Quantum crystallography: The structure and C-C bond length alternation of [18]-annulene.

February 13th, 2026

In my story about one of the molecules of the year, cyclo[48]carbon,[1] I noted that the DFT method used in the literature to model the C-C bond length alternation around the ring (OX B3LYP30[2]) had been re-calibrated against a remeasured crystal structure[3] of C18H18 or [18]-annulene (below) in order to reproduce the observed values for this molecule. Read the rest of this entry »

References

  1. Y. Gao, P. Gupta, I. Rončević, C. Mycroft, P.J. Gates, A.W. Parker, and H.L. Anderson, "Solution-phase stabilization of a cyclocarbon by catenane formation", Science, vol. 389, pp. 708-710, 2025. https://doi.org/10.1126/science.ady6054
  2. M. Vitek, J. Deng, H.L. Anderson, and I. Rončević, "Global Aromatic Ring Currents in Neutral Porphyrin Nanobelts", ACS Nano, vol. 19, pp. 1405-1411, 2024. https://doi.org/10.1021/acsnano.4c14100
  3. Stawski, Wojciech., Zhu, Yikun., Rončević, Igor., Wei, Zheng., Petrukhina, Marina A.., and Anderson, Harry L.., "CCDC 2293565: Experimental Crystal Structure Determination", 2024. https://doi.org/10.5517/ccdc.csd.cc2gzmz2

Molecules of the year 2025: Benzene-busting inverted sandwich.

January 1st, 2026

Sandwich compounds are the colloquial term used for molecules where a metal atom such as an iron dication is “sandwiched” between two carbon-based rings as ligands, most commonly cyclopentadienyl anion (the “bread”) as in e.g. Ferrocene – a molecule first discovered in 1951. An “inverted” sandwich is where the carbon ring is itself sandwiched between two metal ions and one such was reported this year [1] containing benzene in the middle with scandium as the metal. The novelty of the subsequent four-electron reduction of the benzene “filler” and its ring opening to a linear hexadiene unit resulted in this being selected as one “molecule of the year” for 2025.

Read the rest of this entry »

References

  1. L. Zhang, Z. Jiang, C. Zhang, K. Cheng, S. Li, Y. Gao, X. Wang, and J. Chu, "Room Temperature Ring Opening of Benzene by Four-Electron Reduction and Carbonylation", Journal of the American Chemical Society, vol. 147, pp. 25017-25023, 2025. https://doi.org/10.1021/jacs.5c08414

Molecules of the year 2025: Cyclo[48]carbon and others – the onset of bond alternation and the Raman Activity Spectrum.

December 29th, 2025

The annual “Molecules of the Year” selections are available for the year 2025. A theme was elemental allotropes and one such was carbon in the form of C48 stabilised by formation of a catenane C48.M3 (M = red ligand below)[1] – it was not possible however to crystallise C48.M3. When “unmasked” by removal of the M ligand, the true allotrope C48 had a solution half-life of about 1 hour at 20°C. This follows the reports from 2019 onwards of a series of smaller cyclo[n]carbon allotropes, (n=6,10,12,13,14,16,18,20,26)[2],[3] which were only characterised on a solid surface and not in solution.

Read the rest of this entry »

References

  1. Y. Gao, P. Gupta, I. Rončević, C. Mycroft, P.J. Gates, A.W. Parker, and H.L. Anderson, "Solution-phase stabilization of a cyclocarbon by catenane formation", Science, vol. 389, pp. 708-710, 2025. https://doi.org/10.1126/science.ady6054
  2. K. Kaiser, L.M. Scriven, F. Schulz, P. Gawel, L. Gross, and H.L. Anderson, "An sp-hybridized molecular carbon allotrope, cyclo[18]carbon", Science, vol. 365, pp. 1299-1301, 2019. https://doi.org/10.1126/science.aay1914
  3. H. Rzepa, "Cyclo[18]carbon: The Kekulé vibration calculated and hence a mystery!", 2019. https://doi.org/10.59350/jdy16-7rv58

Mechanism of reaction between titanocene pentasulfide and sulfenyl chloride: The effect of continuum solvation on the energy surface.

December 16th, 2025

An investigation of the kinetics of the reaction between titanocene pentasulfide and sulfenyl chloride[1] leading to the formation of the S7 allotrope of sulfur was accompanied by supporting DFT calculations which led to the conclusion that of five possible mechanisms for the reaction, the most probable corresponded to a variant of the concerted σ-bond metathesis (Scheme 1, Mechanism IV, R = Cl). Here we take a closer look at the DFT predictions from the point of view of the impact of continuum solvation on the calculated mechanism.

Read the rest of this entry »

References

  1. P.H. Helou de Oliveira, P.J. Boaler, G. Hua, N.M. West, R.T. Hembre, J.M. Penney, M.H. Al-Afyouni, J.D. Woollins, A. García-Domínguez, and G.C. Lloyd-Jones, "Kinetics of sulfur-transfer from titanocene (poly)sulfides to sulfenyl chlorides: rapid metal-assisted concerted substitution", Chemical Science, vol. 15, pp. 11875-11883, 2024. https://doi.org/10.1039/d4sc02737j

Reinvestigating the reported transition state structure of a concerted triple H-tunneling mechanism.

