Chemistry rich diagrams: do crystal structures carry spin information? Iron-di-imine complexes.

June 18th, 2017

The iron complex shown below forms the basis for many catalysts.[1] With iron, the catalytic behaviour very much depends on the spin-state of the molecule, which for the below can be either high (hextet) or medium (quartet) spin, with a possibility also of a low spin (doublet) state. Here I explore whether structural information in crystal structures can reflect such spin states.

We studied this a few years back and the talk I gave on the topic included some of our first statistical explorations of the CSD (Cambridge structure database). Here I update those searches, using the search query (DOI: 10.14469/hpc/2675) shown below. The di-imine ligand contains only 3-coordinate atoms, whilst the iron is 5-coordinate. The angles subtended at the Fe and group X=NM (any non-metal atom) are as defined below.

The resulting scatterplot is shown below and contains a rich variety of phenomena.

  1. In the bond length region of 1.85-1.95Å one sees three clusters, one arranged on the diagonal indicating both N-Fe lengths are the same and two off the diagonal which indicates one length is ~0.1Å longer than the other.
    • To explain this, one needs to know that 5-coordinate Fe has a trigonal bipyramidal shape in which one X=NM group subtends an (anti-periplanar)  angle of ~180° at Fe with one of the ring nitrogens and the other two X=NM groups each subtend an angle of <120° with the other ring nitrogen. The result is that if the group X has the appropriate (electron withdrawing) properties, the two N-Fe bond lengths are no longer equal. If group X is more passive, the two N-Fe bond lengths may remain more equal.
  2. A second cluster occurs at ~2.00-2.1Å, mostly along the diagonal but with hints of smaller off-diagonal clusters.
  3. A third feature occurs at ~2.1-2.3Å, where now the off-diagonal clusters contain more examples than are on the diagonal itself.

Clearly, there is more going on here than can be explained simply by the orientation of X=NM with respect to the Fe-N bond axis. That something is the spin-multiplicity of the molecule. With the Fe complex shown above, this can be one of doublet (one unpaired electron), quartet (three unpaired electrons) or hextet (five unpaired electrons). To gain insight into how this affects the bond lengths, some calculations are needed, using X=Cl, R=H. Here they are done at the TPSSH/Def2-TZVPP level. In fact it is well-known[2] that the energy separations of low/medium/high spin Fe complexes are highly sensitive to the functional, but TPSSH seems to be amongst the best.‡ This shows that the energy ordering of the three states using this particular method is hextet (0.0, DOI: 10.14469/hpc/2676) < quartet (10.5, DOI: 10.14469/hpc/2677) < doublet (13.2 kcal/mol, DOI: 10.14469/hpc/2678), with the bond lengths shown below (for X=Cl).

We might make tentative hypotheses based on these values:

  1. The off-diagonal bottom left clusters (1 in list above) might arise from doublet states.
  2. The off-diagonal top right clusters (3 in list above) might arise from sextet states.
  3. The cluster (2 in list above) might be quartet states for which X is not sufficiently electronegative to induce bond length discriminations.
  4. It is worth noting that the energy span between the three states for the above molecule is only ~13 kcal/mol, which is small enough to be altered by substituents.

Testing these hypotheses requires knowledge of the spin state of all the entries in any cluster. This information is unfortunately not carried by the CSD, which has relatively little information over and above structural data. Each entry would have to be individually inspected. Indeed the spin state of many of these complexes may not even be known. Nevertheless, it would be great to repeat the graphs shown above as a function of known spin state so that the (again I repeat tentative) hypotheses might be confirmed or refuted.

‡This article evaluates a whole host of functionals against e.g. the spin-state energy separations of the Fe2+ ion. As it happens, TPSSH was not one that was evaluated, but in fact it gives more or less the best match to experiment. Thus Esinglet-Equintet obs = 85.6 kcal/mol, calc 92.4; Etriplet-Equintet obs 56.1, calc 59.5 kcal/mol. A hypothesis therefore is that the TPSSH functional is a reasonable one to go exploring such high-spin species.

References

  1. M.P. Shaver, L.E.N. Allan, H.S. Rzepa, and V.C. Gibson, "Correlation of Metal Spin State with Catalytic Reactivity: Polymerizations Mediated by α‐Diimine–Iron Complexes", Angewandte Chemie International Edition, vol. 45, pp. 1241-1244, 2006. https://doi.org/10.1002/anie.200502985
  2. P. Verma, Z. Varga, J.E.M.N. Klein, C.J. Cramer, L. Que, and D.G. Truhlar, "Assessment of electronic structure methods for the determination of the ground spin states of Fe(<scp>ii</scp>), Fe(<scp>iii</scp>) and Fe(<scp>iv</scp>) complexes", Physical Chemistry Chemical Physics, vol. 19, pp. 13049-13069, 2017. https://doi.org/10.1039/c7cp01263b

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

June 10th, 2017

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.

The collection is at DOI: 10.14469/hpc/2657. Here I track down how some of them are doing 20+ years on.

  1. Formula-To-Mass-To-Formula (f2m2f), which was started in August 1996 and was written by Guillaume Cottenceau, a french undergraduate student visiting London and who wanted to learn to program. I suggested he try Java, and as I recollect sent him out to the business park west of London where Sun Microsystems had an office to learn how to do so (they had only released the development kit a few months earlier!). The applet he wrote still works (being unsigned, you have to jump through a few hoops to allow it to run (but be quick, not many browsers will still let you do so!). The applet also has a benchmark feature. Running the heavy bench now takes ~ 0.4s on a laptop.  I cannot be sure,  but I seem to remember that this one took ~20 seconds back in 1997. 
  2. Guillaume then returned to Paris to finish the above off, but also managed to find the time a year later to produce Jspec, a visualiser for NMR and MS. Darek Bogdal was visiting from Poland in August 1997(8?) and he incorporated these tools into a general spectral display and problem solving resource, which also still mostly works (with no curation!). The bit that does not work depended on the Chime plugin, now long gone and of course replaced in large measure by Jmol and now JSmol. 
  3. Here is an equation setter. The original site has long gone, but I had copied the classes over and it also (mostly) works!
  4. This dates from 1997 by Wyn Locke and Alan Tongue and uses JavaScript plus the spectral viewer to communicate with Chime. All done much better by many others since of course.

