Henry Rzepa's Blog Chemistry with a twist

August 13, 2012

Digital repositories. An update to the update.

Filed under: Chemical IT — Tags: , — Henry Rzepa @ 6:33 pm

A third digital repository has been added to the two I described before. Chempound is a free open-source repository which (unlike DSpace and Figshare) was developed specifically for chemistry.

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July 22, 2012

QR codes and InChI strings.

Filed under: Chemical IT — Tags: , , , , , , , , — Henry Rzepa @ 8:37 am

A month or so ago at a workshop I was attending, a speaker included in his introductory slide a QR (Quick Response) Code. It is a feature of most digital eco-systems that there is probably already “an app for it”. So I thought I would jump on the band wagon by coding an InChI string. Here it is below:

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July 21, 2012

Digital repositories. An update.

I blogged about this two years ago and thought a brief update might be in order now. To support the discussions here, I often perform calculations, and most of these are then deposited into a DSpace digital repository, along with metadata. Anyone wishing to have the full details of any calculation can retrieve these from the repository. Now in 2012, such repositories are more important than ever. 

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July 20, 2012

Origins of the Regioselectivity of Cyclopropylcarbinyl Ring Opening Reactions.

Filed under: Uncategorised — Tags: , , , , , , , — Henry Rzepa @ 1:55 pm

Twenty years are acknowledged to be a long time in Internet/Web terms. In the early days (in 1994), it was a taken that the passage of 1 Web day in the Internet time-warp was ~≡ 7 for the rest of the world (the same factor as applied to the lives of canines). This temporal warping can also be said to apply to computational chemistry. I previously revisited some computational work done in 1992, and here I rediscover another investigation from that year[1] and that era. The aim in this post is to compare not only how the presentation of the results has changed, but how the computational models have as well.

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References

  1. R.A. Batey, P. Grice, J.D. Harling, W.B. Motherwell, and H.S. Rzepa, "Origins of the regioselectivity of cyclopropylcarbinyl ring opening reactions in bicyclo [n.1.0] systems", Journal of the Chemical Society, Chemical Communications, pp. 942, 1992. http://dx.doi.org/10.1039/C39920000942

July 12, 2012

More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.

Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[1]. That was then.

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References

  1. M.S. Baird, J.R. Al Dulayymi, H.S. Rzepa, and V. Thoss, "An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes", Journal of the Chemical Society, Chemical Communications, pp. 1323, 1992. http://dx.doi.org/10.1039/C39920001323

July 5, 2012

Connections in chemistry. Anti-malaria drug ↔ organocatalysis.

Filed under: Chemical IT,Interesting chemistry — Tags: , , , — Henry Rzepa @ 11:30 am

Back in 1994, we published the crystal structure of the molecule below (X=H), a putative anti-malarial drug called halofantrine. Little did we realise that a whole area of organo catalysis based on a thiourea catalyst with a similar motif would emerge a little later. Here is how the two are connected.

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May 18, 2012

“Text” Books in a (higher) education environment.

Text books (is this a misnomer, much like “papers” are in journals?) in a higher-educational chemistry environment, I feel, are at a cross-roads. What happens next?

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February 27, 2012

The blog post as a scientific article: citation management

Sometimes, as a break from describing chemistry, I take to describing the (chemical/scientific) creations behind the (WordPress) blog system. It is fascinating how there do seem increasing signs of convergence between the blog post and the journal article. Perhaps prompted by transclusion of tools such as Jmol and LaTex into Wikis and blogs, I list the following interesting developments in both genres.

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December 11, 2011

Mobile-friendly solutions for viewing (WordPress) Blogs with embedded 3D molecular coordinates.

My very first post on this blog, in 2008, was to describe how Jmol could be used to illustrate chemical themes by adding 3D models to posts. Many of my subsequent efforts have indeed invoked Jmol. I thought I might review progress since then, with a particular focus on using the new generations of mobile device that have subsequently emerged.

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May 4, 2010

A Digital chemical repository – is it being used?

In this previous blog post I wrote about one way in which we have enhanced the journal article. Associated with that enhancement, and also sprinkled liberally throughout this blog, are links to a Digital Repository (if you want to read all about it, see DOI: 10.1021/ci7004737). It is a fairly specific repository for chemistry, with about 5000 entries. These are mostly the results of quantum mechanical calculations on molecules (together with a much smaller number of spectra, crystal structure and general document depositions). Today, with some help (thanks Matt!), I decided to take a look at how much use the repository was receiving.

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