Posts Tagged ‘Acrobat’

Re-inventing the anatomy of a research article.

Saturday, December 29th, 2018

The traditional structure of the research article has been honed and perfected for over 350 years by its custodians, the publishers of scientific journals. Nowadays, for some journals at least, it might be viewed as much as a profit centre as the perfected mechanism for scientific communication. Here I take a look at the components of such articles to try to envisage its future, with the focus on molecules and chemistry.

The formula which is mostly adopted by authors when they sit down to describe their chemical discoveries is more or less as follows:

  1. An introduction, setting the scene for the unfolding narrative
  2. Results. This is where much of the data from which the narrative is derived is introduced. Such data can be presented in the form of:
    • Tables
    • Figures and schemes
    • Numerical and logical data embedded in narrative text
  3. Discussion, where the models constructed from the data are illustrated and new inferences presented. Very often categories 2 and 3 are conflated into one single narrative.
  4. Conclusions, where everything is brought together to describe the essential aspects of the new science.
  5. Bibliography, where previous articles pertinent to the narrative are listed.

In the last decade or so, the management of research data has developed as a field of its own, with three phases:

  1. Setting out a data management plan at the start of the project, often a set of aspirations together with putative actions,
  2. the day-to-day management of the data as it emerges in the form of an electronic laboratory notebook (ELN),
  3. the publication of selected data from the ELN into a repository, together with the registration of metadata describing the properties of the data.

In the latter category, item 8 can be said to be a game-changer, a true disruptive influence on the entire process. The key aspect is that it constitutes independent publication of data to sit alongside the object constructed from 1-5. More disruption emerges from the open citations project, whereby category 5 above can be released by publishers to adopt its own separate existence. So now we see that of the five essential anatomic components of a research article, two are already starting to achieve their own independence. Clearly the re-invention of the anatomy of the research article is well under way already.

Next I take a look at what sorts of object might be found in category 8, drawing very much on our own experience of implementing 7 and 8 over the last twelve years or so. I start by observing that in 2 above, figures are perhaps the object most in need of disruptive re-invention. In the 1980s, authors were much taken by the introduction of colour as a means of conveying information within a figure more clearly; although the significant costs then had to be borne directly by these authors (and with a few journals this persists to this day). By the early 1990s, the introduction of the Web[1] offered new opportunities not only of colour but of an extra dimension (or at least the illusion of one) by means of introducing interactivity for three-dimensional models. Some examples resulting from combining figures from category 2 with 8 above are listed in the table below.

Examples of re-invented data objects from category 2
Example Object title Object DOI Article DOI
1 Figure 9. Catalytic cycle involving one amine …etc. 10.14469/hpc/1854 10.1039/C7SC03595K
2 FAIR Data Figure. Mechanistic insights into boron-catalysed direct amidation reactions 10.14469/hpc/4919 10.1039/C7SC03595K
3 FAIR Data table. Computed relative reaction free energies (kcal/mol-1) of Obtusallene derived oxonium and chloronium cations 10.14469/hpc/1248 10.1021/acs.joc.6b02008
4 (raw) NMR data for Epimeric Face-Selective Oxidations … 10.14469/hpc/1267 10.1021/acs.joc.6b02008
5 Bibliography 10.14469/hpc/1116 10.1021/acs.joc.6b02008

Example 1 illustrates how a figure from category 2 above can be augmented with active hyperlinks specifying the DOI of the data in category 8 from which the figure is derived, thus creating a direct and contextual connection between the research article and the research data it is based upon. These links are embedded only in the Acrobat (PDF) version of the article as part of the production process undertaken by the journal publisher. Download Figure 9 from the link here and try it for yourself or try the entire article from the journal, where more figures are so enhanced.

Example 2 takes this one stage further. The hyperlinks in the published figure in example 1 were embedded in software capable of resolving them, namely a PDF viewer. But that is all that this software allows. By relocating the hyperlink into a Web browser instead, one can add further functionality in the form of Javascripts perhaps better described as workflows (supported by browsers but not supported by Acrobat). There are three such workflows in example 2.

  • The first uses an image map to associate a region of the figure data object defined by a DOI.
  • The second interrogates the metadata specifically associated with the DOI (the same DOIs that are seen in the figure itself) to see if there is any so-called ORE metadata available (ORE= Object Re-use and Exchange). If there is, it uses this information to retrieve the data itself and pass it through to
  • the third workflow represented by a set of JavaScripts known as JSmol. These interpret the data received and construct an interactive visual 3D molecular model representing the retrieved data.

All this additional workflowed activity is implemented in a data repository. It is not impossible that it could also be implemented at the journal publisher end of things, but it is an action that would have to be supported by multiple publishers. Arguably this sort of enhancement is far better suited and more easily implemented by a specialised data publisher, i.e. a data repository.

