Posts Tagged ‘chemical’

Data-round-tripping: wherein the future?

Tuesday, December 7th, 2010

Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say ChemDraw) and the Word processor used to place them into a context (say Microsoft office), via an intermediate storage area known as the clipboard. The round trip between the Macintosh (OS X) versions of these programs had been broken a little while, but it is now fixed! A small victory. This blog reports what happened when such a Mac-created Word document is sent to someone using Microsoft Windows as an OS (or vice versa).

As you might have guessed, the molecular diagram arrives largely dead, and not re-usable. Opening the .docx archive (it is nothing more than a zip file) reveals only a JPEG file residing inside. Nothing that can be chemically repurposed. If the reverse process is undertaken, of creating a chemdraw diagram, and pasting it into Word on Windows, one finds in the .docx two components; a bit-mapped image linked to an active object containing the data. Only the first of these is recognised if the file makes its way to a Macintosh; i.e. the same story, the data is again lost. So the bottom line is that Mac users and Windows users cannot, after all, exchange repurposable molecular diagrams using Word documents using this combination of programs. This is not good.

But let me remind what happened around 1993. The word processor was joined by a program called the Web browser. In 1996, the underlying content carrier, HTML, became XHTML (an instance of XML). Right from day 1 almost, such XHTML could, and frequently was repurposed. A memorable example is that search engines could use it to index the Web. The XHTML easily survived trips to and from clipboards. In 1996, CML joined HTML as a way of carrying chemical information capable of round-tripping without loss (if need be). There are other chemical XML languages in use nowadays, including CDXML used by the ChemDraw program. Word itself now uses XML (the x in .docx). So, after 14 years, why am I still describing the difficulties above? I am frankly at a loss to explain why there is still a need to write this post.

All is not entirely lost. The CML4Word approach is designed to enable (chemical) data round tripping from the outset. Although I do not yet know if the CML created and stored in the Word document using this mechanism is recognised anywhere outside of Word 2007 on Windows?  If anyone can let me know of examples where such a CML-enabled Word document can be used in other environments, I would be very grateful (but not on  OS X, as I know already).

And as I might have mentioned in the previous post on this topic, things may not however be getting better in that other carrier of information and data, the mobile phone/iPad, as exemplified by operating systems such as iOS or Android. Watch this space, as they say.

The oldest reaction mechanism: updated!

Tuesday, September 14th, 2010

Unravelling reaction mechanisms is thought to be a 20th century phenomenon, coincident more or less with the development of electronic theories of chemistry. Hence electronic arrow pushing as a term. But here I argue that the true origin of this immensely powerful technique in chemistry goes back to the 19th century. In 1890, Henry Armstrong proposed what amounts to close to the modern mechanism for the process we now know as aromatic electrophilic substitution [1]. Beyond doubt, he invented what is now known as the Wheland Intermediate (about 50 years before Wheland wrote about it, and hence I argue here it should really be called the Armstrong/Wheland intermediate). This is illustrated (in modern style) along the top row of the diagram.

The mechanism of aromatic electrophilic substitution

In 1887, Armstrong had tabulated the well known ortho/meta/para directing properties of substituents already on the ring towards this reaction[2]. He even offered an explanation, which is not entirely wrong, given that in 1890, the electron had not yet been discovered! That did not stop Armstrong, who invented an entity he called the affinity for the purpose of developing his theories (in this theory, benzene had an inner circle of six affinities, which had a tendency to resist disruption). Armstrong’s description of the properties of the affinity matches that of the (yet to be discovered) electron very closely! But that is enough of history. The mechanism shown above emerged in its present representation (and naming) during the heyday of physical organic chemistry between 1926 – 1940, and of course is an absolute staple of all text books on organic chemistry. But, sacrilege, is it correct? Could what is referred to as an intermediate instead be a transition state? (shown in the bottom pathway of the scheme).

Consider instead the following, in which X is replaced by an acetic acid motif;

Transition state alternative to the Wheland

The two steps, a bond formation between the benzene and E, and the proton abstraction from the benzene by X, are now synchronized into a single step, and the intermediate is now transformed into a transition state. Time to put this theory to the test. X is going to be made trifluoroacetate (R=CF3) and we are going to test it with E= NO+ and F+ (yes, trifluoroacetyl hypofluorite is a known chemical, and it really does fluorinate1 aromatic compounds at -78C). Firstly, E= NO+. A B3LYP/6-311G(d,p) calculation[3]  run in a solvent simulated as dichloromethane, reveals the mid point to indeed be a transition state and NOT an intermediate![4].

