Posts Tagged ‘King’

Wild flowers in West London.

Monday, July 24th, 2017

Bees are having a tough time around the world. Oddly, they are surviving very well in cities. One reason are the wild flower meadows in London and for some summer relief I thought I would tell you the story of the one shown below.

We live in west London, in an area that was farmland as recently as the 1930s and used to produce vegetables and milk for the population of London. When the London underground (the “tube”) was extended into this rural west, housing sprung up around the central and metropolitan lines (Metroland). In our case, the large meadows adjacent to the new housing were left undeveloped due to their propensity to become waterlogged and flooded from the nearby river Brent. Flood prevention schemes have now made such flooding largely a thing of the past and part of the meadows have been turned into a golf course. But the area that you see above is largely left to nature and in the normal course of events the grasses grow copiously and cause the local population to suffer mightily from hay fever between June-August.

Not this year, when a tractor from the local council (Ealing) turned up in March and ploughed the grassy area up! For two months it lay fallow because there was almost no rain in May or June, but after several decent showers the area started to bloom and we all realized that the tractor must also have sown wild flower seeds. Its been a riot of colour for more than a month now and looks likely to continue for a little while yet. The bees love it (it’s not been such a good year for butterflies however). So do the human residents; you can see our house in the background! On a number of occasions now, contemplating the start of a new day, I have wandered out into the meadow, frankly with all thoughts of writing a blog abandoned. Except this one, since I did feel like sharing our pleasure. I cannot share the scent of the flowers however, which is also pretty heady. I should perhaps also mention that rather to the left of the photo above is the river Brent and along its route grows wild mustard in spring and many a bramble bearing luscious fruits in July. Foraging for these is another delight! 

Update on  4th August, 2017. Perivale Park, UB6 9BG

Update on  20th August, 2017. Perivale Park, UB6 9BG

Update on  6th September, 2017. Perivale Park, UB6 9BG

Update on  17th August, 2017. Cayton Green Park. UB6 8BJ.

Update on  11th August, 2017. King George’s Playing Fields, UB1 2QA

Update on  11th August, 2017. Jubilee Park, UB1 2TJ

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What is the future of books?

Friday, April 29th, 2011

At a recent conference, I talked about what books might look like in the near future, with the focus on mobile devices such as the iPad. I ended by asserting that it is a very exciting time to be an aspiring book author, with one’s hands on (what matters), the content. Ways of expressing that content are currently undergoing an explosion of new metaphors, and we might even expect some of them to succeed! But content is king, as they say.

Here I list only some innovative solutions which have emerged in the last year or so, but which also raise important issues which we ignore at our peril.

  1. TouchPress were one of the first publishers to get off the mark with their living books. Their first offering was The Elements, deriving from an earlier interactive display of the periodic table (an example of which can be seen in the entrance to the chemistry building at Imperial College). It is a programmed book, in the sense that the content is expressed using code written by the publisher (very much in the manner of interactive games).
  2. Next to appear were Inkling, who describe their offering as interactive. Their approach is described in a blog written by their founder, Matt Macinnis. There he talks about The Art of Content Engineering, which again makes it sound as if authoring a book is in effect programming it! (I know what he means; if you follow the link to the talk I allude to above, you may spot that it too is, at least in part, programmed, and not simply written). Inkling also promote the book as part of a social network, with readers able to annotate the content, and share that annotation with others.
  3. The latest company to change the way books are both read and authored is Pushpoppress, the heart of which is also an interactive app.
  4. Then there is the epub3 format. This is a free and open standard for e-books. This third revision in particular is meant to enhance interactivity.

Something of a common theme so far. Books are going to be interactive! But what about these issues?

  1. Each of the first three (commercial) publishers above has adopted their own programming format. Although HTML5 may be at the heart of some of this, programming may also mean control (in the sense that the creative industries must put control of their content at the heart of what they do). Each of the first three above sound like a closed system, and extracting re-usable content is, I argue, an essential part of doing science. I am just a tad worried that the approaches exemplified above may not allow this to happen.
  2. Suppose you manage to acquire a chemistry textbook in any of the four approaches listed above. Will they inter-operate, in the sense of being able to extract data from one and perhaps inject it into another? Or will each be a data- or information silo, rigidly controlled by the creative content generator (whoever that is)?
  3. What might an aspiring author, intent on creating interactive content do? Should they go closed/proprietary or open? They will clearly need to retrain themselves. We have indeed come a long way along the road: hand-written manuscript → typed manuscript → word-processed manuscript → interactive app! Like computer games, is the day of the single-authored book rapidly fading, to be replaced by a large team, each with their own tasks to perform?

I end with this question. Is the era of books, just like the Web itself, going to be the app? And who will be able to (find the time) to participate?

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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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