I posed10.59350/rncje-xe063 this question back in 2010: "(Almost) 100 years of Lewis10.1021/ja02261a002 structures: are they still fit for purpose?". I was reminded of this when I came across this relatively recent article10.3390/molecules19021956 describing the structures of three binary sulfur-nitrogen anions, as shown in Figure 1 of their article. These are reproduced below (Scheme 1) along with an additional one reported separately.10.1039/C39780000642…

Metalla-aromatics have been defined as metallacycles that are derived from the formal replacement of a carbon atom in the framework of an organic aromatic ring with a metal fragment.10.1021/acs.chemrev.0c00392. Here I explore whether this simple definition can be broadened to sulfur-nitrogen rings which contain few10.1039/C39850000398,10.1039/c39840000055 if indeed any10.1039/C39910000942,10.1002/cber.19951280103,10.1016/0277-5387(96)00223-9,10.1142/12397 carbon atoms and which also happen to be planar aromatic molecules.

In the previous post10.59350/p8zwp-39q65 we described the orbital interactions involved in stabilising the formation of a Cp2TiS5 complex (figure 1 below, X=S) rather than a Cp2TiS4 complex when Cp2TiCl2 is treated with a mixture of polysulfide dianions - and how these interactions can be "tuned" by variation in the ring atoms. Figure 1. Bis-cyclopentadienyl titanium sulfides. We identified10.59350/p8zwp-39q65 one compound in which one of the Cp ligands itself is replaced by a hindered phenyoxy group (

A recently published article addresses10.1039/D6DT01849A the long standing problem of why transition metals complexes such as e.g. Cp2TiCl2 in the presence of solutions of polysulfide dianions containing sulfur chains of various lengths, can react to form sulfur ring complexes of a specific size, depending on the metal. Thus when the early transition metal is Ti (Cp = cyclopentadienyl) it forms only the six membered ring shown below (X=S), with none of the five-membered/four-sulfur ring present.

I have in the past (around 2012 to be specific) taken an interest in a particular type of sigmatropic pericyclic reaction called the semibullvalene rearrangement.10.59350/cq2a3-g2g35,10.59350/585c3-dpy86,10.59350/8nkna-ycy23. This system can apparently exhibit very long C-C bonds in the region of 2.1Å, in which form it would be called a "frozen" transition state, also referred to a bis-homoaromatic molecule, which in this form is NOT regarded as a sigmatropic pericyclic transition state.

(Some) chemists have a strange fascination with bonds between two specified atoms - more exactly how short or how long can such a bond get? I asked a slight different question10.59350/rzepa.29383 of a molecule known as nitrosobenzene dimer, noting that both nitrogens were both connected to each other and carried a (formal) positive charge; one might naively imagine that the coulomb repulsion between two positive atoms might result in a repulsion which would greatly lengthen the bond between them (it does not, but it does weaken it).

Metadata is an essential way of enabling the discoverability and impact of scholarly resources such as (research) data and associated objects. It must adhere to a precisely described schema describing its properties,10.14454/qdd3-ps68 and such a conformant metadata record is an mandatory component of a (research) data repository. Access to the record is by resolving the DOI (Digital object identifier) for any repository item, as for example:

In the previous post,10.59350/jhsbq-sfs70 I noted the photochemical isomerisation of a pyrimidone into what is called the bicyclic Dewar form, being part of a solar energy storage system.10.1126/science.aec6413 A colleague (thanks Alan!) has recollected a very similar example dating from 196510.1039/C19650000468 in which a similar molecule known as a diazepinone 72 (scheme below) is converted by light into a Dewar form…

MOST is a chemical method of converting photonic or light energy into storable thermal energy which can be released on demand. A recent breakthrough in such methods has been reported10.1126/science.aec6413 in which a pyrimidone molecule is efficiently converted by 310nm light into the isomeric Dewar pyrimidone. This molecule is thermally stable, but when protonated, rapidly releases thermal (enthalpic) energy in converting down to protonated pyrimidone - the energy release is sufficiently rapid that it can boil water and reaching energy storage levels previously inaccessible to MOST systems.

A little while back, I wrote about anomeric-like effects in the sulfur ring S7.10.59350/rzepa.28407 I had started that exploration by retrieving the crystal structure from the ICSD (Inorganic crystal structure database) and then optimising these coordinates using a DFT method (MN15L/Def2-TZVPP to be precise). In demonstrating this effect to a student, I decided to create an initial guess for the molecule coordinates not from the crystal structure but by drawing and then minimising using a simple molecular mechanics force field - and only then subjecting it to DFT re-optimisation.10.14469/hpc/15924 It turns out the result was quite surprising in one respect and so here I tell the rest of the story.

