Henry Rzepa's Blog Chemistry with a twist

May 16, 2018

Ten years on: Jmol and WordPress.

Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on how ten years of progress in technology has required changes and the challenge of how any necessary changes might be kept “under the hood” of this blog.


June 10, 2017

Twenty one years of chemistry-related Java apps: RIP Java?

In an earlier post, I lamented the modern difficulties in running old instances of Jmol, an example of an application program written in the Java programming language. When I wrote that, I had quite forgotten a treasure trove of links to old Java that I had collected in 1996-7 and then abandoned. Here I browse through a few of the things I found.


May 29, 2017

Curating a nine year old journal FAIR data table.

As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[1]



  1. H.S. Rzepa, "Wormholes in chemical space connecting torus knot and torus link π-electron density topologies", Phys. Chem. Chem. Phys., vol. 11, pp. 1340-1345, 2009. http://dx.doi.org/10.1039/b810301a

April 6, 2017

The conformation of enols: revealed and explained.

Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.


February 2, 2017

Revisiting (and maintaining) a twenty year old web page. Mauveine: The First Industrial Organic Fine-Chemical.

Almost exactly 20 years ago, I started what can be regarded as the precursor to this blog. As part of a celebration of this anniversary,[1] I revisited the page to see whether any of it had withstood the test of time. Here I recount what I discovered.



  1. P.W. May, S.A. Cotton, K. Harrison, and H.S. Rzepa, "The ‘Molecule of the Month’ Website—An Extraordinary Chemistry Educational Resource Online for over 20 Years", Molecules, vol. 22, pp. 549, 2017. http://dx.doi.org/10.3390/molecules22040549

October 31, 2016

The smallest C-C-C angle?

Is asking a question such as “what is the smallest angle subtended at a chain of three connected 4-coordinate carbon atoms” just seeking another chemical record, or could it unearth interesting chemistry?


February 14, 2015

How many water molecules does it take to ionise HCl?

Filed under: Interesting chemistry,reaction mechanism — Tags: , , , , — Henry Rzepa @ 4:26 pm

According to Guggemos, Slavicek and Kresin, about 5-6![1]. This is one of those simple ideas, which is probably quite tough to do experimentally. It involved blasting water vapour through a pinhole, adding HCl and measuring the dipole-moment induced deflection by an electric field. They found “evidence for a noticeable rise in the dipole moment occurring at n56“.



  1. N. Guggemos, P. Slavíček, and V.V. Kresin, "Electric Dipole Moments of Nanosolvated Acid Molecules in Water Clusters", Physical Review Letters, vol. 114, 2015. http://dx.doi.org/10.1103/PhysRevLett.114.043401

November 1, 2014

Blasts from the past. A personal Web presence: 1993-1996.

Egon Willighagen recently gave a presentation at the RSC entitled “The Web – what is the issue” where he laments how little uptake of web technologies as a “channel for communication of scientific knowledge and data” there is in chemistry after twenty years or more. It caused me to ponder what we were doing with the web twenty years ago. Our HTTP server started in August 1993, and to my knowledge very little content there has been deleted (it’s mostly now just hidden). So here are some ancient pages which whilst certainly not examples of how it should be done nowadays, give an interesting historical perspective. In truth, there is not much stuff that is older out there!


September 16, 2014

Electronic notebooks: a peek into the future?

ELNs (electronic laboratory notebooks) have been around for a long time in chemistry, largely of course due to the needs of the pharmaceutical industries. We did our first extensive evaluation probably at least 15 years ago, and nowadays there are many on the commercial market, with a few more coming from opensource communities. Here I thought I would bring to your attention the potential of an interesting new entrant from the open community.


June 8, 2014

Test of JSmol in WordPress: the background story.

A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. It relied on Java as the underlying software (first introduced in 1996), or almost 20 years ago. Like most software technologies, much has changed, and Java itself (as a compiled language) has had to move to improve its underlying security. In the last year, the Java code itself (in this case Jmol) has needed to be digitally signed in a standard manner, and this meant that many an old site that used unsigned older versions has started to throw up increasingly alarming messages.


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