Posts Tagged ‘Chemical nomenclature’

Long C=C bonds.

Thursday, December 1st, 2016

Following on from a search for long C-C bonds, here is the same repeated for C=C double bonds.

sq

The query restricts the search to each carbon having just two non-metallic substituents. To avoid conjugation with these, they each are 4-coordinated; the carbons themselves are three-coordinated. Further constraints are the usual no disorder, no errors and R < 0.1 and the C=C distance > 1.4Å (the standard value is ~1.32-1.34Å). The search query is deposited as DOI: 10.14469/hpc/1959[1]

c_c

The apparent longest example is LIRVEN, DOI: 10.5517/CC4R2MK[2] with a value of 1.589Å, longer than most C-C single bonds! Closer inspection reveals the presence of lithium cations, and so the molecule bearing the C=C bond must sustain two negative charges. So this apparent C=C bond is in fact anionic, with one electron going into each of the π* orbitals, thus lengthening the CC bond. Not a true example of a neutral C=C bond[3] but it now becomes interesting for what its spin state might be. Is it a biradical or a triplet for example? One to be investigated further I fancy! Another example of this type is QUKCEE[4]

10-5517cc4r2mk-lirven

This next FAZWIM has a C=C length of 1.546Å. It is an old structure (1986), and comes without attached hydrogen atoms. Although drawn with no hydrogens on the central C=C bond, the length suggests this molecule is simply mis-assigned.fazwin-diag fazwim

The final example I will highlight is pretty ordinary looking and published in 2016 as a private communication; ALOVOO, DOI: 10.5517/CCDC.CSD.CC1LJSWS[5] with a C=C length of 1.443Å. Again no obvious reason for the bond to be longer than normal.‡†

10-5517ccdc-csd-cc1ljsws-alovoo

In hunting for such unusual deviations from the norm, the most obvious explanation is normally some anomaly in the crystallographic analysis. Although the CSD (crystal structure database) is a very heavily curated resource, it seems unlikely that each deposition would be carefully inspected for its chemistry, and this must be our task here. But such anomalies can themselves point to interesting or unusual chemistry, which in  turn can be subjected to quantum computation to see if either the unusual value can be replicated or other reasons identified.  In this case, this exercise can been conducted by a human, but one can easily envisage the entire process being automated on a far larger scale.  The future?


In fact the stoichiometry shows each “double bond” is actually a di-anion, with two electrons entering each of the the π* orbitals.

A calculation on the singlet state for the structure as drawn (ωB97XD/Def2-TZVPP, DOI: 10.14469/hpc/1960) gives a bond length of 1.342Å, i.e. that expected for a double bond. The triplet state is similar in energy, but with a much longer central bond length of 1.476Å, DOI: 10.14469/hpc/1962 but the geometry at the carbons is planar and not bent as shown above. The quintet state is 1.45Å and is again planar, doi 10.14469/hpc/1963. So calculations on FAZWIM strongly suggest the structure as shown is an error.

‡†The computed value is 1.324Å, perfectly normal. DOI: 10.14469/hpc/1966[6]

References

  1. H. Rzepa, "Long C=C bonds", 2016. https://doi.org/10.14469/hpc/1959
  2. Matsuo, T.., Watanabe, H.., Ichinohe, M.., and Sekiguchi, A.., "CCDC 141348: Experimental Crystal Structure Determination", 2000. https://doi.org/10.5517/cc4r2mk
  3. T. Matsuo, H. Watanabe, M. Ichinohe, and A. Sekiguchi, "Reduction of the 1,4,5,8-tetrasila-1,4,5,8-tetrahydroanthracene derivative with lithium metal. Isolation and characterization of the tetralithium salt of a tetraanion, and observation of an Si–H⋯Li+ interaction", Inorganic Chemistry Communications, vol. 2, pp. 510-512, 1999. https://doi.org/10.1016/s1387-7003(99)00136-7
  4. T. Matsuo, H. Watanabe, and A. Sekiguchi, "A Novel Tetralithium Salt of a Tetraanion and a Dilithium Salt of a Dianion, Formed by the Reduction of the Tetrasilylethylene Moiety. Synthesis, Characterization, and Observation of an Si-H···Li+ Interaction", Bulletin of the Chemical Society of Japan, vol. 73, pp. 1461-1467, 2000. https://doi.org/10.1246/bcsj.73.1461
  5. M.E. Light, S. Bain, and J. Kilburn, "CCDC 1475906: Experimental Crystal Structure Determination", 2016. https://doi.org/10.5517/ccdc.csd.cc1ljsws
  6. H. Rzepa, "ALOVOO", 2016. https://doi.org/10.14469/hpc/1966

Global initiatives in research data management and discovery: searching metadata.

Monday, March 7th, 2016

The upcoming ACS national meeting in San Diego has a CINF (chemical information division) session entitled "Global initiatives in research data management and discovery". I have highlighted here just one slide from my contribution to this session, which addresses the discovery aspect of the session.

Data, if you think about it, is rarely discoverable other than by intimate association with a narrative or journal article. Even then, the standard procedure is to identify the article itself as being of interest, and then digging out the "supporting information", which normally takes the form of a single paginated PDF document. If you are truly lucky, you might also get a CIF file (for crystal structures). But such data has little life of its own outside of its parent, the article. Put another way, it has no metadata it can call its own (metadata is data about an object, in this case research data). An alternative is to try to find the data by searching conventional databases such as CAS,  Beilstein/Reaxys or CSD, and there of course the searches can be very precise. But (someone) has to pay the bills for such accessibility.