November 21st, 2025

Substituting a deuterium isotope (2H) for a normal protium hydrogen isotope can slow the rate of a chemical reaction if this atom is involved in the reaction mode. The magnitude of the effect, referred to as a kinetic isotope effect or KIE is normally 2-7, but higher values of 20 or even more are sometimes observed due to a phenomenon known as proton tunnelling. So a recent report[1] of a 1H/2H of ~2440 for the following palladium catalysed reaction caught my eye:

Read the rest of this entry »

References

  1. Q. Wu, P. Liu, X. Zhang, C. Fan, Z. Chen, R. Qin, Y.Q. Gao, Y. Zhao, and N. Zheng, "Catalytic Hydrogenation Dominated by Concerted Hydrogen Tunneling at Room Temperature", ACS Central Science, vol. 11, pp. 2180-2187, 2025. https://doi.org/10.1021/acscentsci.5c00943

Short B-H…H-O Interactions in crystal structures – a short DFT Exploration using B3LYP+D4 and r2scan-3c

October 27th, 2025

In the previous post,[1] I was commenting that the transition state for borohydride reduction of a ketone contained some close contacts between the hydrogen of the borohydride and the hydrogen of water. A systematic search of the CSD reveals a modest number of such contacts have been observed in crystal structures (Table).  Since it is always good to have a reality check for constructed transition states, here I take a look at some of compounds showing the closest H…H contacts in the experimental database of structures.

Read the rest of this entry »

References

  1. H. Rzepa, "The mechanism of borohydride reductions. Part 2: 4-t-butyl-cyclohexanone – Dispersion induced stereochemistry.", 2025. https://doi.org/10.59350/x5k75-t2m40

The mechanism of borohydride reductions. Part 2: 4-t-butyl-cyclohexanone – Dispersion induced stereochemistry.

October 21st, 2025

Part one of this topic was posted more than ten years ago.[1] I clearly forgot about it, so belatedly, here is part 2 – dealing with the stereochemistry of the reduction of tert-butyl-cyclohexanone by borohydride in water. The known stereochemistry is nicely summarised in this article, along with an extensive  history of possible explanations of the reasons for the stereochemical preference.[2] Put simply, the hydride nucleophile attacks the carbonyl from an axial rather than equation direction with a ratio of 10:1 (ΔΔG 1.37 kcal/mol). So does the model I previously proposed[1] support this and give any indication of why the stereochemistry is axial?

Read the rest of this entry »

References

  1. H. Rzepa, "Part 1: ethanal.", 2015. https://doi.org/10.59350/aqrgh-jw887
  2. R. Kobetić, V. Petrović-Peroković, V. Ključarić, B. Juršić, and D.E. Sunko, "Selective Reduction of Cyclohexanones with NaBH<sub>4</sub> in β-Cyclodextrin, PEG-400, and Micelles", Supramolecular Chemistry, vol. 20, pp. 379-385, 2008. https://doi.org/10.1080/10610270701268815

Alternative reactions of the N≡N “triple bond” in a nitric oxide dimer: forming the trimer N3O3.

September 3rd, 2025

In the previous post[1] I mooted the possibility that a high energy form of the dimer of nitric oxide 1 might nonetheless be able to be detected using suitable traps (such as hydrogenation or cycloaddition). However, an interesting alternative is that this species could be trapped by nitric oxide itself. According to [2] in an article entitled “Decomposition of nitric oxide at elevated pressures” the rate of this termolecular reaction 3NO → N2O + NO2 are said to obey third order kinetics. One plausible mechanism for this process is shown below.

Read the rest of this entry »

References

  1. H. Rzepa, "Hydrogenating the even more mysterious N≡N triple bond in a nitric oxide dimer.", 2025. https://doi.org/10.59350/rzepa.29626
  2. T. Melia, "Decomposition of nitric oxide at elevated pressures", Journal of Inorganic and Nuclear Chemistry, vol. 27, pp. 95-98, 1965. https://doi.org/10.1016/0022-1902(65)80196-8

Hydrogenating the even more mysterious N≡N triple bond in a nitric oxide dimer.

August 25th, 2025

Previously[1] I looked at some of the properties of the mysterious dimer of nitric oxide  1 – not the known weak dimer but a higher energy form with a “triple” N≡N bond. This valence bond isomer of the weak dimer was some 24 kcal/mol higher in free energy than the two nitric oxide molecules it would be formed from. An energy decomposition analysis (NEDA) of 1 revealed an interaction energy[2] of +4.5 kcal/mol for the two radical fragments, compared to eg -27 kcal/mol for the equivalent analysis of the N=N double bond in nitrosobenzene dimer[3] So here I take a look at another property of N≡N bonds via their hydrogenation energy (Scheme), mindful that the dinitrogen molecule requires forcing conditions to hydrogenate, in part because of the unfavourable entropy terms (See Wiki and also here for a calculation of ΔG298).

Read the rest of this entry »

References

  1. H. Rzepa, "The even more mysterious N≡N triple bond in a nitric oxide dimer.", 2025. https://doi.org/10.59350/rzepa.29429
  2. H. Rzepa, "N2O2 as strong dimer? bent NEDA 0 1 0 2 0 -2 Total Interaction (E) : 4.520 Wiberg NN bond index 1.0072 NN stretch 2604 cm-1", 2025. https://doi.org/10.14469/hpc/15468
  3. H. Rzepa, "Nitrosobenzene dimer NEDA=2, 0,1 0,1 0,1 Total Interaction (E) : -27.564", 2025. https://doi.org/10.14469/hpc/15444

The spin-offs from adding citations to blog posts.

August 19th, 2025

I started adding citations to my blog posts around 2012 using the Kcite plugin. Rogue Scholar is a service that monitors registered blog sources and adds all sorts of value to the original post, including identifying such citations and creating a list of them.

Read the rest of this entry »