Wheland as a transition state. Click image for animation

There is one crucial aspect to this transition state that Armstrong himself made a point of. In the Wheland intermediate proper, the aromaticity of the benzene ring must be disrupted. As a transition state, it need not be (at least not completely). Thus the two bonds labeled as a have calculated lengths of ~1.415Å, only slightly longer than the aromatic length, and certainly not single bonds as implied by the Wheland intermediate! Notice also the significant motion by the hydrogen, which implies the reaction would be subject to a kinetic isotope effect (this would normally be interpreted in terms of the second stage of the stepwise reaction shown along the top a being rate limiting, but this result shows this need not be so). Thus, if the structure is favourable, this veritable old mechanism can be redesigned to give a new, 21st century look to a 19th century staple! By the way, the free energy of activation for this reaction is calculated as ~22 kcal/mol, a perfectly viable thermal reaction. No doubt, by suitable design of the group X, this might be reduced.

Now on to E=F+[5]. This looks a little different. F+ is now a much more voracious electrophile than the nitrosonium cation, and it therefore jumps ahead of the second mechanistic step, with no motion of the hydrogen being involved at this stage (one might also imagine making X a better base to swing things the other way).

Transition state E=F+ leading to Wheland Intermediate. Click for  3D model.

Genuine Wheland intermediate for E=F+ Click for 3D model

Now a full blown Armstrong/Wheland intermediate does indeed form (10042/to-5174); an intimate ion pair if you will, even in the relatively non polar dichloromethane as modelled solvent. The structure  (shown above) is rather unexpected.  This reaction has ΔG of ~5 kcal/mol,  which is significantly lower than for the E=NO+ system.

Chemistry is full of surprises, and it is always a wonder how a slightly different take on even the oldest of reactions can reveal something new.

Reference.

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p>1. Umemoto, T.; Mukono, T.. 1-Acylamido-2-fluoro-4-acylbenzenes. Jpn. Kokai Tokkyo Koho  (1986), Patent number JP61246156.

References

  1. "Proceedings of the Chemical Society, Vol. 6, No. 85", Proceedings of the Chemical Society (London), vol. 6, pp. 95, 1890. https://doi.org/10.1039/pl8900600095
  2. H.E. Armstrong, "XXVIII.—An explanation of the laws which govern substitution in the case of benzenoid compounds", J. Chem. Soc., Trans., vol. 51, pp. 258-268, 1887. https://doi.org/10.1039/ct8875100258
  3. "C 8 H 6 F 3 N 1 O 3", 2010. http://doi.org/10042/to-5172
  4. S.R. Gwaltney, S.V. Rosokha, M. Head-Gordon, and J.K. Kochi, "Charge-Transfer Mechanism for Electrophilic Aromatic Nitration and Nitrosation via the Convergence of (ab Initio) Molecular-Orbital and Marcus−Hush Theories with Experiments", Journal of the American Chemical Society, vol. 125, pp. 3273-3283, 2003. https://doi.org/10.1021/ja021152s

On the importance of Digital repositories in Chemistry

Friday, April 3rd, 2009

The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it yourself. Even after 15 years of the  (chemical) Web, this can be distressingly difficult to achieve (or can it be that it is only myself who wishes to view molecules in their  native mode?).  Thus the standard mechanism is to seek out on journal pages that disarming little entry entitled  supporting information and to hope that you might find something useful embedded there.  Embedded is the correct description, since the information is often found within the confines of an Acrobat file, and has to be extracted from there.  Indeed, that is what  I had to resort to in order to write one of the blog entries below. I ground my teeth whilst doing so. 
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So is there a better way? We think so! The  digital repository. If you click on this you should see the entry directly. What can you do there? Well, if you have suitable programs, you can download eg a Checkpoint file of the calculation that created the molecule model and re-activate it there. Or you can download just the CML file for viewing in any CML-compliant program (such as e.g. Jmol). Or you can check up on the InCHi string or the InChI Key of the molecule.

What about the specific entry above? Well, it corresponds to the calculation for the π4 + π2 cycloaddition described in the blog entry below. You can now verify for yourself the assertions made in that entry, ie that the rotation mode is disrotatory, or that the bond is forming antarafacially. You do not need to take my word for it! If the Digital repository is too much trouble for you, click on the graphic instead to get a similar result.

We now regularly put such links into journal articles, in the form of Web-enhanced tables and figures, so that it is literally just one click away from such an article to having a vibrant molecule dancing in front of you. All (chemistry) journals should do this. If they do not yet, then contact their editor in chief when you next submit an article and ask them why not!

See also the blog by Peter Murray-Rust.