Archive for the ‘Interesting chemistry’ Category

3-Methyl-5-phenylpyrazole: a crystallographic enigma?

Thursday, May 19th, 2022

Previously, I explored the unusual structure of a molecule with a hydrogen bonded interaction between a phenol and a pyridine. The crystal structure name was RAKQOJ and it had been reported as having almost symmetrical N…H…O hydrogen bonds. This feature had been determined using neutron diffraction crystallography, which is thought very reliable at determining proton positions. Another compound with these characteristics is 3-methyl-5-phenylpyrazole or MEPHPY01.[1] Here the neutron study showed it to apparently have the structure represented below, where the solid N-H lines indicate a proton equidistant between two nitrogens.



  1. F.H. Moore, A.H. White, and A.C. Willis, "3-Methyl-5-phenylpyrazole: a neutron diffraction study", Journal of the Chemical Society, Perkin Transactions 2, pp. 1068, 1975.

C2N2: a 10-electron four-atom molecule displaying both Hückel 4n+2 and Baird 4n selection rules for ring aromaticity.

Thursday, April 7th, 2022

The previous examples of four atom systems displaying two layers of aromaticity illustrated how 4 (B4), 8 (C4) and 12 (N4) valence electrons were partitioned into 4n+2 manifolds (respectively 2+2, 6+2 and 6+6). The triplet state molecule B2C2 with 6 electrons partitioned into 2π and 4σ electrons, with the latter following Baird’s aromaticity rule.[1],[2]. Now for the final missing entry; as a triplet C2N2 has 10 electrons, which now partition into 4 + 6. But would that be 4π + 6σ or 4σ + 6π? Well, in a way neither! Read on.



  1. N.C. Baird, "Quantum organic photochemistry. II. Resonance and aromaticity in the lowest 3.pi..pi.* state of cyclic hydrocarbons", Journal of the American Chemical Society, vol. 94, pp. 4941-4948, 1972.
  2. M. Rosenberg, C. Dahlstrand, K. Kilså, and H. Ottosson, "Excited State Aromaticity and Antiaromaticity: Opportunities for Photophysical and Photochemical Rationalizations", Chemical Reviews, vol. 114, pp. 5379-5425, 2014.

Sir Geoffrey Wilkinson: An anniversary celebration. 23 March, 2022, Burlington House, London.

Thursday, March 24th, 2022

The meeting covered the scientific life of Professor Sir Geoffrey Wilkinson from the perspective of collaborators, friends and family and celebrated three anniversaries, the centenary of his birth (2021), the half-century anniversary of the Nobel prize (2023) and 70 years almost to the day (1 April) since the publication of the seminal article on Ferrocene (2022).[1]



  1. G. Wilkinson, M. Rosenblum, M.C. Whiting, and R.B. Woodward, "THE STRUCTURE OF IRON BIS-CYCLOPENTADIENYL", Journal of the American Chemical Society, vol. 74, pp. 2125-2126, 1952.

A four-atom molecule exhibiting simultaneous compliance with Hückel 4n+2 and Baird 4n selection rules for ring aromaticity.

Tuesday, March 22nd, 2022

Normally, aromaticity is qualitatively assessed using an electron counting rule for cyclic conjugated rings. The best known is the Hückel 4n+2 rule (n=0,1, etc) for inferring diatropic aromatic ring currents in singlet-state π-conjugated cyclic molecules and a counter 4n rule which infers an antiaromatic paratropic ring current for the system. Some complex rings can sustain both types of ring currents in concentric rings or regions within the molecule, i.e. both diatropic and paratropic regions. Open shell (triplet state) molecules have their own rule; this time the molecule has a diatropic ring current if it follows a 4n rule, often called Baird’s rule. But has a molecule which simultaneously follows both Hückel’s AND Baird’s rule ever been suggested? Well, here is one, as indeed I promised in the previous post.


More aromatic species with four atoms. B4 and N4.

Saturday, March 19th, 2022

I discussed in the previous post the small molecule C4 and how of the sixteen valence electrons, eight were left over after forming C-C σ-bonds which partitioned into six σ and two π. So now to consider B4. This has four electrons less, and now the partitioning is two σ and two π (CCSD(T)/Def2-TZVPPD calculation, FAIR DOI: 10.14469/hpc/10157). Again both these sets fit the Hückel 4n+2 rule (n=0).

Molecule of the year 2021: Infinitene.

Thursday, December 16th, 2021

The annual “molecule of the year” results for 2021 are now available … and the winner is Infinitene.[1],[2] This is a benzocirculene in the form of a figure eight loop (the infinity symbol), a shape which is also called a lemniscate [3] after the mathematical (2D) function due to Bernoulli. The most common class of molecule which exhibits this (well known) motif are hexaphyrins (hexaporphyrins; porphyrin is a tetraphyrin)[4],[5],[6], many of which exhibit lemniscular topology as determined from a crystal structure. Straightforward annulenes have also been noted to display this[7] (as first suggested here for a [14]annulene[8]) and other molecules show higher-order Möbius forms such as trefoil knots.[9],[10] This new example uses twelve benzo groups instead of six porphyrin units to construct the lemniscate. So the motif is not new, but this is the first time it has been constructed purely from benzene rings. (more…)