The recent report10.1126/science.aea3321 of what is termed a "half-Möbius" molecule is generating a lot of excitement. It was generated as part of a project to make odd-numbered cyclocarbons on STM (scanning tunnelling microscope) surfaces. I had discussed even-numbered cyclocarbons in another post10.59350/g4309-gv10910.1126/science.aea3321 they were focussing on C13 and a precursor to this was to be C13Cl2. As part of the microscopy, they noticed this latter species was asymmetric (chiral) and so started the story of a "half-Möbius" molecule (molecules with twists in their topology are of course chiral).

A few posts back, I contemplated the curly arrows appropriate for the formation of nitrosobenzene dimer from nitrosobenzene, 10.59350/rzepa.28849 and commented on the odd nature of the N=N double bond formed in this process.10.59350/rzepa.29383. Odd, because the valence bond representation of this dimer (1 below10.1021/ja00827a021) has two formally positive adjacent nitrogen atoms. An energy decomposition analysis (NEDA10.1021/acs.organomet.5b00429) of species…

In my story about one of the molecules of the year, cyclocarbon,10.1126/science.ady6054 I noted that the DFT method used in the literature to model the C-C bond length alternation around the ring (OX B3LYP3010.1021/acsnano.4c14100) had been re-calibrated against a remeasured crystal structure10.5517/ccdc.csd.cc2gzmz2 of C18H18 or -annulene (below) in order to reproduce the observed values for this molecule. -annulene A noteworthy aspect of this structure is the six hydrogen atoms pointing into the centre of the ring, which come into very close contact with each other.

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 10.1021/jacs.5c08414 containing benzene in the middle with scandium as the metal.

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)10.1126/science.ady6054 - 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.

An investigation of the kinetics of the reaction between titanocene pentasulfide and sulfenyl chloride10.1039/d4sc02737j 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).

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.

In the previous post,10.59350/x5k75-t2m40 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.

Part one of this topic was posted more than ten years ago.10.59350/aqrgh-jw887[.cite] 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 explanation of the reasons for the stereochemical preference.10.1080/10610270701268815 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).

In the previous post10.59350/rzepa.29626 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 10.1016/0022-1902(65)80196-8 in an article entitled "Decomposition of nitric oxide at elevated pressures…

Previously10.59350/rzepa.29429 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 energy10.14469/hpc/15468 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 dimer10.14469/hpc/15444 So here I take a look at another property of N≡N bonds…

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. I show the results for the previous blog10.59350/rzepa.29523 here. Martin Fenner has just added some interesting new features10.53731/yjq4w-5yr32 which I thought would be useful to share with you here.

Two years ago, I posted on the topic "Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry (IJC)".10.59350/xqerh-wam97  The IJC had been founded in 1998,10.1080/00987913.2000.10764578  in part at least to "re-invent" the scholarly journal by elevating research data to being a more integrated part of the overall article, rather than as the previously conventional addendum of SI (Supporting Information)‡.

Previously, I pondered about the strange N=N double bond in nitrosobenzene dimer10.59350/rzepa.29383 as a follow up to commenting on the curly arrow mechanism of the dimerisation.10.59350/rzepa.28849. By the same curly arrow method, one can produce the below, showing how the simpler nitric oxide radical could potentially dimerise to a species with a N≡N triple bond!  This involves a total of six electrons entering the N-N region, and hence raises the question of whether these all move in a single concerted/synchronous bond forming reaction, or whether they might go in (asynchronous) stages.

In the previous post,10.59350/rzepa.29383 I introduced the N=N double bond in nitrosobenzene dimer, arguing that even though it was a formal double bond, its bond dissociation energy made it nonetheless a very weak double bond! This was backed up by a technique known as energy decomposition analysis or EDA. Here I use a variant of this method  known as  NEDA to look at some other strained alkenes, including the famously non-existent tetra t-Butyl ethene.

In an earlier blog, I discussed10.59350/rzepa.28849 the curly arrows associated with the known dimerisation of nitrosobenzene, and how the N=N double bond (shown in red below) forms in a single concerted process. One of the properties of this molecule is that the equilibrium between the monomer and dimer can be detected10.1002/mrc.1260251118, with significant concentrations of the dimer observed below 10°C. This dimer can even be crystalised, with around 20 well defined crystal structures known for the dimeric structure in the current version of the  CSD crystal structure dataset.