That said, many of the other links at DOI: 10.14469/hpc/2657 no longer work. In truth I am slightly surprised a few still do! 

Quite possibly these screen shots may be the only visual images that can be created in the very near future, as all but very specialised web browsers drop “plug-in” (aka Java) support. So perhaps it will be RIP Java, at least for the in-browser frame mode (but certainly not for the stand-alone application mode).

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Posted in Historical | 5 Comments »

How to search data repositories for FAIR chemical content and data: SubjectScheme

June 8th, 2017

As data repositories start to flourish, it is reasonable to ask questions such as what sort of chemistry can be found there and how can I find it? Here I give an updated[1] worked example of a digital repository search for chemical content and also pose an important issue for the chemistry domain.

Firstly, I should say this search is restricted just to those data repositories that submit indexing terms (metadata) to DataCite, which is the agency that will be used to conduct the searches. Each type of metadata is defined by a prefix or operator field (much in the same way that an advanced Google search can be prefixed with an operator, e.g. author:♥). I will use just two such DataCite field prefixes† here as exemplars (there are many more).

  1. media: This specifies the media type for the data being searched. For restriction to chemistry one takes advantage of the chemical/x- media type, as described previously.[2]
  2. SubjectScheme: This is a new declaration, as specified in the DataCite V4 metadata schema.[3] The subject scheme in effect declares a subject-specific term, and is designed to be used by domains such as chemistry.

This latter is best illustrated by one specific example of a search which I will dissect here:
https://search.datacite.org/works?query=media:chemical\/x\-gaussian*+SubjectScheme:inchikey+subject:XZYDALXOGPZGNV-UHFFFAOYSA-M+media:chemical\/x\-mnpub*‡

  1. https://search.datacite.org/works?query= queries the DataCite MDS† (metadata store).
  2. media:chemical\/x\-gaussian* defines a media type which contains the string chemical/x-gaussian, with the * being a wild-card which allows any characters to follow this string. This now is specifying any data repository where Gaussian files have been deposited and assigned this media type.
  3. + represents a Boolean AND operator.
  4. SubjectScheme:inchikey restricts a subject search to a subjectScheme having the value inchikey, whilst
  5. subject:XZYDALXOGPZGNV-UHFFFAOYSA-M defines the value of the subject itself.
  6. media:chemical/x-mnpub completes the search definition, this relating to the mandatory additional presence of an Mpublish[4] file indicating (spectroscopic, probably NMR) data readable by the MestreNova program.

One hit with these restrictions has doi: 10.14469/HPC/2635 and clicking the button on the landing page for this object labelled metadata resolves to e.g.
https://data.datacite.org/application/vnd.datacite.datacite+xml/10.14469/hpc/2635,
and downloads the metadata record for this object. Part of this record looks a bit like:

This brings me to the important issue for the chemistry domain, which is to agree upon a core set of SubjectSchemes for implementation in data repositories with domain-specific chemical content. The two subjects above, the InChI and the InChIKey seem obvious candidates for inclusion. But how the list is extended and how the SubjectScheme is specified are now matters for the community to discuss. Perhaps the IUPAC GoldBook is one starting point for the SubjectScheme URIs. Watch this space.

‡The \ syntax indicates an “escaped” character. Thus in chemicalx\-gaussian a \ ensured that the following / is treated as part of the search string, and not as part of the search syntax. Likewise \- ensures the minus character is part of the string and not a syntactic negation. The current list of characters requiring escaping is + - & | ! ( ) { } [ ] ^ " ~ * ? : \ /

† The documentation lists common fields, but there are far more specified in V4 of their schema. The ones you see used here are not (yet?) documented at https://search.datacite.org/help.html

♥ This Google page has a rich plethora of powerful searches, which I suggest almost no-one knows about!

References

  1. H.S. Rzepa, A. Mclean, and M.J. Harvey, "InChI As a Research Data Management Tool", Chemistry International, vol. 38, pp. 24-26, 2016. https://doi.org/10.1515/ci-2016-3-408
  2. H.S. Rzepa, P. Murray-Rust, and B.J. Whitaker, "The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World Wide Web Information Exchange", Journal of Chemical Information and Computer Sciences, vol. 38, pp. 976-982, 1998. https://doi.org/10.1021/ci9803233
  3. DataCite Metadata Working Group., "DataCite Metadata Schema Documentation for the Publication and Citation of Research Data v4.0", DataCite e.V., 2016. https://doi.org/10.5438/0012
  4. M.J. Harvey, A. McLean, and H.S. Rzepa, "A metadata-driven approach to data repository design", Journal of Cheminformatics, vol. 9, 2017. https://doi.org/10.1186/s13321-017-0190-6

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Posted in Chemical IT | 1 Comment »

FAIR Research data: Gravitational waves as an example from the astrophysics community.

June 2nd, 2017

In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.

  1. The original report in 2016[1] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.
  2. The second instance[2] also cites (Ref 89) a DOI: 10.7935/K5H41PBP
  3. Today† a third instance was reported[3] with data cited (Ref 180) as DOI: 10.7935/K53X84K2
  4. Sixth instance in 2017[4], Data (Ref 80) DOI: 10.7935/K5B8566F.
  5. A complete list of events is available at losc.ligo.org/events/

Each of these datasets is beautifully presented, with interactive components making the data very accessible and indeed FAIR. Recently, guidelines for how to cite data have emerged and the FORCE11 organisation has interpreted them for authors, publishers and journal editors, and repository administrators and it is good that the data for these detections has adhered to these principles. When implemented, it will identify e.g. Refs 116, 89 or 180 in the above articles with attributes that will trigger something called EventData with the objective that it retrieves and exposes the activity that occurs around research data objects and brings to light links between publications and data, citations, software, reuse, documentation, etc. At the moment I presume that these three data citations do not yet trigger any EventData. However, there are plans to for both CrossRef and DataCite to implement search procedures to find such EventData. When this service goes live, I intend to explore its potential; watch this space.

I did one other check on each of the datasets:

These download the metadata associated with each dataset. Ideally this could contain a host of information about the data and in particular its creators (i.e. the ORCID of each of the many authors describing how the data was acquired and interpreted). I show just the last as an example in full (the others are similar). Its pretty minimal.