Example 3 does the same thing for a table.

Example 4 enhances in a different manner. Conventionally NMR data is added to the supporting information file associated with a journal article, but such data is already heavily processed and interpreted. The raw instrumental data is never submitted to the journal and is pretty much always possibly only available by direct request from the original researchers (at least if the request is made whilst the original researchers are still contactable!). The data repository provides a new mechanism for making such raw instrumental (and indeed computational) data an integral part of the scientific process.

Example 5 shows how a bibliography can be linked to a secondary bibliography (citations 35 and 36 in this example in the narrative article) and perhaps in the future to Open Citations semantic searches for further cross references.

So by deconstructing the components of the standard scientific article, re-assembling some of them in a better-suited environment and then linking the two sets of components to each other, one can start to re-invent the genre and hopefully add more tools for researchers to use to benefit their basic research processes. The scope for innovation seems considerable. The issue of course is (a) whether publishers see this as a viable business model or whether they instead wish to protect their current model of the research article and whether (b) authors wish to undertake the learning curve and additional effort to go in this direction. As I have noted before, the current model is deficient in various ways; I do not think it can continue without significant reinvention for much longer. And I have to ask that if reinvention does emerge, will science be the prime beneficiary?

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

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Managing (open) NMR data: a working example using Mpublish.

Monday, August 1st, 2016

In March, I posted from the ACS meeting in San Diego on the topic of Research data: Managing spectroscopy-NMR, and noted a talk by MestreLab Research on how a tool called Mpublish in the forthcoming release of their NMR analysis software Mestrenova could help. With that release now out, the opportunity arose to test the system.

I will start by reminding that NMR data associated with a published article is (or should be) openly free: one should not need a subscription to the journal to access it (although one might in order to find it). Now, NMR data as it emerges from a spectrometer is highly sophisticated, comprising a collection of (sometimes) binary proprietary files containing the measured free induction decays (FID). Turning this raw data into an interpretable NMR spectrum, the visual form of the data that so appeals to human beings, is non trivial. This requires what may be highly sophisticated software and that in turn means that it may be a commercial product. Of course there are also examples of non-commercial open software packages that are best-of-breed; indeed in its early life-cycle MestreNova was known as MESTREC before becoming a commercial product. Could one achieve the benefits of both open and fully functional NMR data with no loss from the original instrument coupled with the ability to apply top-quality software for its analysis in an open manner? This is a demonstration of how Mpublish achieves this.

  1. Invoke the URL data.datacite.org/chemical/x-mnpub/10.14469/hpc/1087 from a browser
  2. This action queries the metadata deposited with DataCite for the doi 10.14469/hpc/1087 and retrieves the first instance of any file associated with that dataset that has the format type chemical/x-mnpub. You can directly view this metadata by invoking just data.datacite.org/10.14469/hpc/1087 where you can find both mnpub and mnova formats listed. A command such as data.datacite.org/chemical/x-mnpub/10.14469/hpc/1087 allows the file retrieval to be incorporated into automated workflows based just on the doi and the media type desired. Note my parenthetical comment above about finding data; here you only need its doi to retrieve it!
  3. The URL above downloads a small text file with the suffix .mnpub which contains in essence two components:

    • A URL pointing directly to an .mnova file at the repository for which the doi has been issued
    • A signature key derived used to verify that the public key of the publisher (the data repository in this instance) was counter-signed by Mestrelab.
  4. If you now download the application program and install it (but for the purpose of this demonstration, ignore any requests to try to license the program. Use it unlicensed) and open the .mnpub file using it, you should get the below.The application program has checked the signature key, and if valid, proceeds to download a full data file (a .mnova file in this case), and to analyze and display it within the program. The data is fully active; it can be manipulated and analysed. Notice in the picture below, the red arrow points to the state of the license, in this case not present.
    mn
  5. It is also possible to apply this procedure to the raw data as it emerges from the (Bruker) spectrometer, and compressed into a .zip archive. The MestreNova software will automatically process the contents by applying various default parameters, although the result may not correspond exactly to that present in e.g. the equivalent .mnova file (which may have had specific parameters applied).

It is my hope that anyone who records NMR data and processes it using software such as MestreNova will now consider using the mechanism above to accompany their submitted articles, rather than just automatically pasting a static image of the spectrum into a PDF file as "supporting information". This is part of what is meant by "managed research data" (RDM).

One cannot help but note that many types of scientific instrument nowadays come with bespoke software for analysing the data they produce. Very often this software is unavailable to anyone who has not purchased the instrument itself. To make the data available to others, the processed data and its visual interpretation often have to be reduced, with much consequent information loss, to a lowest common denominator format such as Acrobat/PDF. Here we see a mechanism for avoiding any such information loss whilst enabling, for that dataset only, the full potential for (re)analysing the data. It will be interesting to see if other examples of this model or its equivalent emerge in the near future.

