Posts Tagged ‘http’

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

Saturday, November 1st, 2014

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!

  1. This page was written in May 1994 as a journal article, although it did have to be then converted into a Word document to actually be submitted.[1] Because it introduced hyperlinks to a chemical audience, we wanted to illustrate these in the article itself! Hence permission was obtained from the RSC for an HTML version to be “self-archived” on our own servers where the hyperlinks were supposed to work (an early example of Open Access publishing!). I say supposed because quite a few of them have now “decayed”. We were aware of course that this might happen, but back in 1994, no-one knew how quickly this would happen. What is interesting is that the HTML itself (written by hand then) has survived pretty well! I will leave you to decide how much the message itself has decayed.
  2. This HTML actually predates the above; it was written around November 1993 and represented the very first lecture notes I converted into this form (on the topic of NMR spectroscopy). A noteworthy aspect is the scarce use of colour images. At the start of 1994, the bandwidth available on our campus was pretty limited (the switches were 10 Mbps only) and a request went out to reduce the bit-depth of any colour images to 4-bits to help conserve that bandwidth! I rather doubt anyone took much notice however, and the policy was forgotten just a few months later.
  3. In 1996, I had two visitors to the group, Guillaume Cottenceau, a french undergraduate student, and Darek Bogdal, a Polish researcher who wanted to learn some HTML. Together they produced this, which was an interactive tutorial to accompany the NMR lecture notes previously mentioned. These pages introduce the Java applet (yes, it was very new in 1996), which Guillaume had written and which Darek then made use of. And hey, what do you know, the applet still works (although you might have to coerce your browser into accepting an unsigned applet).
  4. Here is a programming course that I had been running with Bryan Levitt for a few years, now recast into HTML web pages some time in 1994-5. This particular project I still hold dear, since it expanded upon the NMR lectures by getting the students to synthesize a FID (free induction decay) using the program they wrote, and then perform a Fourier Transform on it. I even encouraged students to present their results in HTML (I cannot now remember how many did). This link is to the computing facilities we offered students in 1994 for this project, ah those were the times! In 1996, the programming course was replaced by one on chemical information technologies, and here students were most certainly expected to write HTML. Some of the best examples are still available. And to illustrate how things happen in cycles, that course itself is now gone to be replaced by, yes, a programming course (but using Python, and not the original Fortran).
  5. In tracking down the materials for the programming course described above, I re-discovered something far older. It is linked here and is (some of) the Fortran source code I wrote as a PhD student in 1974 1972. So I will indulge in a short digression. My Ph.D. involved measuring rate constants, and the accepted method for analysing the raw kinetic data was using graph paper. For first order rate behaviour, this required one to measure a value at time=∞, which is supposed to be measured after ten half-lives. I was too impatient to wait that long, and worked out that a non-linear least squares analysis did not require the time=∞ value; indeed this value could be predicted accurately from the earlier measurements. So in 1974, I wrote this code to do this; no graph paper for me! Also for good measure is a least squares analysis of the Eyring equation. And you get proper standard deviations for your errors. In retrospect I should have commercialised this work, but in 1974, almost no-one paid money for software! What a change since then. I must try recompiling this code to see if it still works! And for good measure, here is a Huckel MO program I wrote in 1984 or earlier (I did compile this recently and found it works) and here is a little program for visualising atomic orbitals.
  6. In January 1994, I was asked to create a web page for the WATOC organisation. This certainly predated the web sites for e.g. the RSC, the ACS, indeed famous sites such as the BBC and Tesco (a large supermarket chain) which only started up in mid 1994. The WATOC site itself moved a few years ago.
  7. This is one of those wonderfully naive things I started in 1994, and which did not last long (in my hands). Nowadays, the concept lives on as MOOCs. Note again the almost complete expiry of the hyperlinks.
  8. This is a project we also started in 1994, Virtual reality[2],[3]. The idea was that if HTML was text-markup, VRML was going to be 3D markup. VRML itself never quite caught on, but it is having a new life as a 3D printing language!
  9. And by 1995, I felt confident enough in my ability to (edit) HTML, that we started a virtual conference in organic chemistry (we did four of them in the end). I remember the first one involved contributors sending me a Word version of their poster, and I did all the work in converting it into HTML. Such virtual conferences still run, but in truth most participants still prefer to travel long distances to go drink a beer with their chums, rather than hack HTML.

I am going to stop now, since this is far too much wallowing in the past. But at least all this stuff is not (yet) lost to posterity.

