Henry Rzepa's Blog Chemistry with a twist

March 18, 2014

Five things you did not know about (fork) handles.

Filed under: Chemical IT — Tags: , , , , , — Henry Rzepa @ 4:23 pm

OK, you have to be British to understand the pun in the title, a famous comedy skit about four candles. Back to science, and my mention of some crystal data now having a DOI in the previous post. I thought it might be fun to replicate the contents of one of my ACS slides here.


October 13, 2013

Blasts from the past and present: altmetrics.

I reminisced about the wonderfully naive but exciting Web-period of 1993-1994. This introduced the server-log analysis to us for the first time, and hits-on-a-web-page. One of our first attempts at crowd-sourcing and analysis was to run an electronic conference in heterocyclic chemistry and to look at how the attendees visited the individual posters and presentations by analysing the server logs.


September 15, 2013

A two-publisher model for the scientific article: narrative+shared data.

I do go on rather a lot about enabling or hyper-activating[1] data. So do others[2]. Why is sharing data important?



  1. O. Casher, G.K. Chandramohan, M.J. Hargreaves, C. Leach, P. Murray-Rust, H.S. Rzepa, R. Sayle, and B.J. Whitaker, "Hyperactive molecules and the World-Wide-Web information system", Journal of the Chemical Society, Perkin Transactions 2, pp. 7, 1995. http://dx.doi.org/10.1039/P29950000007
  2. R. Van Noorden, "Data-sharing: Everything on display", Nature, vol. 500, pp. 243-245, 2013. http://dx.doi.org/10.1038/nj7461-243a

July 5, 2013

150,000,000 DFT calculations on 2,300,000 compounds!

The title of this post summarises the contents of a new molecular database: www.molecularspace.org[1] and I picked up on it by following the post by Jan Jensen at www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called “The Harvard Clean Energy Project: Large-scale computational screening and design of organic photovoltaics on the world community grid“. It reminds of a 2005 project by Peter Murray-Rust et al at the same sort of concept[2] (the World-Wide-Molecular-Matrix, or WWMM[3]), although the new scale is certainly impressive. Here I report my initial experiences looking through molecularspace.org



  1. J. Hachmann, R. Olivares-Amaya, S. Atahan-Evrenk, C. Amador-Bedolla, R.S. Sánchez-Carrera, A. Gold-Parker, L. Vogt, A.M. Brockway, and A. Aspuru-Guzik, "The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid", The Journal of Physical Chemistry Letters, vol. 2, pp. 2241-2251, 2011. http://dx.doi.org/10.1021/jz200866s
  2. P. Murray-Rust, H.S. Rzepa, J.J.P. Stewart, and Y. Zhang, "A global resource for computational chemistry", Journal of Molecular Modeling, vol. 11, pp. 532-541, 2005. http://dx.doi.org/10.1007/s00894-005-0278-1
  3. P. Murray-Rust, S.E. Adams, J. Downing, J.A. Townsend, and Y. Zhang, "The semantic architecture of the World-Wide Molecular Matrix (WWMM)", Journal of Cheminformatics, vol. 3, 2011. http://dx.doi.org/10.1186/1758-2946-3-42

June 24, 2013

Research data and the “h-index”.

Filed under: Chemical IT — Tags: , , , , — Henry Rzepa @ 1:41 pm

The blog post by Rich Apodaca entitled “The Horrifying Future of Scientific Communication” is very thought provoking and well worth reading. He takes us through disruptive innovation, and how it might impact upon how scientists communicate their knowledge. One solution floated for us to ponder is that “supporting Information, combined with data mining tools, could eliminate most of the need for manuscripts in the first place“. I am going to juxtapose that suggestion on something else I recently discovered. 


June 5, 2013

Computers 1967-2013: a personal perspective. Part 5. Network bandwidth.

In a time of change, we often do not notice that Δ = ∫δ. Here I am thinking of network bandwidth, and my personal experience of it over a 46 year period.


June 2, 2013

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.


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.


February 9, 2010

To blog or to publish. That is the question.

Scientists write blogs for a variety of reasons. But these do probably not include getting tenure (or grants). For that one has to publish. And I will argue here that a blog is not currently accepted as a scientific publication (for more discussion on this point, see this article by Maureen Pennock and Richard Davis). For chemists, publication means in a relatively small number of high-impact journals. Anything more than five articles a year in such journals, and your tenure is (probably) secure (if not your funding).


Older Posts »

Powered by WordPress