 
 
 

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Data nightmares: B40 and counting its π-electrons

Saturday, July 19th, 2014

Whilst clusters of carbon atoms are well-known, my eye was caught by a recent article describing the detection of a cluster of boron atoms, B40 to be specific.[1] My interest was in how the σ and π-electrons were partitioned. In a C40, one can reliably predict that each carbon would contribute precisely one π-electron. But boron, being more electropositive, does not always play like that. Having one electron less per atom, one might imagine that a fullerene-like boron cluster would have no π-electrons. But the element has a propensity[2] to promote its σ-electrons into the π-manifold, leaving a σ-hole. So how many π-electrons does B40 have? These sorts of clusters are difficult to build using regular structure editors, and so coordinates are essential. The starting point for a set of coordinates with which to compute a wavefunction was the supporting information. Here is the relevant page: B401 The coordinates are certainly there (that is not always the case), but you have to know a few tricks to make them usable.

  1. Open Adobe Reader, select the coordinates and copy
  2. Paste into any application which recognises text. I used an old stalwart on the Mac, BBedit. It is reliable!
  3. But no, it produces a row of skull&crossbones characters (the authors of the program clearly have a sense of humour) B402
  4. Thinking that BBedit might have let me down (for the first time), I tried Word. A little less humour, but the same result. B403
  5. There are lots of web sites out there that claim to convert PDF files directly to Word files. Again, no luck, the coordinates are now entirely missing! B404
  6. Right, time for the big guns. Adobe Acrobat XI converts .PDF to .DOC, and (if you jump through a lot of hoops to register etc) they even give you a 30 day trial. Well, at least it gives numbers. But notice that the line breaks are missing, and all the numbers flow from one line to another.B405
  7. Another copy/paste from Word to BBedit, and now I have all the numbers, and adding 40 line breaks is all that is needed (there is sometimes some skill in knowing where to add them by the way).‡ The time taken from step 1 to step 7 was about 90 minutes (including a necessary cup of tea to recover from steps 1-5, and the realisation that the time was not wasted, since I could blog the experience!).

Well, I am sure you know what is coming next; my usual rant about how little most chemists truly value data and particularly its integrity and its semantics. And how little almost all journals understand data. Notice that the original article was published in Nature Chemistry. Note also a new journal from that stable, Scientific Data. The journal clearly thinks there is mileage in receiving scholarly articles about scientific data, and what they call data descriptors (they even got me to write a data descriptor a year or so back). Its a shame then that the same publisher allowed the decimation of the core data related to an article about B40.

They have a widely read blog, perhaps they can comment?

One more point to make about data: a phrase has recently been coined: deposition with recognition. Here, I show how my own data has been recognised:

There are various other ways as well, and perhaps I will leave this to another post. To return to the chemistry (where we should have been at the start). I ran the calculation (B3LYP+D3/TZVP) and published the newly enhanced data, citing it in the usual way.[3],[4]† To answer my question, for the D2d geometry, B40 has 24 π-electrons (there is some ambiguity, it could be 26). On average, the boron retains only ~0.65s, balanced by ~2.35p electrons. The most stable π-pair is shown below. At the centre of the ring is a strongly diatropic ring current (NICS = -42 ppm)[5] suggesting aromaticity (26 electrons = 4n+2).

B40-29

I conclude by pondering whether the properties of any such boron cluster may in time prove to be directly related to the number of σ-to-π promotions.

‡ Sadly, line breaks in lists of atom coordinates date back to an era of about 50 years ago when text files were first treated differently from binary files. Three different “standards” emerged for specifying a line break (DOS, Mac and Unix) in a text file and much confusion has there been ever since when moving these text files across operating systems. The modern way of doing it is to make line breaks redundant by instead marking up the file. The standard chemical markup, invented in 1996, and formally published in 1999[6], is CML. You will find such CML coordinates in the deposited data from this calculation.[3] You will not have any problems with line breaks!

†Publication assigns a DataCite DOI. This takes about 48 hours to propagate to CrossRef, which is here used by the KCite WordPress plugin to retrieve the metadata and compose a citation. If KCite queries CrossRef before the metadata has propagated, it does not generate a citation. If you are reading this and see no citation, please revisit after 48 hours have elapsed.

The diatropicity is inverted to paratropicity (NICS = +28 ppm) when two electrons are removed to create the dication.[7] This inversion is normally a good test of aromaticity/antiaromaticity.