Now there is an area that this otherwise magnificent example of open data sharing could improve upon. In a forthcoming post, I will show how rich metadata population of a chemistry dataset can be used to enhance it and also to trigger EventData as noted above.

‡For a famous chemical controversy involving gravitational fields, see here.

References

  1. B. Abbott, R. Abbott, T. Abbott, M. Abernathy, F. Acernese, K. Ackley, C. Adams, T. Adams, P. Addesso, R. Adhikari, V. Adya, C. Affeldt, M. Agathos, K. Agatsuma, N. Aggarwal, O. Aguiar, L. Aiello, A. Ain, P. Ajith, B. Allen, A. Allocca, P. Altin, S. Anderson, W. Anderson, K. Arai, M. Arain, M. Araya, C. Arceneaux, J. Areeda, N. Arnaud, K. Arun, S. Ascenzi, G. Ashton, M. Ast, S. Aston, P. Astone, P. Aufmuth, C. Aulbert, S. Babak, P. Bacon, M. Bader, P. Baker, F. Baldaccini, G. Ballardin, S. Ballmer, J. Barayoga, S. Barclay, B. Barish, D. Barker, F. Barone, B. Barr, L. Barsotti, M. Barsuglia, D. Barta, J. Bartlett, M. Barton, I. Bartos, R. Bassiri, A. Basti, J. Batch, C. Baune, V. Bavigadda, M. Bazzan, B. Behnke, M. Bejger, C. Belczynski, A. Bell, C. Bell, B. Berger, J. Bergman, G. Bergmann, C. Berry, D. Bersanetti, A. Bertolini, J. Betzwieser, S. Bhagwat, R. Bhandare, I. Bilenko, G. Billingsley, J. Birch, I.A. Birney, O. Birnholtz, S. Biscans, A. Bisht, M. Bitossi, C. Biwer, M. Bizouard, J. Blackburn, C. Blair, D. Blair, R. Blair, S. Bloemen, O. Bock, T. Bodiya, M. Boer, G. Bogaert, C. Bogan, A. Bohe, P. Bojtos, C. Bond, F. Bondu, R. Bonnand, B. Boom, R. Bork, V. Boschi, S. Bose, Y. Bouffanais, A. Bozzi, C. Bradaschia, P. Brady, V. Braginsky, M. Branchesi, J. Brau, T. Briant, A. Brillet, M. Brinkmann, V. Brisson, P. Brockill, A. Brooks, D. Brown, D. Brown, N. Brown, C. Buchanan, A. Buikema, T. Bulik, H. Bulten, A. Buonanno, D. Buskulic, C. Buy, R. Byer, M. Cabero, L. Cadonati, G. Cagnoli, C. Cahillane, J.C. Bustillo, T. Callister, E. Calloni, J. Camp, K. Cannon, J. Cao, C. Capano, E. Capocasa, F. Carbognani, S. Caride, J.C. Diaz, C. Casentini, S. Caudill, M. Cavaglià, F. Cavalier, R. Cavalieri, G. Cella, C. Cepeda, L.C. Baiardi, G. Cerretani, E. Cesarini, R. Chakraborty, T. Chalermsongsak, S. Chamberlin, M. Chan, S. Chao, P. Charlton, E. Chassande-Mottin, H. Chen, Y. Chen, C. Cheng, A. Chincarini, A. Chiummo, H. Cho, M. Cho, J. Chow, N. Christensen, Q. Chu, S. Chua, S. Chung, G. Ciani, F. Clara, J. Clark, F. Cleva, E. Coccia, P. Cohadon, A. Colla, C. Collette, L. Cominsky, M. Constancio, A. Conte, L. Conti, D. Cook, T. Corbitt, N. Cornish, A. Corsi, S. Cortese, C. Costa, M. Coughlin, S. Coughlin, J. Coulon, S. Countryman, P. Couvares, E. Cowan, D. Coward, M. Cowart, D. Coyne, R. Coyne, K. Craig, J. Creighton, T. Creighton, J. Cripe, S. Crowder, A. Cruise, A. Cumming, L. Cunningham, E. Cuoco, T.D. Canton, S. Danilishin, S. D’Antonio, K. Danzmann, N. Darman, C. Da Silva Costa, V. Dattilo, I. Dave, H. Daveloza, M. Davier, G. Davies, E. Daw, R. Day, S. De, D. DeBra, G. Debreczeni, J. Degallaix, M. De Laurentis, S. Deléglise, W. Del Pozzo, T. Denker, T. Dent, H. Dereli, V. Dergachev, R. DeRosa, R. De Rosa, R. DeSalvo, S. Dhurandhar, M. Díaz, L. Di Fiore, M. Di Giovanni, A. Di Lieto, S. Di Pace, I. Di Palma, A. Di