Blog Syn sheds light on IBX oxidation

Blog Syn – the site publishing crowdsourced verification of synthetic procedures – is only 3 investigations old but is already showing signs of maturing into a valuable resource for the synthetic community.

Their 3rd investigation into the reliability of IBX oxidations of arylmethanes detailed some disappointing results in attempts to repeat published procedures. To their credit, the (high profile) authors of the original work engaged the contributors in a discussion of the variables in the experimental procedures.

In a follow-up post to the discussion, the Blog Syn contributors propose that the active species in the oxidation is actually a hydrated version of the IBX oxidant and that the presence of water is critical in the reaction.

This is fascinating stuff. The site had come under some heavy criticism recently for questioning peer-reviewed results without subjecting itself to the same process. But here’s the real beauty of a community-based discussion – we can all learn something new, and maybe even improve our understanding of chemistry.

Blog Syn #003A – Secret Ingredient

A paramagnetic/diamagnetic molecular switch

Fraser Stoddart’s group have reported a catenane molecule that can be oxidised to a stable paramagnetic radical state. The oxidation states of the molecule are easily configurable, so this structure has significant potential for use in data storage on the molecular level.

From the Chemistry World article:

The key to the stability of the new radical compound is the mechanical bond that links the two macrocycles, forcing the charged species to remain close. And that proximity means that the molecule never oxidises to a fully charged species but stops at the paramagnetic species •7+. That, says Barnes, is because the molecule is trying to minimise the charge in the centre where the two catenanes link. ‘The charged units have no choice but to interact with one another,’ explains Barnes, so it holds on to that remaining electron to reduce the charge repulsion.

But while the •7+ species is paramagnetic, all the other charged species are diamagnetic, as the electrons spins pair. Using cyclic voltammetry it is possible to quickly switch between the paramagnetic and diamagnetic states by adding and removing electrons. And it is this simple switching that could be the key to a potential application of the material: memory storage.

DOI: 10.1126/science.1228429

‘Square’ four-stranded DNA structure found in cells

A Paper in Nature Chemistry this week reports the first observation of a G-quadruplex structure of DNA in cells. Nature News has a summary of the discovery that hints at the possibility that these DNA structures may have important biological functions.

A G-quadruplex comprises four guanines from different places along a G-rich strand held together by a special type of hydrogen bonding to form a compact square structure that interrupts the DNA helix.

In a paper published online today in Nature Chemistry, researchers led by Shankar Balasubramanian at the University of Cambridge, UK, provide strong evidence that G-quadruplexes do occur in cells.

For those without subscription access, the Nature Chemistry paper is available for free for the rest of this week.

ChemDraw magic: shortcuts you know and the rest you don’t

We’re a bit late to this, but it really is essential viewing for anyone who uses ChemDraw software on a daily basis.

Pierre Morieux uses ChemDraw like most gamers play games: with lots of keyboard shortcuts and hotkeys. After being featured on In the Pipeline, Pierre has landed a job with ChemDraw publisher Perkin Elmer. Chemjobber has an interview with Pierre about his background and how he turned his skills to his advantage.

When you watch the video above, be ready to take notes.

Blog Syn: crowdsourcing synthetic procedures

Our aim is to highlight the most interesting advances in synthetic chemistry. As well as featuring journal articles we are going to start highlighting developments from outside the published literature. And, as an ideal example of chemistry moving from literature to practice…

There are few more uncertain things in organic synthesis than attempting to reproduce a literature procedure. Despite the high ideals of the scientific process, there is a high degree of variation in the quality of published procedures, and it’s not always obvious which are dubious. So when a reaction fails, have you made an error in reproducing the conditions, or is the published prep at fault?

A group of chemists are attempting to address this problem by crowdsourced checking of published methods in a new blog/journal/discussion site called Blog Syn.

Hello, synthetic chemists! Welcome to Blog Syn, a new chemical literature review site.

We don’t just discuss the methods, we put them to the test!

Stay tuned to this page as we figure out exactly how to structure this new venture. In the meantime, if this sounds like something you’d like to be involved in, drop us a message in the comments.

blog-syn.blogspot.co.uk