References

  1. H. Zhai, Y. Zhao, W. Li, Q. Chen, H. Bai, H. Hu, Z.A. Piazza, W. Tian, H. Lu, Y. Wu, Y. Mu, G. Wei, Z. Liu, J. Li, S. Li, and L. Wang, "Observation of an all-boron fullerene", Nature Chemistry, vol. 6, pp. 727-731, 2014. https://doi.org/10.1038/nchem.1999
  2. H.S. Rzepa, "The distortivity of π-electrons in conjugated boron rings", Physical Chemistry Chemical Physics, vol. 11, pp. 10042, 2009. https://doi.org/10.1039/b911817a
  3. H.S. Rzepa, "Gaussian Job Archive for B40", 2014. https://doi.org/10.6084/m9.figshare.1111454
  4. H.S. Rzepa, "B 40", 2014. https://doi.org/10.14469/ch/24884
  5. H.S. Rzepa, "Gaussian Job Archive for B40", 2014. https://doi.org/10.6084/m9.figshare.1111518
  6. P. Murray-Rust, and H.S. Rzepa, "Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles", Journal of Chemical Information and Computer Sciences, vol. 39, pp. 928-942, 1999. https://doi.org/10.1021/ci990052b
  7. H.S. Rzepa, "Gaussian Job Archive for B40(2+)", 2014. https://doi.org/10.6084/m9.figshare.1111534

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Science publishers (and authors) please take note.

Monday, October 24th, 2011

I have for perhaps the last 25 years been urging publishers to recognise how science publishing could and should change. My latest thoughts are published in an article entitled “The past, present and future of Scientific discourse” (DOI: 10.1186/1758-2946-3-46). Here I take two articles, one published 58 years ago and one published last year, and attempt to reinvent some aspects. You can see the result for yourself (since this journal is laudably open access, and you will not need a subscription). The article is part of a special issue, arising from a one day symposium held in January 2011 entitled “Visions of a Semantic Molecular Future” in celebration of Peter Murray-Rust’s contributions over that period (go read all 15 articles on that theme in fact!).

Here I want to note just two features, which I have also striven to incorporate into many of the posts this blog (which in one small regard I have attempted to formulate as an experimental test-bed for publishing innovations). Scalable-Vector-Graphics (SVG) emerged around the turn of the millennium as a sort of HTML for images. To my knowledge, no science publisher has yet made it an intrinsic part of their publishing process (although gratifyingly all modern browsers support at least a sub-set of the format). Until now (perhaps). Thus 10.1186/1758-2946-3-46 contains diagrams in SVG, but you will need to avoid the Acrobat version, and go straight to the HTML version to see them. However, what sparked my noting all of this here was the recent announcement by Amazon that they are adopting a new format for their e-books, which they call Kindle Format 8 or KF8 (the successor to their Mobi7 format). To quote: “Technical and engineering books are created more efficiently with Cascading Style Sheet 3 formatting, nested tables, boxed elements and Scalable Vector Graphics“. This is wrapped in HTML5 to be able to provide (inter alia) a rich interactive experience for the reader. In fairness, there is also the more open epub3 which strives for the same. Other features of HTML5 include embedded chemistry using WebGL and the same mechanisms are being used for the construction of modern chemical structure drawing packages.

It remains to be seen how much of all of this will be adopted by mainstream chemistry publishers. Here, we do get into something of a cyclic argument. I suspect the publishers will argue that few of the authors that contribute to their journals will send them copy in any of these new formats and that it would be too expensive for them to re-engineer these articles with little or no help from such authors. The chemistry researchers who do the writing (perhaps composition might be a better word?) might argue there is little point in adopting innovative formats if the publishers do not accept them (I will point out that my injection of SVG into the above article did have some teething problems). For example, you will not find SVG noted in any of the “instructions for authors” in most “high impact journals” (or, come to that, HTML5).

If one looks at the 25 year old period, in 1986 all chemistry journals were distributed exclusively on paper. My office shelves still show the scars of bearing the weight of all that paper. Move on 25 years, and all journals almost without exception are now distributed electronically. I suspect the outcome in many a reader’s hands is simply that they (rather than the publisher) now bear the printing costs themselves (despite or perhaps because of the introduction of electronic binders such as Mendeley). But it will only be when the article itself grows out of its printable constraints, and hops onto mobile devices such as Kindles and iPads in the promised (scientifically) interactive and data-rich form, that the true revolution will start taking place.

A final observation: you will not readily obtain the interactive features of 10.1186/1758-2946-3-46 on e.g. an iPad or Kindle because the Java-based Jmol is not supported on either. But Jmol has now been ported to Android, and its certainly one to watch.

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(Hyper)activating the chemistry journal.

Monday, September 7th, 2009

The science journal is generally acknowledged as first appearing around 1665 with the Philosophical Transactions of the Royal Society in London and (simultaneously) the French Academy of Sciences in Paris. By the turn of the millennium, around 10,000 science and medical journals were estimated to exist. By then, the Web had been around for a decade, and most journals had responded to this new medium by re-inventing themselves for it. For most part, they adopted a format which emulated paper (Acrobat), with a few embellishments (such as making the text fully searchable) and then used the Web to deliver this new reformulation of the journal. Otherwise, Robert Hooke would have easily recognized the medium he helped found in the 17th century.

