Cyclo[6] and [10]carbon. The Kekulé vibrations compared.

September 3rd, 2019

In the previous post, I looked at the so-called Kekulé vibration of cyclo[18]carbon using various quantum methods and basis sets.  Because some of these procedures can take a very long time,  I could not compare them using the same high-quality consistent atom basis set for the carbon (Def2-TZVPP). Here I try to start to do this using the smaller six and ten carbon rings to see what trends might emerge. FAIR data are at DOI: 10.14469/hpc/6069

Read the rest of this entry »

Cyclo[18]carbon: The Kekulé vibration calculated and hence a mystery!

August 30th, 2019

I have discussed the vibration in benzene known as the Kekulé mode in other posts, the first of which was all of ten years ago. It is a stretching mode that lengthens three of the bonds in benzene (a [6]-annulene) and shortens the other three, thus leading to a cyclohexatriene motif (see below). This vibration is real (+ve force constant) in benzene itself, which indicates that distorting the structure from six to three-fold symmetry leads to an increase in energy. Benzene therefore has a symmetrising influence, and it comes as a surprise to most to learn that this is actually due to the σ rather than the π-electrons! But there are good reasons to believe that as the ring size of the annulene increases, the Kekulé vibration will evolve from a real mode into an imaginary (-ve force constant) vibration representing a transition state for mutating the single and double bonds. At some point therefore, the more symmetrical geometry of the annulene in which all the bonds are of equal length will change into one of lower symmetry, in which BLA (bond length alternation) occurs and the symmetrical form becomes a transition state for this process.

Read the rest of this entry »

A Non-nitrogen Containing Morpholine Isostere; an application of FAIR data principles.

August 4th, 2019

In the pipeline reports on an intriguing new ring system acting as an isostere for morpholine. I was interested in how the conformation of this ring system might be rationalised electronically and so I delved into the article.[1] Here I recount what I found.

Read the rest of this entry »

References

  1. H. Hobbs, G. Bravi, I. Campbell, M. Convery, H. Davies, G. Inglis, S. Pal, S. Peace, J. Redmond, and D. Summers, "Discovery of 3-Oxabicyclo[4.1.0]heptane, a Non-nitrogen Containing Morpholine Isostere, and Its Application in Novel Inhibitors of the PI3K-AKT-mTOR Pathway", Journal of Medicinal Chemistry, vol. 62, pp. 6972-6984, 2019. http://dx.doi.org/10.1021/acs.jmedchem.9b00348

CH…O hydrogen bonding competing with layered dispersion attractions.

July 19th, 2019

I have previously looked at the topic of hydrogen bonding interactions from the hydrogen of chloroform Here I generalize C-H…O interactions by conducting searches of the CSD (Cambridge structure database) as a function of the carbon hybridisation. I am going to jump straight to a specific molecule XEVJIR (DOI: 10.5517/cc5fgpq) identified from the searches appended to this post as interesting for further inspection.[1]

Read the rest of this entry »

References

  1. K.S. Huang, M.J. Haddadin, M.M. Olmstead, and M.J. Kurth, "Synthesis and Reactions of Some Heterocyclic Azacyanines1", The Journal of Organic Chemistry, vol. 66, pp. 1310-1315, 2001. http://dx.doi.org/10.1021/jo001484k

Metadata. Why?

July 2nd, 2019

I have had some interesting discussions recently regarding metadata. What emerges is that it can be quite a broadly defined concept and it is clear that a variety of answers might be obtained when asking the simple question “what is it useful for?” Here I set out some of my answers to that question.

Read the rest of this entry »

Anniversaries: The World-Wide-Web at 30 and 25 (+ CERN’s LHC as a bonus).

