is the strategy?.
From Organic Letters the title "Exploring the Unique Reactivity of Diazoesters: An Efficient Approach to Chiral Amino Acids" (doi) and from the abstract "The development of a "..." is described.". And the graphical abstract: no trace of an amino acid.
From Tetrahedron letters the title "A practical method for the regeneration of Kaiser-oxime resin" (DOI) and from the would-be abstract "We report here a simple procedure for the regeneration of the Kaiser-oxime resin". In the meanwhile the reader remains clueless about what the "practical method" is all about.
Of course Trevor Laird and his colleagues should just assume control over their shops and simply demand relevant titles and abstracts. The are the boss after all. Right?

Polymer film autolocomotion

14 January 2013 - Making It Move part X

PPyActuatorLanger2013.PNGSo what else can be made to move by sheer chemical force. In what must be part 10 in our Making-It-Move sequel - Ma, Guo, Anderson and Langer are moving around a piece of water-responsive polymer film (DOI).

A polymer film was created by Pyrrole electropolymerisation in a pentaerythritol ethoxylate / boron trifluoride etherate / isopropyl alcohol system. In this way polypyrrole (PPy) gets embedded in a polyol / borate interpenetrating network according to the idealised equation 2ROH + 2BF3 -> RO-BF2--OR + BF4- + H+. In this system both phases act as each other's counterion.

The polyol/borate phase is good at reversibly absorbing water. When a flat film is left on a moist surface the bottom part, absorbing water, swells more than the top part making the film buckle and move away from the surface. Due to mechanical instability the buckled film will eventually fall over and in a next phase the the other side of the film faces the wet surface and the process repeats itself. Hence, locomotion!.

The numbers: a cycle takes 5 minutes and can repeat itself hundreds of times. The force exerted is 80 times higher than mammalian skeletal muscle. The film can lift a 9.5 g object by 2 mm in 3 seconds. Optimal film thickness ranges between 15 and 40 micron.

In another exploit the film was slammed against a piezoelectric polyvinylidene difluoride film and again exposed to the wet surface. The repeated bending and stretching made the film generate a cool 5 nano Watt of power. This does not sound like much but the researchers are confident their invention will one day power a euphemistically called ultralow-power device. movie!

Design of Experiments and chemistry

12 January 2013 - DoE

PrincipalComponentAnalysisMurry2012.PNGA fun anecdote from past experience while working in industry. In optimizing chemical reactions I have worked with chemists who insisted on randomly selecting their reaction parameters. Ten experiments were performed with a random set of lets say reaction temperature, stoichiometry and choice of base. The best performing reaction was then presented to management as the 'optimized reaction'. Why? For the chemist it conveniently lifted the burden of rationalizing the outcome of the reaction. Did management want more optimizations? Ten new random experiments were selected from the magicians hat.

Murray et al. are also industrial chemists but represent the other extreme of the quality scale. In the latest issue of OPRD they play an interesting numbers game (DOI). In a concept article the key question they pose: how do you optimise a chemical reaction knowing that even with a limited set of variables the number of unique reactions can easily run in the thousands. Case at hand: a typical Suzuki reaction has 7 continuous variables (stoichiometry for reactants, base, water, precatalyst loading, metal:ligand ratio, concentration and temperature ) resulting in 128 variable sets with just two levels. Adding 500 ligands, 2 Pd precursors, 4 bases and 100 solvents (all discrete variables and industrially relevant) increases the number to a staggering 51.2 million. As Murray points out, even on a 10 mg test scale 512 Kg of starting material would be required.

Solution: a combination of Design of Experiments and Principal Component Analysis. Testing a bunch of very similar ligands is nonsensical. What you would like to have is a set of ligands the occupy different spots in so-called ligand space defined by three axes of measurable chemical properties such as Hansen solubility parameter, boiling point or a bond length. With for example 9 representative ligands occupying the corners of a cube and one in the centre the best performing reaction will reveal where in ligand space the opportunities are. Through a method of iterations the reaction can then be further refined. Murray boasts that by using this method optimizing a Buchwald-Hartwig amination only required 35 reactions.