In 1994, a small group of us thought that one could, and indeed should go further than emulated paper. We argued [1] that journals should be activated by delivering not merely the logic of a scientific argument, but also the data on which it might have been based. Of course, we encountered the usual problem; doing this might cost publishers more in production resources, and in the absence of a market prepared to pay the extra, the business model did not make sense (to the publishers). Well, 15 years later, and most publishers are indeed now thinking about how their journals can be enhanced. A number of interesting projects (the RSC’s Project Prospect is one which strives to bring science alive) have emerged. Another is the topic of this blog; the activation of the journal with molecular coordinates and data using the Jmol applet.

Initially (~2005), this project met with resistance from publishers, and the issue really amounted to what the definitive version of a scientific article should be. Should that definitive version be printable? That model, after all had served the community well for more than 300 years! And journals from the very beginning are still as readable now as when first published. In other words, print lasts! But print is pretty limiting after all. For a start, it is limited to 2D static representations. Molecules, by and large, do their magic in a dynamic three dimensions (4D in an Einsteinian sense). But print is also expensive; not merely to produce, but to transport paper around the world.

From the turn of the millennium, a number of publishers, amongst them the American Chemical Society, started to evolve the scientific article such that the pre-eminent version would now be considered to be the HTML form (perhaps as a prelude to phasing out print entirely? See an interesting commentary by a journal editor) and perhaps a digital Acrobat form which would be deemed to loose some of its functionality once printed (again see here for how Acrobat can be used to enhance things). Again however, a chicken-and-egg scenario resulted. To enhance the articles with extra functionality (such as data), they would need to find authors prepared to put the extra work into preparing the material. In fact, most authors already do that, but they call it supporting information. This is often highly data rich, covering materials such as spectra, coordinates and other information nowadays provided to researchers for analysis. Unfortunately, what has been missing is the education of authors to provide this information in a proper digital form which can be easily re-used by others, and on a Web page, converted automatically to nice interactive models. Most spectra which form part of the supporting information are in fact still scanned versions of printed spectra!

Enter computational chemists. Nowadays, they live in a world that truly does not need printing! Almost all of their data is already suitably digital. So perhaps it is no surprise to find that when enhanced journal articles started appearing around 2005, many were produced by this group of chemists. By now perhaps you are wondering what such an article might look like. Well, the remainder of this blog will be devoted to listing some examples. You will also notice that they come exclusively from our own publications. Perhaps someone will find the time to collect a far more representative set to better illustrate the diversity of this form, and how it is evolving. Meanwhile, you might wish to take a look at the following.

Part 1: The early days: 1994 onwards

These examples all relied on a browser plugin called Chime, which is no longer with us! Hence the pages designed to invoke it no longer display properly. But the data associated with the articles is still there!

  1. An early 1994 example of (hyper)activating a journal article can be seen here as the preliminary communication and
  2. in 1995 here as the final full article. I am told that this was the article that actually inspired the developers of Chime to enhance (Netscape) with a chemical plugin.
  3. This one from 1998 illustrates how articles can decay in functionality when Chime is no longer available.
  4. An ab initio and MNDO-d SCF-MO Computational Study of Stereoelectronic Control in Extrusion Reactions of R2I-F Iodine (III) Intermediates, M. A. Carroll, S. Martin-Santamaria, V. W. Pike, H. S. Rzepa and D. A. Widdowson, Perkin Trans. 2, 1999, 2707-2714 with the supporting information here.
  5. Huckel and Mobius Aromaticity and Trimerous transition state behaviour in the Pericyclic Reactions of [10], [14], [16] and [18] Annulenes. Sonsoles Martên-Santamarêa, Balasundaram Lavan and H. S. Rzepa, J. Chem. Soc., Perkin Trans 2, 2000, 1415. with the supporting information here.
  6. Peter Murray-Rust, H. S. Rzepa and Michael Wright, “Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content”, New J. Chem., 2001, 618-634. DOI: 10.1039/b008780g. This article broke new ground in that the supporting information was something of a misnomer. It was expressed entirely in XML, including all the chemistry data, and used XSLT transforms on the fly to regenerate the article. In that sense, it was actually a superset of the published article. It would be fair to say that this article was rather ahead of its time (although it does seem appropriate to publish it in a new journal!).
  7. M. Jakt, L. Johannissen, H. S. Rzepa, D. A. Widdowson and R. Wilhelm, “A Computational Study of the Mechanism of Palladium Insertion into Alkynyl and Aryl Carbon-Fluorine bonds”, Perkin Trans. 2, 2002, 576-581 and supporting information.
  8. P. Murray-Rust and H. S. Rzepa, chapter in “Handbook of Chemoinformatics. Part 2. Advanced Topics.”, ed. J. Gasteiger and T. Engel, 2003, Vol 1, was not enhanced per se, but did lay out the principles of how it might/should be done.
  9. K. P. Tellmann, M. J. Humphries, H. S. Rzepa and V. C. Gibson, “An experimental and computational study of β-H transfer between organocobalt complexes and 1-alkenes”, Organometallics, 2004, 23, 5503-5513. DOI: 10.1021/om049581h and supporting information.