Virgilio, G. Dojcinoski, V. Dolique, F. Donovan, K. Dooley, S. Doravari, R. Douglas, T. Downes, M. Drago, R. Drever, J. Driggers, Z. Du, M. Ducrot, S. Dwyer, T. Edo, M. Edwards, A. Effler, H. Eggenstein, P. Ehrens, J. Eichholz, S. Eikenberry, W. Engels, R. Essick, T. Etzel, M. Evans, T. Evans, R. Everett, M. Factourovich, V. Fafone, H. Fair, S. Fairhurst, X. Fan, Q. Fang, S. Farinon, B. Farr, W. Farr, M. Favata, M. Fays, H. Fehrmann, M. Fejer, D. Feldbaum, I. Ferrante, E. Ferreira, F. Ferrini, F. Fidecaro, L. Finn, I. Fiori, D. Fiorucci, R. Fisher, R. Flaminio, M. Fletcher, H. Fong, J. Fournier, S. Franco, S. Frasca, F. Frasconi, M. Frede, Z. Frei, A. Freise, R. Frey, V. Frey, T. Fricke, P. Fritschel, V. Frolov, P. Fulda, M. Fyffe, H. Gabbard, J. Gair, L. Gammaitoni, S. Gaonkar, F. Garufi, A. Gatto, G. Gaur, N. Gehrels, G. Gemme, B. Gendre, E. Genin, A. Gennai, J. George, L. Gergely, V. Germain, A. Ghosh, A. Ghosh, S. Ghosh, J. Giaime, K. Giardina, A. Giazotto, K. Gill, A. Glaefke, J. Gleason, E. Goetz, R. Goetz, L. Gondan, G. González, J.G. Castro, A. Gopakumar, N. Gordon, M. Gorodetsky, S. Gossan, M. Gosselin, R. Gouaty, C. Graef, P. Graff, M. Granata, A. Grant, S. Gras, C. Gray, G. Greco, A. Green, R. Greenhalgh, P. Groot, H. Grote, S. Grunewald, G. Guidi, X. Guo, A. Gupta, M. Gupta, K. Gushwa, E. Gustafson, R. Gustafson, J. Hacker, B. Hall, E. Hall, G. Hammond, M. Haney, M. Hanke, J. Hanks, C. Hanna, M. Hannam, J. Hanson, T. Hardwick, J. Harms, G. Harry, I. Harry, M. Hart, M. Hartman, C. Haster, K. Haughian, J. Healy, J. Heefner, A. Heidmann, M. Heintze, G. Heinzel, H. Heitmann, P. Hello, G. Hemming, M. Hendry, I. Heng, J. Hennig, A. Heptonstall, M. Heurs, S. Hild, D. Hoak, K. Hodge, D. Hofman, S. Hollitt, K. Holt, D. Holz, P. Hopkins, D. Hosken, J. Hough, E. Houston, E. Howell, Y. Hu, S. Huang, E. Huerta, D. Huet, B. Hughey, S. Husa, S. Huttner, T. Huynh-Dinh, A. Idrisy, N. Indik, D. Ingram, R. Inta, H. Isa, J. Isac, M. Isi, G. Islas, T. Isogai, B. Iyer, K. Izumi, M. Jacobson, T. Jacqmin, H. Jang, K. Jani, P. Jaranowski, S. Jawahar, F. Jiménez-Forteza, W. Johnson, N. Johnson-McDaniel, D. Jones, R. Jones, R. Jonker, L. Ju, K. Haris, C. Kalaghatgi, V. Kalogera, S. Kandhasamy, G. Kang, J. Kanner, S. Karki, M. Kasprzack, E. Katsavounidis, W. Katzman, S. Kaufer, T. Kaur, K. Kawabe, F. Kawazoe, F. Kéfélian, M. Kehl, D. Keitel, D. Kelley, W. Kells, R. Kennedy, D. Keppel, J. Key, A. Khalaidovski, F. Khalili, I. Khan, S. Khan, Z. Khan, E. Khazanov, N. Kijbunchoo, C. Kim, J. Kim, K. Kim, N. Kim, N. Kim, Y. Kim, E. King, P. King, D. Kinzel, J. Kissel, L. Kleybolte, S. Klimenko, S. Koehlenbeck, K. Kokeyama, S. Koley, V. Kondrashov, A. Kontos, S. Koranda, M. Korobko, W. Korth, I. Kowalska, D. Kozak, V. Kringel, B. Krishnan, A. Królak, C. Krueger, G. Kuehn, P. Kumar, R. Kumar, L. Kuo, A. Kutynia, P. Kwee, B. Lackey, M. Landry, J. Lange, B. Lantz, P. Lasky, A. Lazzarini, C. Lazzaro, P. Leaci, S. Leavey, E. Lebigot, C. Lee, H. Lee, H. Lee, K. Lee, A. Lenon, M. Leonardi, J. Leong, N. Leroy, N. Letendre, Y. Levin, B. Levine, T. Li, A. Libson, T. Littenberg, N. Lockerbie, J. Logue, A. Lombardi, L. London, J. Lord, M. Lorenzini, V. Loriette, M. Lormand, G. Losurdo, J. Lough, C. Lousto, G. Lovelace, H. Lück, A. Lundgren, J. Luo, R. Lynch, Y. Ma, T. MacDonald, B. Machenschalk, M. MacInnis, D. Macleod, F. Magaña-Sandoval, R. Magee, M. Mageswaran, E. Majorana, I. Maksimovic, V. Malvezzi, N. Man, I. Mandel, V. Mandic, V. Mangano, G. Mansell, M. Manske, M. Mantovani, F. Marchesoni, F. Marion, S. Márka, Z. Márka, A. Markosyan, E. Maros, F. Martelli, L. Martellini, I. Martin, R. Martin, D. Martynov, J. Marx, K. Mason, A. Masserot, T. Massinger, M. Masso-Reid, F. Matichard, L. Matone, N. Mavalvala, N. Mazumder, G. Mazzolo, R. McCarthy, D. McClelland, S. McCormick, S. McGuire, G. McIntyre, J. McIver, D. McManus, S. McWilliams, D. Meacher, G. Meadors, J. Meidam, A. Melatos, G. Mendell, D. Mendoza-Gandara, R. Mercer, E. Merilh, M. Merzougui, S. Meshkov, C. Messenger, C. Messick, P. Meyers, F. Mezzani, H. Miao, C. Michel, H. Middleton, E. Mikhailov, L. 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Research data: Gravitational waves as an example from the astrophysics community.