References

  1. H.S. Rzepa, B.J. Whitaker, and M.J. Winter, "Chemical applications of the World-Wide-Web system", Journal of the Chemical Society, Chemical Communications, pp. 1907, 1994. https://doi.org/10.1039/c39940001907
  2. O. Casher, and H.S. Rzepa, "Chemical collaboratories using World-Wide Web servers and EyeChem-based viewers", Journal of Molecular Graphics, vol. 13, pp. 268-270, 1995. https://doi.org/10.1016/0263-7855(95)00053-4
  3. O. Casher, C. Leach, C.S. Page, and H.S. Rzepa, "Advanced VRML based chemistry applications: a 3D molecular hyperglossary", Journal of Molecular Structure: THEOCHEM, vol. 368, pp. 49-55, 1996. https://doi.org/10.1016/s0166-1280(96)90535-7

Tags:, , , , , , , , , , , , , , , , , , , ,
Posted in Chemical IT, Historical | No Comments »

Carbobenzene: benzene with a difference

Friday, April 16th, 2010

Some molecules, when you first see them, just intrigue. So it was with carbobenzene, the synthesis of a derivative of which was recently achieved by Remi Chauvin and co-workers (DOI: 10.1002/chem.200601193). Two additional carbon atoms have been inserted into each of the six C-C bonds in benzene.

Carbobenzene

The structure shows two resonance forms, which remind one of Kekulé and of course benzene itself. Counting reveals 18π-electrons in the conventional π sense, but with a further set of 12 π-electrons located in the plane of the ring, and orthogonal to the first set. Since both could be cyclically conjugated, we can say that the first set belongs to a 4n+2 count, and should set up diatropic ring currents resulting in aromaticity, whilst the second set would belong to the 4n category, and might set up paratropic ring currents in the plane of the system. The lowest occupied molecular orbitals of each set look as follows.

The lowest MO for the 18π-electron set. Click for 3D

Lowest occupied molecular orbital for the 12π-electron set. Click for 3D

Experimentally, the molecule is found to be aromatic. One way of quantifying this is via the so-called dissected NICS magnetic response index (DOI: 10.1021/ol016217v). At the ring centroid, NICS(0,1,2,3)zz (respectively 0,1,2,3Å above the plane of the ring) are found to be -49, -46, -38 and -28 ppm (DOI: http://10042/to-4878).  The un-dissected NICS (which includes all σ-current contributions) were -18, -16.6, -13 and -9 ppm. This both confirms diatropicity (for which NICS is strongly negative) and also suggests that the 12-electron π-framework is opposing the 18-electron π-framework.

Another, less common way to study the aromaticity is to look at the delocalization of the electrons using the ELF technique.

ELF function evaluated using only the 18 π electrons. Click for 3D

 –

ELF function evaluated using only the 12 σ-electrons. Click for 3D

The 18-electron set bifurcate (break up into smaller basins), at the threshold of 0.87 shown above (the ELF function has a maximum of 1.0 and a minimum of 0.0), a high value which is typical of aromatic systems (benzene bifurcates at ~0.9). In contrast, the 12-electron set break up well before a value of 0.1 (shown), a low value which tends to indicate anti-aromaticity.

There are many other ways of exploring the properties of such aromatic molecules, but the two above tend to suggest that carbobenzene has two personalities, one aromatic, the other antiaromatic, and with the former dominant. This gives it an interesting twist on benzene itself, and makes one wonder whether this dual Janus-like personality could be exploited in some interesting fashion.

Tags:, , , ,
Posted in General | 3 Comments »

Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog

Saturday, April 12th, 2008

A lemniscular molecular orbital

Click on the static image to get an active model. The code used to obtain the above was:

  1. This line is best added to the theme header by editing the file /wp-content/themes/default/header.php to add the following line in the header:

    <script src="../Jmol/Jmol.js" type="text/javascript"></script>

  2. <img onclick="jmolInitialize('../Jmol/','JmolAppletSigned.jar');jmolSetAppletColor('yellow');
    jmolApplet([500,500],'load http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2009/08/HV2-62.jvxl;isosurface translucent;zoom 5;moveto 4 0 2 0 90 70;');"  alt="A lemniscular molecular orbital" src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2008/04/14-knot.jpg" />

    where of course the uploads directory needs to be modified to correspond to your own content, and the file and script following it also correspond to the effect you wish to achieve.

The path wp-content/uploads/2009/08/ is that created by the built-in editor using the Add media file upload mechanism. The Jmol directory is located at the level above that of the blog itself. The JVXL file is created from either the corresponding (Gaussian) output file, or a CUB file created using a program such as Gaussview. Any suitable surface can be displayed using JVXL. In addition to MOs, we have also displayed ELF (Electron localization function) isosurfaces and molecular vibrations. For the latter, use a script of the form

'load wp-content/uploads/2008/04/vibration.log; frame 9; vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 10;animation mode loop;'

where the vibration you want is contained in e.g. frame 9.

There does appear to be a display bug with the above; the Jmol model replaces the window rather than being inlined in it. Once the model is displayed, just refresh the page to return to the blog entry.

A recent addition is the display of non-covalent-interaction (NCI) surfaces, which are colour coded by using the values in one cube of points to colorize a second cube.

'load wp-content/uploads/2011/05/isobornyl1.xyz;isosurface wp-content/uploads/2011/05/isobornyl1.jvxl colorscheme translucent bgyor;'

Tags:, , , , , , , ,
Posted in Chemical IT, Interesting chemistry | 8 Comments »