Part 2: 2005.

These four examples all now invoke Jmol, which downloads upon request and hence does not rely on the presence of any browser plugin. The four articles were submited with supporting information in the form of HTML. These were associated with the main article, but were not formal part of that article. In that sense, they represent an incarnation of the traditional model, with all the data firmly resident in the supporting information.

  1. Gibson, Vernon C.; Marshall, Edward L.; Rzepa, H. S. ” A computational study on the ring-opening polymerization of lactide initiated by β-diketiminate metal alkoxides: The origin of heterotactic stereocontrol”, J. Am. Chem. Soc., 2005, 127, 6048-6051. DOI: 10.1021/ja043819b and supporting information.
  2. H. S. Rzepa, Mobius aromaticity and delocalization”, Chem. Rev., 2005, 105, 3697 – 3715. DOI: 10.1021/cr030092l and supporting information.
  3. H. S. Rzepa, “Double-twist Mšbius Aromaticity in a 4n+2 Electron Electrocyclic Reaction”, 2005, Chem Comm, 5220-5222. DOI: 10.1039/b510508k The supporting information is also available directly.
  4. H. S. Rzepa, “A Double-twist Mobius-aromatic conformation of [14]annulene”, Org. Lett., 2005, 7, 637 – 4639. DOI: 10.1021/ol0518333 and supporting information.

Part 3: 2006 onwards

The supporting information has now been assimilated into the main body of the article proper, and within these confines contribute components such as enhanced figures or tables (i.e. enhanced with data)