June 2nd, 2017

In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.

  1. The original report in 2016[1] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.
  2. The second instance[2] also cites (Ref 89) a DOI: 10.7935/K5H41PBP
  3. Today a third instance was reported[3] with data cited (Ref 180) as DOI: 10.7935/K53X84K2

Each of these datasets is beautifully presented, with interactive components making the data very accessible and indeed FAIR. Recently, guidelines for how to cite data have emerged and the FORCE11 organisation has interpreted them for authors, publishers and journal editors, and repository administrators and it is good that the data for these detections has adhered to these principles. When implemented, it will identify e.g. Refs 116, 89 or 180 in the above articles with attributes that will trigger something called EventData with the objective that it retrieves and exposes the activity that occurs around research data objects and brings to light links between publications and data, citations, software, reuse, documentation, etc. At the moment I presume that these three data citations do not yet trigger any EventData. However, there are plans to for both CrossRef and DataCite to implement search procedures to find such EventData. When this service goes live, I intend to explore its potential; watch this space.

I did one other check on each of the datasets:

These download the metadata associated with each dataset. Ideally this could contain a host of information about the data and in particular its creators (i.e. the ORCID of each of the many authors describing how the data was acquired and interpreted). I show just the last as an example in full (the others are similar). Its pretty minimal.

Now there is an area that this otherwise magnificent example of open data sharing could improve upon. In a forthcoming post, I will show how rich metadata population of a chemistry dataset can be used to enhance it and also to trigger EventData as noted above.

‡For a famous chemical controversy involving gravitational fields, see here.

References

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Yancey, M. Yap, H. Yu, H. Yu, M. Yvert, A. Zadrożny, M. Zanolin, T. Zelenova, J. Zendri, M. Zevin, L. Zhang, M. Zhang, T. Zhang, Y. Zhang, C. Zhao, M. Zhou, Z. Zhou, X. Zhu, A. Zimmerman, M. Zucker, J. Zweizig, and . , "GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2", Physical Review Letters, vol. 118, 2017. https://doi.org/10.1103/physrevlett.118.221101

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Tautomeric polymorphism.

June 1st, 2017

Conformational polymorphism occurs when a compound crystallises in two polymorphs differing only in the relative orientations of flexible groups (e.g. Ritonavir). At the Beilstein conference, Ian Bruno mentioned another type;  tautomeric polymorphism, where a compound can crystallise in two forms differing in the position of acidic protons. Here I explore three such examples.

The term occurs in the title of this article,[1] for a compound known as Omeprazole.

When the bottom structure (the 6-methoxy) is used to search the CSD, two separate series are found. The first of these is UDAVIF (DOI:  10.5517/ccp82qq,  6-Methoxy-2-((4-methoxy-3,5-dimethyl-2-pyridinyl)methylsulfinyl)-1H-benzimidazole). There is no information regarding the absolute configuration of the chiral S-centre. Although the downloaded coordinates show it as R it is probably a racemic mixture. A note added to the structure declares disorder: “Omeprazole exists as solid solutions of the two tautomers. The structure is mixed 5-methoxy/6-methoxy with occupancies 0.078:0.922“, which indicates 7.8% is present as in the upper structure above. 

The second hit is VAYXOI (DOI: 10.5517/ccp82pp, rac-6-Methoxy-2-(((4-methoxy-3,5-dimethyl-2-pyridinyl)methyl)sulfinyl)-1H-benzimidazole) which now contains no disorder; the contaminating 5-methoxy tautomer is no longer present. Perhaps not quite a true tautomeric polymorph, since the 5-methoxy tautomer is never observed in pure form.

This does occur with a second example. DEBFAR[2] represents the keto form on the right which crystallises from methanol, whilst YUYDOL as the enol form on the left crystallises from n-hexane. 

Calculations shed some light on this behaviour. DEBFAR has a computed (DOI: 10.14469/hpc/2591)  dipole moment of 11D, whereas YUYDOL (DOI: 10.14469/hpc/2590) is 2.5D. In chloroform solutions (~half way between the two solvent polarities), the keto form is ~6.1 kcal/mol lower in ΔG than the enol. The crystal packing for the two forms is very different and the differences in this packing must clearly amount to >6.1 kcal/mol to over-ride the lesser stability of DEBFAR in solution.


The final example [3] is illustrated using scheme 2 from that article, one entitled tautomeric species of 4-hydroxynicotinic acid:

The original diagram has two unfortunate bond errors which are NOT reproduced above (and which perhaps are a good topic for discussion in tutorials with students), along with an unusual interpretation of the term tautomerism. The blue arrows above are mine and I suggest the isomerism between the connected species is resonance isomerism, and not tautomerism. So three possible different true tautomers then. Five crystal structures are reported which I list below.

  1. 10.5517/cctswjz (KUXPUP, 4-oxo-1,4-dihydropyridine-3-carboxylic acid, no H2O),  10.5517/ccdc.csd.cc1kfyxv (KUXPUP01 no H2O) and 10.5517/ccdc.csd.cc1kfyzx (KUXPUP02 no H2O)
  2. 10.5517/ccx59s4 (AVEMUK, 4-Oxo-1,4-dihydropyridine-3-carboxylic acid hemihydrate) and  10.5517/ccdc.csd.cc1kfz21 (AVEMUK01)
  3. 10.5517/ccdc.csd.cc1kfz54 (AKIHIN, 4-hydroxypyridin-1-ium-3-carboxylate monohydrate) 
  4. 10.5517/ccdc.csd.cc1kfz10 (AKIHAF, 4-hydroxypyridin-1-ium-3-carboxylate)

KUXPUP and AVEMUK differ only in the presence of one solvent water molecule and both represent tautomer 2 above. AKIHIN and AKIHAF similarly represent tautomer 3 above; both are represented as 3a in the CSD and not as 3b. There are no examples of tautomer 1 in the crystal structure database; it may only exist in the gas phase. So the equilibrium 2 ⇌ 3 is another genuine example of tautomeric polymorphism, with the keto form favoured by more polar solvents, as was noted for the previous example.

With this last article,[3] comprehensive calculations at a good level were reported, including modelling the periodic cell using the Crystal program and including corrections such as BSSE (basis set superposition error) and dispersion terms. I was hopeful that this might lead me to something as simple as the computed dipole moments of the (isolated) species (as I reported above for the previous system), but these were not mentioned in the text of the article. Unfortunately, the supporting information also had no details of any such calculations, which left me frustrated again at how difficult it can be in (it has to be said) the vast majority of articles which report calculations to get details of such calculations. 

Tautomeric polymorphism remains a very rare phenomenon. SciFinder for example only has 19 references citing it (2 of which are to conference talks). Perhaps the most intriguing[4] claims that 2-thiobarbituric acid has the richest collection of tautomeric polymorphs with five. Since no calculations are reported there, I might try these out and report back here.

Postscript:  Here is some analysis of 2-thiobarbituric.

  1. THBARB (DOI 10.5517/cctbxcd, 10.5517/cctbxfg  and 10.5517/cctbxgh) are three polymorphs of  the keto tautomer, the isolated molecule having a small calculated dipole moment (DOI: 10.14469/hpc/2632).
  2. PABNAJ (DOI: 10.5517/cctbxbc) is a polymorph in the enol form, with a much larger calculated dipole moment (DOI: 10.14469/hpc/2633)
  3. PABNIR (DOI: 10.5517/cctbxdf) is a mixed polymorph with one enol paired with one keto form. 