June 15th, 2019

 

The World-Wide-Web is currently celebrating its 30th anniversary; you can get the T-shirt in the CERN visitor centre!  Five years on, in May 1994, the first Web conference took place (WWW94) at CERN and now celebrating its own 25th anniversary. That 1994 conference also had various break-out sessions, one of which summarised the state of chemistry on the web at the time. You can see my general but entirely personal impressions written after the workshop (DOI: 10.14469/hpc/5850), with a chemistry specific version at DOI: 10.14469/hpc/5851.  A real trip down memory lane and an indication of how much has happened in 25 years!

Read the rest of this entry »

ChemRxiv. Why?

June 5th, 2019

In August 2016, the launch of a chemistry pre-print service ChemRxiv was announced. I was phoned a day or so later by a staff journalist at C&E News for my opinion. The only comment that was retained for their report was my instantaneous feeling that “the community needed a chemistry pre-print server like one needed a hole in the head“. I had been there before you see, recollecting a pre-print server launched by the ChemWeb service around 1996 or 1997 and which lasted only about two years before being withdrawn due to the low quality of the preprints. So what do I think of ChemRxiv now in 2019?

Read the rest of this entry »

Diatomics with eight valence-electrons: formation by radioactive decay.

June 2nd, 2019

This is a follow up to my earlier post about C⩸N+, itself inspired by this ChemRxiv pre-print[1] which describes a chemical synthesis of singlet biradicaloid C2 and its proposed identification as such by chemical trapping.

Read the rest of this entry »

References

  1. K. Miyamoto, S. Narita, Y. Masumoto, T. Hashishin, M. Kimura, M. Ochiai, and M. Uchiyama, "Room-Temperature Chemical Synthesis of C2", 2019. http://dx.doi.org/10.26434/chemrxiv.8009633.v1

Startling bonds: revisiting C⩸N+, via the helium bond in N≡C-He+.

May 27th, 2019

Although the small diatomic molecule known as dicarbon or C2 has been known for a long time, its properties and reactivity have really only been determined via its very high temperature generation. My interest started in 2010, when I speculatively proposed here that the related isoelectronic species C⩸N+ might sustain a quadruple bond. Shortly thereafter, a torrent of theoretical articles started to appear in which the idea of a quadruple bond to carbon was either supported or rejected. Clearly more experimental evidence was needed. The recent appearance of a Chemrxiv pre-print entitled “Room-temperature chemical synthesis of C2“.[1] claims to provide just this! Using the synthetic scheme outlined below, they trapped “C2” with a variety of reagents (see Figure 2A in their article), concluding that the observed reactivity best matched that of singlet “biradicaloid” C2 sustaining a quadruple bond.

Read the rest of this entry »

References

  1. K. Miyamoto, S. Narita, Y. Masumoto, T. Hashishin, M. Kimura, M. Ochiai, and M. Uchiyama, "Room-Temperature Chemical Synthesis of C2", 2019. http://dx.doi.org/10.26434/chemrxiv.8009633.v1

An Ambimodal Trispericyclic Transition State: the effect of solvation?

May 2nd, 2019

Ken Houk’s group has recently published this study of cycloaddition reactions, using a combination of classical transition state location followed by molecular dynamics trajectory calculations,[1] and to which Steve Bachrach’s blog alerted me. The reaction struck me as being quite polar (with cyano groups) and so I took a look at the article to see what both the original[2] experimental conditions were and how the new simulations compared. The reaction itself is shown below.

Read the rest of this entry »

References

  1. X. Xue, C.S. Jamieson, M. Garcia-Borràs, X. Dong, Z. Yang, and K.N. Houk, "Ambimodal Trispericyclic Transition State and Dynamic Control of Periselectivity", Journal of the American Chemical Society, vol. 141, pp. 1217-1221, 2019. http://dx.doi.org/10.1021/jacs.8b12674
  2. C.Y. Liu, and S.T. Ding, "Cycloadditions of electron-deficient 8,8-disubstituted heptafulvenes to electron-rich 6,6-disubstituted fulvenes", The Journal of Organic Chemistry, vol. 57, pp. 4539-4544, 1992. http://dx.doi.org/10.1021/jo00042a039