  1. A. P. Dove, V. C. Gibson, E. L. Marshall, H. S. Rzepa, A. J. P. White and D. J. Williams, “Synthetic, Structural, Mechanistic and Computational Studies on Single-Site β-Diketiminate Tin(II) Initiators for the Polymerization of rac-Lactide”, J. Am. Chem. Soc., 2006,128, 9834-9843. DOI: 10.1021/ja061400a The enhancement can be seen in Figure 11.
  2. O. Casher and H. S. Rzepa, “SemanticEye: A Semantic Web Application to Rationalise and Enhance Chemical Electronic Publishing”, J. Chem. Inf. Mod., 2006, 46, 2396-2411. DOI: 10.1021/ci060139e
  3. H S. Rzepa and M. E. Cass, “A Computational Study of the Nondissociative Mechanisms that Interchange Apical and Equatorial Atoms in Square Pyramidal Molecules”, Inorg. Chem., 2006, 45, 3958–3963. DOI 10.1021/ic0519988. Interactive table at 10.1021/ic0519988/ic0519988.html
  4. M. E. Cass and H. S. Rzepa, “In Search of The Bailar Twist and Ray-Dutt mechanisms that racemize chiral tris-chelates: A computational study of Sc(III), V(III), Co(III), Zn(II) and Ga(III) complexes of a ligand analog of acetylacetonate”, Inorg. Chem., 2007, 49, 8024-8031. DOI: 10.1021/ic062473y The enhancement can be seen in Figure 2
  5. H. S. Rzepa, “Lemniscular Hexaphyrins as examples of aromatic and antiaromatic Double-Twist Möbius Molecules”, Org. Lett., 2008, 10, 949-952.DOI:10.1021/ol703129z The enhancement can be seen in Web Table 1.
  6. D. C. Braddock and H. S. Rzepa, “Structural Reassignment of Obtusallenes V, VI and VII by GIAO-based Density functional prediction”, J. Nat. Prod., 2008, DOI: 10.1021/np0705918 and WEO1.
  7. S. M. Rappaport and H S. Rzepa, “Intrinsically Chiral Aromaticity. Rules Incorporating Linking Number, Twist, and Writhe for Higher-Twist Möbius Annulenes”, J. Am. Chem. Soc., 2008, 130,, 7613-7619. DOI: 10.1021/ja710438j and WEO1 to 4
  8. C. S. M. Allan and H. S. Rzepa, “AIM and ELF Critical point and NICS Magnetic analyses of Möbius-type Aromaticity and Homoaromaticity in Lemniscular Annulenes and Hexaphyrins”, J. Org. Chem., 2008, 73, 6615-6622. DOI: 10.1021/jo801022b and WEO1
  9. C. S. M. Allan and H. S. Rzepa, “Chiral aromaticities. Möbius Homoaromaticity”, J. Chem. Theory. Comp., 2008, 4, 1841-1848. DOI: 10.1021/ct8001915 and WEO1
  10. C. S. M Allan and H. S. Rzepa, “The structure of Polythiocyanogen: A Computational investigation”, Dalton Trans., 2008, 6925 – 6932. DOI: 10.1039/b810147g and enhanced Table
  11. H. S. Rzepa, “Wormholes in Chemical Space connecting Torus Knot and Torus Link π-electron density topologies”, Phys. Chem. Chem. Phys., 2009, 1340-1345. DOI: 10.1039/b810301a and enhanced Table.
  12. H. S. Rzepa, “The Chiro-optical properties of a Lemniscular Octaphyrin”, Org. Lett., 2009, 11, 3088-3091. DOI: 10.1021/ol901172g
  13. C. S. Wannere, H. S. Rzepa, B. C. Rinderspacher, A. Paul, H. F. Schaefer III, P. v. R. Schleyer and C. S. M. Allan, “The geometry and electronic topology of higher-order Möbius charged Annulenes”, J. Phys. Chem., 2009, DOI: 10.1021/jp902176a and enhanced table
  14. H. S. Rzepa, “The distortivity of π-electrons in conjugated Boron rings.”, Phys. Chem. Chem. Phys., 2009, DOI: 10.1039/B911817A and enhanced table.
  15. H. S. Rzepa, “The importance of being bonded”, Nature Chem., 2009, DOI: 10.1038/nchem.373 and the exploratorium.
  16. King Kuok Hii, J.L.Arbour, H.S.Rzepa, A.J.P.White, “Unusual Regiodivergence in Metal-Catalysed Intramolecular Cyclisation of γ-Allenols”, Chem. Commun, 2009, DOI: 10.1039/b913295c and enhanced table.
  17. L. F. V. Pinto, P. M. C. Glória, M. J. S. Gomes, H. S. Rzepa, S. Prabhakar, A. M. Lobo. “A Dramatic Effect of Double Bond Configuration in N-Oxy-3-aza Cope Rearrangements – A simple synthesis of functionalised allenes”, Tet. Lett., 2009, 50, 3446-3449. DOI: 10.1016/j.tetlet.2009.02.228 and interactive table.
  18. H. S. Rzepa and C. S. M. Allan, “Racemization of isobornyl chloride via carbocations: a non-classical look at a classic mechanism”, J. Chem. Educ., 2010, DOI: 10.1021/ed800058c and interactive table.
  19. K. Abersfelder, A. J. P. White, H. S. Rzepa, and D. Scheschkewitz “A Tricyclic Aromatic Isomer of Hexasilabenzene”, Science, 2010, DOI: 10.1126/science.1181771 and interactive table.
  20. A. C. Spivey, L. Laraia, A. R. Bayly, H. S. Rzepa and A. J. P. White “Stereoselective Synthesis of cis- and trans-2,3-Disubstituted Tetrahydrofurans via Oxonium−Prins Cyclization: Access to the Cordigol Ring System”, Org. Lett., 2010, DOI 10.1021/ol9024259 and interactive table.
  21. J. Kong, P. v. R. Schleyer and H. S. Rzepa, “Successful Computational Modeling of Iso-bornyl Chloride Ion-Pair Mechanisms”, J. Org. Chem., 2010, DOI: 10.1021/jo100920e and interactive table.