The relative free-energies of the isolated molecules are 0.0 (keto) and 9.0 (enol). The keto-enol pair is 0.4 kcal/mol more stable than the isolated components. This again shows the effect that crystal packing can have on the relative energies and also shows that a  simple inspection of the dipole moment may cast light on the polymorphism.

 

References

  1. P.M. Bhatt, and G.R. Desiraju, "Tautomeric polymorphism in omeprazole", Chemical Communications, pp. 2057, 2007. https://doi.org/10.1039/b700506g
  2. Y. Akama, M. Shiro, T. Ueda, and M. Kajitani, "Keto and Enol Tautomers of 4-Benzoyl-3-methyl-1-phenyl-5(2H)-pyrazolone", Acta Crystallographica Section C Crystal Structure Communications, vol. 51, pp. 1310-1314, 1995. https://doi.org/10.1107/s0108270194007389
  3. S. Long, M. Zhang, P. Zhou, F. Yu, S. Parkin, and T. Li, "Tautomeric Polymorphism of 4-Hydroxynicotinic Acid", Crystal Growth & Design, vol. 16, pp. 2573-2580, 2016. https://doi.org/10.1021/acs.cgd.5b01639
  4. M. Chierotti, L. Ferrero, N. Garino, R. Gobetto, L. Pellegrino, D. Braga, F. Grepioni, and L. Maini, "The Richest Collection of Tautomeric Polymorphs: The Case of 2‐Thiobarbituric Acid", Chemistry – A European Journal, vol. 16, pp. 4347-4358, 2010. https://doi.org/10.1002/chem.200902485

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CH⋅⋅⋅π Interactions between methyl and carbonyl groups in proteins: a small molecule check.

May 29th, 2017

Derek Lowe highlights a recent article[1] postulating CH⋅⋅⋅π interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD).

The search query (DOI: 10.14469/hpc/2594) is shown below.

  1. The distance refers to that between the (normalised) position of a hydrogen on a 4-coordinated carbon atom and the centroid of a carbonyl group substituted with R=C or H. 
  2. The angle is that subtended at the centroid. An approach orthogonal to the axis of the carbonyl group will have a value of 1.0 for the sine.
  3. The torsion relates to the angle between the H…centroid and C-R vectors. The absolute value is constrained to 70-110° to filter only approaches towards the π-system of the carbonyl.
  4. The search is further restricted to no disorder, no errors and R < 0.05. 

The two most interesting hits, both revealing short distances and ~orthogonal approaches to the π-system are:

Remember however that such “outliers” must always be carefully inspected. There are more numerous interactions in the region 2.4-2.6Å with a sine(angle) of >0.9 and and a close orthogonal approach to the π-system (green dots) which probably qualify for the title above. There seem many interesting but still putative small-molecule candidates for this proposed interaction postulated for proteins. 

Postscript:  Here the results of the search above with R= any of H,C,N,O,F,Cl up to values of the distance <2.4Å, which show a range of interesting (green) points.

References

  1. F.A. Perras, D. Marion, J. Boisbouvier, D.L. Bryce, and M.J. Plevin, "Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins", Angewandte Chemie International Edition, vol. 56, pp. 7564-7567, 2017. https://doi.org/10.1002/anie.201702626

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Challenges in reliably representing the chemistry of crystal structures.

May 29th, 2017

The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science. It also addresses the theme here of the issues that might arise in assigning identifiers for any given molecule.

The structure was represented as shown[1] by the original authors, in which the bonding from S to Sn is indicated with both solid lines (a bond) and dotted lines (an “interaction”).

Why would this matter? Well, to enable any entry in the Cambridge structure database as findable (the F of FAIR) it has to be given a unique identifier. There are in general three such identifiers assigned by the CCDC:

  1. The Refcode, in this case XONHIS. These six or seven letter codes are historically the oldest, and started off at least with an attempt if possible to assign some semantic inference from the name, even if only occasionally. 
  2. The CCDC deposition number, in this case 650011. This is the number that an author will receive immediately upon deposition, and you often find these identifiers quoted in supporting information files
  3. The DOI (digital object identifier), in this case 10.5517/ccptd3z, which can be used to view the structure even if access to the full CSD is not available to the user. In that sense, the DOI is the FAIRest of the first three of these identifiers.
  4. However, CCDC reported that they are considering adding a 4th very common identifier, based on the InChI (International chemical identifier), which comes as a full string and with the structure of the molecule at least in part inferrable from it, together with  a shortened (almost) unique string which has the advantage of being “Googlable”. Both are helpfully FAIR.

It is this 4th identifier that is at issue here. InChIs are derived from atom connection tables; you need to define all bonds present in the molecule. And it is here that the dotted “bond”/”interaction” above becomes a problem. This is the representation shown in the CSD database, which reveals that all the Sn…S interactions are classified as “bonds”, along with some creative(!) representations of the C…S bonds.

So the InChI will very much depend on whether all the Sn…S contacts are termed as bonds or as interactions. To help clarify that, it is useful to show the typical range of lengths of such contacts. Below is a simple search for all Sn and S systems where the pair are either close in space (< 3.5Å) or have a bond specified between the two atoms.

The main cluster occurs at ~2.5Å, but there is some evidence of a second peak at about 3.0Å. The third distribution up to 3.5Å is probably a continuum of very weak dispersion interaction, which most molecules exhibit. The values for XONHIS are 2.521 and 2.996Å, which match the two clusters above.

So perhaps a quantum calculation can shed some light (DOI: 10.14469/hpc/2593)? The values on the right are the optimised bond lengths which are pretty similar to the crystal structure. On the left are the calculated Wiberg bond orders (B3LYP+D3BJ/Def2-TZVPP/chloroform calculation). These reveal both “bonds” have an order less than 1. The value of ~0.6 is probably not contentious, but it does graphically show that when a compound is indexed as having a “single bond” between two atoms, the quantitative bond order may be substantially less. What however would one make of a bond order of 0.214? Should it be classified as a bond, albeit a much weaker one than normal? Or should it instead simply be a rather strong “interaction” which is not classified as a bond? And perhaps one should have in mind the question “how sensitive is this result to the quantum mechanical procedure used?”