  1. K. Itami, M. Krzeszewski, and H. Ito, "Infinitene: A Helically Twisted Figure-Eight [12]Circulene Topoisomer", 2021.
  2. M. Krzeszewski, H. Ito, and K. Itami, "Infinitene: A Helically Twisted Figure-Eight [12]Circulene Topoisomer", Journal of the American Chemical Society, vol. 144, pp. 862-871, 2021.
  3. C.S.M. Allan, and H.S. Rzepa, "Chiral Aromaticities. AIM and ELF Critical Point and NICS Magnetic Analyses of Möbius-Type Aromaticity and Homoaromaticity in Lemniscular Annulenes and Hexaphyrins", The Journal of Organic Chemistry, vol. 73, pp. 6615-6622, 2008.
  4. H. Rath, J. Sankar, V. PrabhuRaja, T.K. ChandrashekarPresent address: The D, B.S. Joshi, and R. Roy, "Figure-eight aromatic core-modified octaphyrins with six meso links: syntheses and structural characterization", Chemical Communications, pp. 3343, 2005.
  5. H. Rath, J. Sankar, V. PrabhuRaja, T.K. Chandrashekar, and B.S. Joshi, "Aromatic Core-Modified Twisted Heptaphyrins[]:  Syntheses and Structural Characterization", Organic Letters, vol. 7, pp. 5445-5448, 2005.
  6. S. Shimizu, N. Aratani, and A. Osuka, "meso-Trifluoromethyl-Substituted Expanded Porphyrins", Chemistry - A European Journal, vol. 12, pp. 4909-4918, 2006.
  7. T. Perera, F.R. Fronczek, and S.F. Watkins, "2,9,16,23-Tetrakis(1-methylethyl)-5,6,11,12,13,14,19,20,25,26,27,28-dodecadehydrotetrabenzo[a,e,k,o]cycloeicosene", Acta Crystallographica Section E Structure Reports Online, vol. 67, pp. o3493-o3493, 2011.
  8. H.S. Rzepa, "A Double-Twist Möbius-Aromatic Conformation of [14]Annulene", Organic Letters, vol. 7, pp. 4637-4639, 2005.
  9. G.R. Schaller, F. Topić, K. Rissanen, Y. Okamoto, J. Shen, and R. Herges, "Design and synthesis of the first triply twisted Möbius annulene", Nature Chemistry, vol. 6, pp. 608-613, 2014.
  10. S.M. Bachrach, and H.S. Rzepa, "Cycloparaphenylene Möbius trefoils", Chemical Communications, vol. 56, pp. 13567-13570, 2020.

Protein-Biotin complexes. Crystal structure mining.

Sunday, December 12th, 2021

In the previous post, I showed some of the diverse “non-classical”interactions between Biotin and a protein where it binds very strongly. Here I take a look at two of these interactions to discover how common they are in small molecule structures.


Biotin’s biggest lesson is the importance of nonclassical H-bonds in protein−ligand complexes.

Saturday, November 27th, 2021

The title comes from the abstract of an article[1] analysing why Biotin (vitamin B7) is such a strong and effective binder to proteins, with a free energy of (non-covalent) binding approaching 21 kcal/mol. The author argues that an accumulation of both CH-π and CH-O together with more classical hydrogen bonds and augmented by a sulfur centered hydrogen bond, oxyanion holes and water solvation, accounts for this large binding energy.



  1. D.B. McConnell, "Biotin’s Lessons in Drug Design", Journal of Medicinal Chemistry, vol. 64, pp. 16319-16327, 2021.

First came Molnupiravir – now there is Paxlovid as a SARS-CoV-2 protease inhibitor. An NCI analysis of the ligand.

Saturday, November 13th, 2021

Earlier this year, Molnupiravir hit the headlines as a promising antiviral drug. This is now followed by Paxlovid, which is the first small molecule to be aimed by design at the SAR-CoV-2 protein and which is reported as reducing greatly the risk of hospitalization or death when given within three days of symptoms appearing in high risk patients.


Herapathite: an example of (double?) serendipity.

Thursday, October 14th, 2021

On October 13, 2021, the historical group of the Royal Society of Chemistry organised a symposium celebrating ~150 years of the history of (molecular) chirality. We met for the first time in person for more than 18 months and were treated to a splendid and diverse program about the subject. The first speaker was Professor John Steeds from Bristol, talking about the early history of light and the discovery of its polarisation. When a slide was shown about herapathite[1] my “antennae” started vibrating. This is a crystalline substance made by combining elemental iodine with quinine in acidic conditions and was first discovered by William Herapath as long ago as 1852[2] in unusual circumstances. Now to the serendipity!



  1. B. Kahr, J. Freudenthal, S. Phillips, and W. Kaminsky, "Herapathite", Science, vol. 324, pp. 1407-1407, 2009.
  2. W.B. Herapath, "XXVI. On the optical properties of a newly-discovered salt of quinine, which crystalline substance possesses the power of polarizing a ray of light, like tourmaline, and at certain angles of rotation of depolarizing it, like selenite", The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, vol. 3, pp. 161-173, 1852.