We are now starting to see quite different solutions to finding data (the F in FAIR data, the other letters representing accessibility, interoperability and re-usability). These solutions depend on metadata being a part of the solution from the outset, rather than any afterthought produced as a commercial solution. The collection of metadata is part of the overall process called RDM, or research data management, perhaps even the most important part of it. In exchange for identifying metadata about one's data, one gets back a "receipt" in the form of a persistent identifier for the data, more commonly known as a DOI. The agency that issues the DOI also undertakes to look after the donated metadata, and to make it searchable. The table below shows eight searches of such metadata, one example of how to acquire statistics relating to the usage of the data and one search of how to find repositories containing the data.

Search queries enabled by the use of metadata in data publication
# Search query* Instances retrieved:
1 http://search.datacite.org/ui?q=alternateIdentifier:InChIKey:*  InChI identifier
2 http://search.datacite.org/ui?q=alternateIdentifier:InChI:*  InChI key 
3 http://search.datacite.org/ui?q=alternateIdentifier:InChIKey:CULPUXIDFLIQBT-UHFFFAOYSA-N InChI key CULPUXIDFLIQBT-UHFFFAOYSA-N 
4 http://search.datacite.org/ui?q=ORCID:0000-0002-8635-8390+alternateIdentifier:InChIKey:* ORCID 0000-0002-8635-8390 AND (boolean) InChI key.
5 http://search.datacite.org/ui?q=ORCID:0000-0002-8635-8390+alternateIdentifier:InChI:InChI=1S/C9H11N5O3* ORCID 0000-0002-8635-8390 AND (boolean) + InChI string 1S/C9H11N5O3 with the * wild.
6 http://search.datacite.org/ui?q=has_media:true&fq=prefix:10.14469 Has content media for Publisher 10.14469 (Imperial College)
7 http://search.datacite.org/ui?q=format:chemical/x-* Data format type chemical/x-* 
8 http://search.datacite.org/api?&q=prefix:10.14469& fq=alternateIdentifier:InChIKey:*& fl=doi,title,alternateIdentifier& wt=json&rows=15
http://api.labs.datacite.org/works?q=prefix:10.14469+AND+alternateIdentifier:InChIKey:*
First 15 hits in JSON format, batch query mode
9 http://stats.datacite.org/?fq=datacentre_facet:"BL.IMPERIAL – Imperial College London" resolution statistics for publisher 10.14469 (Imperial College) per month
10 http://service.re3data.org/search?query=&subjects[]=31 Chemistry Research data repository search for Chemistry (135 hits)

In this instance the three MIME media types are chemical/x-wavefunction, chemical/x-gaussian-checkpoint and chemical/x-gaussian-log. See[1] for chemical MIME (multipurpose internet media extensions).


Anyone familiar with the standard ways of finding data (CAS, CSD, Reaxys) will appreciate that the above does not yet have the finesse to find eg sub-structures of chemical structures, synthetic procedures or molecular properties. My including it here is primarily to show some of the potential such systems have, and to remark particularly that the batch query capability of this infrastructure could indeed be used in the future to construct much more sophisticated systems.  Oh, and to the end-user at least, the searches shown above do not require institutional licenses to use. Both the data and its metadata is free, mostly with a CC0 or CC BY 3.0 license for re-use (the R of FAIR).

If more of interest related to this topic emerges at the ACS session,  I will report back here.

References

  1. 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

Mesomeric resonance in substituted benzenes: a crystallographic reality check.

Wednesday, August 26th, 2015

Previously, I showed how conjugation in dienes and diaryls can be visualised by inspecting bond lengths as a function of torsions. Here is another illustration, this time of the mesomeric resonance on a benzene ring induced by an electron donating substituent (an amino group) or an electron withdrawing substituent (cyano).

Scheme

In both cases, you can see this resonance showing as a lengthening of the C(ipso)-C(ortho) and C(meta)-C(para) bonds, and a contracting of the C(ortho)-C(meta) bonds. Does this reflect in the measured structures? The usual search is applied (R < 5%, no disorder, no errors) and qualified with the following:

  1. The amino has three bonds, and can bear either H, or 4-bonded carbon only.
  2. R on the ring can be either H or C.
  3. Three distances are defined.

Scheme

The results of a search are shown below; the hotspot shows the C-C(ortho) distance is close to 1.40Å, whilst the corresponding value for C(ortho)-C(meta) is 1.38Å, a contraction of ~0.02Å. The contraction is smaller for phenols (~0.01Å).

Scheme

The C(ortho)-C(meta) vs C(meta)-C(para) amino plot shows a cluster of hotspots for which the former (1.38Å) is  shorter than the latter (~1.39Å) but the effect is less clear cut as the distance from the substituent increases.

Scheme

For an electron withdrawing cyano substituent, C(ipso)-C(ortho) at 1.395Å is longer than C(ortho)-C(meta) at 1.385Å, although the difference seems smaller than for the amino substituent. The (ortho)-C(meta) to C(meta)-C(para) comparison is similar.

Scheme

Scheme

These searches take but a few minutes to perform, and do serve as a reality check on the oft-seen mesomeric π-resonance shown in all organic text books.