Why does this distinction matter? Well, the InChI algorithm is based on simple connectivity; are two atoms connected by a bond or not? There are no nuances here. At the moment, this decision can be made by an algorithm based on the distance between any atom pair (whether computed or measured), but more often I suspect it derives from a “molfile” which is often derived from a human-drawn representation using a structure drawing program. It does rather boil down to the individual preferences of the human drawing the molecule. Due in part to such uncertainties, it was estimated that only 22% of structures in the CSD can be used to generate a reliable InChI. Hydrogen bonds are almost always classified as non-bonds, which means their presence is rarely systematically flagged during the indexing of the structures. Organometallics often pose some of the greatest representational problems (there are many others).

I will end by observing another class of structure that I deal with, “reaction transition states”. As you might imagine these forms are full of pairs of atoms with ambiguous bond lengths and hence connectivity. We currently have no truly reliable method for assigning useful identifiers to them. So lots of challenges for the future then!

 

References

  1. R. Reyes-Martínez, R. Mejia-Huicochea, J.A. Guerrero-Alvarez, H. Höpfl, and H. Tlahuext, "Synthesis, heteronuclear NMR and X-ray crystallographic studies of two dinuclear diorganotin(IV) dithiocarbamate macrocycles", Arkivoc, vol. 2008, pp. 19-30, 2007. https://doi.org/10.3998/ark.5550190.0009.503

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Curating a nine year old journal FAIR data table.

May 29th, 2017

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]

The story started a few days ago when I was contacted by the learned society publisher of that article, noting they were “just checking our updated HTML view and wanted to test some of our old exceptions“. I should perhaps explain what this refers to. The standard journal production procedures involve receiving a Word document from authors and turning that into XML markup for the internal production processes. For some years now, I have found such passive (i.e. printable only) Word content unsatisfactory for expressing what is now called FAIR (Findable, accessible, inter-operable and re-usable) data. Instead, I would create another XML expression (using HTML), which I described as Interactive Tables and then ask the publisher to host it and add that as a further link to the final published article. I have found that learned society publishers have not been unwilling to create an “exception” to their standard production workflows (the purely commercial publishers rather less so!). That exceptional link is http://www.rsc.org/suppdata/cp/b8/b810301a/Table/Table1.html but it has now “fallen foul of the java deprecation“. 

Back in 2008 when the table was first created, I used the Java-based Jmol program to add the interactive component. That page, when loaded, now responds with the message:

This I must emphasise is nothing to do with the publisher, it is the Jmol certificate that has been revoked. That of itself requires explanation. Java is a powerful language which needs to be “sandboxed” to ensure system safety. But commands can be created which can access local file stores and write files out there (including potentially dangerous ones). So it started to become the practise to sign the Java code with the developer certificate to ensure provenance for the code. These certificates are time-expired and around 2015 the time came to renew it. Normally, when such a certificate is renewed, the old one is allowed to continue operation. On this occasion the agency renewing the certificate did not do this but revoked the old one instead (Certificate has been revoked, reason: CESSATION_OF_OPERATION, revocation date: Thu Oct 15 23:11:18 BST 2015). So all instances of Jmol with the old certificate now give the above error message. 

The solution in this case is easy; the old Jmol code (as JmolAppletSigned.jar) is simply replaced with the new version for which the certificate is again valid. But simply doing that alone would merely have postponed the problem; Java is now indeed deprecated for many publishers, which is a warning that it will be prohibited at some stage in the future.‡ So time to bite the bullet and remove the dependency on Java-Jmol, replacing it with JSmol which uses only JavaScript.

Changing published content is in general not allowed; one instead must publish a corrigendum. But in this instance, it is not the content that needs changing but the style of its presentation (following the principle of the Web of a clear-cut separation of style and content). So I set out to update the style of presentation, but I was keen to document the procedures used. I did this by commenting out non-functional parts of the style components of my original HTML document (as <!– comment –>) and adding new ones. I describe the changes I made below.

  1. The old HTML contained the following initialisation code: jmolInitialize(".","JmolAppletSigned.jar");jmolSetLogLevel('0'); which was commented out.
  2. New scripts to initialize instead JSmol were added, such as:
    <script src="JSmol.min.js" type="text/javascript"> </script>
  3. I added further scripts to set up controls to add interactivity.
  4. The now deprecated buttons had been invoked using a Jmol instance:  jmolButton('load "7-c2-h-020.jvxl";isosurface "" opaque; zoom 120;',"rho(r) H")
  5. which was replaced by the JSmol equivalent, but this time to produce a hyperlink rather than a button (to allow the greek ρ to appear, which it could not on a button): <a href="javascript:show_jmol_window();Jmol.script(jmolApplet0,'load 7-c2-020.jvxl;isosurface &quot;&quot; translucent;spin 3;')">ρ(r)</a>,
  6. Some more changes were made to another component of the table, the links to the data repository. Originally, these quoted a form of persistent identifier known as a Handle; 10042/to-800. Since the data was deposited in 2008, the data repository has licensed further functionality to add DataCite DOIs to each entry. For this entry,  10.14469/ch/775. Why? Well, the original Handle registration had very little (chemically) useful registered metadata, whereas DataCite allows far richer content. So an extra column was added to the table to indicate these alternate identifiers for the data.
  7. We are now at the stage of preparing to replace the Java applet at the publishers site with the Javascript version, along with the amended HTML file. The above link, as I write this post, still invokes the old Java, but hopefully it will shortly change to function again as a fully interactive table.
  8. I should say that the whole process, including finding a solution and implementing it took 3-4 hours work, of which the major part was the analysis rather than its implementation.