  22. A. Smith, H. S. Rzepa, A. White, D. Billen, K. K. Hii, “Delineating Origins of Stereocontrol in Asymmetric Pd-Catalyzed α-Hydroxylation of 1,3-Ketoesters”, J. Org. Chem., 2010, 75, 3085-3096. DOI: 10.1021/jo1002906 and interactive table.
  23. H. S. Rzepa “The rational design of helium bonds”, Nature Chem., 2010, 2, 390-393. DOI: 10.1038/NCHEM.596 and web enhanced table.
  24. P. Rivera-Fuentes, J. Lorenzo Alonso-Gómez, A. G. Petrovic, P. Seiler, F. Santoro, N. Harada, N. Berova, H. S. Rzepa, and F. Diederich, “Enantiomerically Pure Alleno–Acetylenic Macrocycles: Synthesis, Solid-State Structures, Chiroptical Properties, and Electron Localization Function Analysis”, Chem. Eur. J., 2010, DOI: 10.1002/chem.201001087 and interactive figure
  25. H. S. Rzepa, “The Nature of the Carbon-Sulfur bond in the species H-CS-OH”, J. Chem. Theory. Comput., 2010, 49, DOI: 10.1021/ct100470g and interactive table.
  26. H. S. Rzepa, “Can 1,3-dimethylcyclobutadiene and carbon dioxide co-exist inside a supramolecular cavity?”, Chem. Commun., 2010, DOI: 10.1039/C0CC04023A and interactive table
  27. M. R. Crittall, H. S. Rzepa, and D. R. Carbery, “Design, Synthesis, and Evaluation of a Helicenoidal DMAP Lewis Base Catalyst”, Org. Lett., 2011, DOI: 10.1021/ol2001705 and interactive table
  28. H. S. Rzepa, “The past, present and future of Scientific discourse”, J. Cheminformatics, 2011, 3, 46. DOI: 10.1186/1758-2946-3-46 and interactive figure 3, figure 4 and figure 5.
  29. H. S. Rzepa, “A computational evaluation of the evidence for the synthesis of 1,3-dimethylcyclobutadiene in the solid state and aqueous solution”, Chem. Euro. J., 2012, in press.
  30. J. L. Arbour, H. S. Rzepa, L. A. Adrio, E. M. Barreiro, P. G. Pringle and K. K. (Mimi) Hii, “Silver-catalysed enantioselective additions of O-H and N-H to C=C bonds: Non-covalent interactions in stereoselective processes”, Chem. Euro. J., 2012, in press, Web table 1 and Web table 2.
  31. H. S. Rzepa, “Chemical datuments as scientific enablers”, J. Chemoinformatics, submitted.
  32. A. P. Buchard, F. Jutz, F. M. R. Kember, H. S. Rzepa, C. K. Williams, C.K., “Experimental and Computational Investigation of the Mechanism of Carbon Dioxide/Cyclohexene Oxide Copolymerization Using A Dizinc Catalyst”, in press. Interactivity box
  33. D. C. Braddock, D. Roy, D. Lenoir, E. Moore, H. S. Rzepa, J. I-Chia Wu and P. von R. Schleyer, “Verification of Stereospecific Dyotropic Racemisation of Enantiopure d and l-1,2-Dibromo-1,2-diphenylethane in Non-polar Media”, Chem. Comm., 2012, just published. DOI: 10.1039/C2CC33676F and interactivity box.
  34. K. Leszczyńska, K. Abersfelder, M. Majumdar, B. Neumann, H.-G. Stammler, H. S. Rzepa, P. Jutzi and D. Scheschkewitz, “The Cp*Si+ Cation as a Stoichiometric Source of Silicon, Chem. Comm., 2012, 48, 7820-7822. DOI: 10.1039/c2cc33911k. Cites links to 10042/to-13974, 10042/to-13982, 10042/to-13969, 10042/20028, 10042/to-13973, 10042/to-13985
  35. H. S. Rzepa, “A computational evaluation of the evidence for the synthesis of 1,3-dimethylcyclobutadiene in the solid state and aqueous solution”, Chem. Euro. J., 2013, 4932-4937. DOI: 10.1002/chem.201102942 and WebTable
  36. H. S. Rzepa, “Chemical datuments as scientific enablers”, J. Chemoinformatics, 2013, 4, DOI: 10.1186/1758-2946-5-6. The interactivity box is integrated into the body of the article.
  37. M. J. Cowley, V. Huch, H. S. Rzepa, D. Scheschkewitz, “A Silicon Version of the Vinylcarbene – Cyclopropene Equilibrium: Isolation of a Base-Stabilized Disilenyl Silylene”, 2013, Nature Chem., in press and Webtable.
  38. M. J. S. Gomes, L. F. V. Pinto, H. S. Rzepa, S. Prabhakar, A. M. Lobo, “N-Heteroatom Substitution Effects in 3-Aza-Cope Rearrangements”, Chemistry Central, 2013, 7:94. doi:10.1186/1752-153X-7-94 and Table.
  39. H. S. Rzepa and C. Wentrup, “Mechanistic Diversity in Thermal Fragmentation Reactions: a Computational Exploration of CO and CO2 Extrusions from Five-Membered Rings”, J. Org. Chem., DOI: 10.1021/jo401146k and Table.
  40. D. C. Braddock, J. Clarke and H. S. Rzepa “Epoxidation of Bromoallenes Connects Red Algae Metabolites by an Intersecting Bromoallene Oxide – Favorskii Manifold”, Chem. Comm., 2013, DOI: 10.1039/C3CC46720A and Table.
  41. M. J. Fuchter, Ya-Pei Lo and H. S. Rzepa, “Mechanistic and chiroptical studies on the desulfurization of epidithiodioxopiperazines reveal universal retention of configuration at the bridgehead carbon atoms”, J. Org. Chem., 2013, in press. doi: 10.1021/jo401316a and table.

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

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Posted in Chemical IT, Interesting chemistry | 6 Comments »

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. 
blog11
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.

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