It might be interesting to speculate how long the curated table will last before it too needs further curation. There are some specifics in the files which might be a cause for worry, namely the so-called JVXL isosurfaces which are displayed. These are currently only supported by Jmol/JSmol. They were originally deployed because iso-surfaces tend to be quite large datafiles and JVXL used a remarkably efficient compression algorithm (“marching cubes”) which reduces their size ten-fold or more. Should JSmol itself become non-operational at some time in the (hopefully) far future (which we take to be ~10 years!) then a replacement for the display of JVXL will need to be found. But the chances are that the table itself will decay “gracefully”, with the HTML components likely to outlive most of the other features. The data repository quoted above has itself now been available for ~12 years and it too is expected to survive in some form for perhaps another 10. Beyond that period, no-one really knows what will still remain. 

You may well ask why the traditional journal model of using paper to print articles and which has survived some 350 years now, is being replaced by one which struggles to survive 10 years without expensive curation. Obviously, a 3D interactive display is not possible on paper. But one also hears that publishers are increasingly dropping printed versions entirely. One presumes that the XML content will be assiduously preserved, but re-working (transforming, as in XSLT) any particular flavour of XML into another publishers systems is also likely to be expensive. Perhaps in the future the preservation of 100% of all currently published journals will indeed become too expensive and we might see some of the less important ones vanishing for ever?†

‡Nowadays it is necessary to configure your system or Web browser to allow even signed valid Java applets to operate. Thus in the Safari browser (which still allows Java to operate, other popular browsers such as Chrome and Firefox have recently removed this ability), one has to go to preferences/security/plugin-settings/Java, enter the URL of the site hosting the applet and set it to either “ask” (when a prompt will always appear asking if you want to accept the applet) or “on” when it will always do so. How much longer this option will remain in this browser is uncertain.

†In the area of chemistry, an early pioneer was the Internet Journal of Chemistry, where the presentation of the content took full advantage of Web-technologies and was on-line only. It no longer operates and the articles it hosted are gone.

References

  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. https://doi.org/10.1039/b810301a

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Conference report: an example of collaborative open science (reaction IRCs).

May 25th, 2017

It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.‡

Steven Kirk  contacted me with the following query: Do you know of any open-access database of calculated IRCs with coverage of as broad a range of classes of chemical reactions as possible? I recollected that about six years ago, I was exploring the use of iTunesU as a system for delivering course content in a rich-media format. I produced animations for about 115 reactions (many of which as it happens were taken from this blog, but quite a number were also unique to that project) and placed them into iTunesU, and now sending the URL https://itunes.apple.com/gb/course/id562191342 to Steven.

I should at this point explain something of the structure of such an iTunesU course.

  1. An essential feature is the course icon, seen below on the left. Since the course is hosted by Imperial College, it had to be an officially approved icon. I am sure you can believe me if I tell you that this took a month or so to obtain, with a fair bit of persistence required!
  2. I also had to get approval to place the iTunes app on all the teaching computers so that students could open the course. Believe me again when I tell you that I had to persuade the Apple lawyers in Cupertino to release a special license for this app to persuade our administrators here to install it on the Windows teaching clusters. Another few months had passed by.
  3. When creating an entry (using e.g. https://itunesu.itunes.apple.com/coursemanager/ ) one has to specify values for various descriptors, also often called metadata. Thus any one entry has fields for name and description, with the popularity added by Apple. Only a few words are visible in the description field, which can be expanded in iTunes using the i button.
  4. Steven meanwhile had replied asking if the original data that was used to generate the IRC might be available. Specifically his second question was “So the DOIs are only stamped into the animation’s bitmaps, or are they also somewhere in the metadata?“. That little i button is not easy to spot, and there is no indication, in the event, of what information it might actually contain.
  5. Here it is expanded. The contents are unstructured text, into which I have placed the required DOI.
  6. The lesson here is that I had fortunately had the foresight to include a link to the IRC data in anticipation of just such a question from someone in the future. But black mark to Apple here; the text cannot be selected and copied into a clipboard! It is fairly unFAIR data, since it can only be inter-operated (the I of FAIR) by a human re-typing it by hand. And the human has also to recognise the pattern of a DOI; a machine could not obtain this information easily. Moreover Steven is a Linux user; he does not readily have access to the iTunes app on this operating system!
  7. Also, there were 115 such entries, and now the prospect was rearing that each would have to be hand processed. Moreover, because the text was unstructured, there was no guarantee that I would have adopted the same pattern for all 115 entries.
  8. Fortunately Steven was on the ball. I quote again: it turns out iTunes isn’t needed at all. A service I found on the web http://picklemonkey.net/feedflipper-home/ takes an ITunes URL and converts it to an RSS feed. Opening this feed in Firefox and RSSOwl respectively let me save the feed as XML and HTML (both attached).
  9. This is currently where we stand (Steven’s first email was two days ago), but it’s not finished yet. Depending on how assiduous I was five years ago, some DOIs to the data may be acquired from the list. Sometimes I simply wrote e.g. See http://www.ch.imperial.ac.uk/rzepa/blog/?p=6816 knowing that the links to the data were there instead. I can already see that some descriptions have neither a DOI nor a link to the blog. More detective work will be needed, unfortunately.

How might the situation described above been avoided? Well, Apple in iTunesU only provided in effect one metadata field, and this was an unstructured one. Anything went in that field. Had they provided (or had the course creator been able to configure it themselves) there might have been another field entitled say “data source“. This could moreover been made a mandatory field and a structured one. Thus it might have only accepted known types of persistent identifier, such as a DOI. Further, the system could have checked that the DOI was actually resolvable. Before you ask, I did log a “bug” with Apple asking this be done, but nothing ever was. With such a tool to hand, I might have achieved data sources for all the 115 entries. The resulting XML (as generated above) could have been used to automate the retrieval of all 115 datasets describing this course. 

At this stage then, Steven can follow-up his interest in building a reaction IRC library and analysing it. I will do all I can to encourage Steven not to make the mistakes I did and to ensure that any further data that is required to augment the library does not suffer the problems above. On the other hand, I console myself that in two days, much of the data for the course I created five years ago was salvageable; I wonder how many other iTunesU courses there are for which that can be said!

I will let (with some blushing) the final word be Steven’s: You are one of the few chemists who has both pioneered and built the principles of ‘open chemistry’ into their actual scientific work. I visit your blog occasionally knowing that there is a very high probability I could download and tinker with the results of real calculations.

‡Might I assure all the speakers that I concentrated totally on their talks rather than incoming emails!

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