In the previous post10.59350/rzepa.28993 I followed up on an article published on the theme "Physical Organic Chemistry: Never Out of Style"10.1021/acs.joc.5c00426 in which Paul Rablen presented the case that the amount of o (ortho) product in electrophilic substitution of a phenyl ring bearing an EWG (electron withdrawing group) is often large enough to merit changing the long held rule-of-thumb for EWGs from being just meta directors into being…

The title of this post comes from an article published as a special virtual issue on the theme "Physical Organic Chemistry: Never Out of Style"10.1021/acs.joc.5c00426 There, Paul Rablen presents the case that the amount of o (ortho) product in electrophilic substitution of a phenyl ring bearing an EWG (electron withdrawing group) is often large enough to merit changing the long held rule-of-thumb for EWGs from being just meta directors into…

This is just a few insights  I have got from some of the talks I attended.  As usual, this does not represent a  NOT a report on the WATOC congress itself but  simply some aspects that caught my personal eye. Frank Neese talked about his Bubblepole approximation for large molecules.10.1021/acs.jpca.4c07415 And he was not kidding - large. Lets say a DFT calculation at the Def2-TZVPP basis set level (often the level used in this blog).

The WATOC congresses occur every three years and in 2025 the main event  starts tomorrow in Oslo, Norway, the 13th in the series which started in 1987.  The day before something new - a session just for early career researchers or "Young WATOC". As an "old" WATOCer, I dropped into the opening session and was delighted to find a packed auditorium, with literally standing room only comprising mostly young researchers in their 20s.

I am in the process of revising my annual lecture to first year university students on the topic of "curly arrows". I like to start my story in 1924, when Robert Robinson published the very first examplegg9g as an illustration of why nitrosobenzene undergoes electrophilic bromination in the para position of the benzene ring. I follow this up by showing how "data mining" can be used to see if this supports his assertion.

Tom recently emailed me this question: Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once? Intrigued, I first set out to find out how many substances, as Chemical Abstracts refers to the them, there were as of 5 June, 2025. There is a static estimate here…

I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems  that I had described had an odd number of atoms and that I had not looked any even numbered rings. Thus hexasulfur is a smaller (known) ring version of S8, by far the best known allotrope of this element of course.

Last year I reminisced on the occasion of the 40th Anniversary of the Macintosh computer.10.59350/f11dr-93t29 Four decades of advances in technology now mean I can do a fair amount of computational quantum modelling on a recent Mac (one from 2022 with M1 processor),  and since then they have only got even (~2 or 3 times) faster with the M4 processor. Many of the calculations done for these blogs have included at least one or two that were done on the Mac.

In this series of posts about the electronic effects in small sulfur rings10.59350/rzepa.28615 I have explored increasingly large induced geometric effects. Here is the largest so far, for the compound S7I1+10.1021/ic50225a048 The calculated geometry10.14469/hpc/15236 is shown below, with the crystallographic values in parentheses - the two matching very well. The calculated NBO7 stereoelectronic analysis identifies an especially strong donor (S7) interaction with an acceptor S4-S7, the E(2) energy being 36.9 kcal/mol.

The two previous  posts10.59350/rzepa.28515,10.59350/rzepa.28407 on the topic of anomeric effects in 7-membered sulfur rings illustrated how orbital interactions between the lone pairs in the molecules and S-S bonds produced widely varying S-S bond lengths in the molecules, some shorter than normal and some longer. Here we extend this to an unknown molecule shown below. The usual  MN15L/Def2-TZVPP calculation10.14469/hpc/15235 gives the calculated geometry shown below.

The monosulfoxide of cyclo-heptasulfur was reported along with cycloheptasulfur itself in 1977,10.1002/anie.197707161 along with the remarks that "The δ modification of S7 contains bonds of widely differing length: this has never been observed before in an unsubstituted molecule. and "the same effect having also been observed in other sulfur rings (S8O, S7I1+ and S7O)." Here I take a look at the last of these other molecules, the monosulfoxide of S7, as a follow up to the commentary on S7 itself.10.59350/rzepa.28407…

Way back in 1977, the crystal structure of the sulfur ring S7 was reported.10.1002/anie.197707151 The authors noted that "The δ modification of S7 contains bonds of widely differing length: this has never been observed before in an unsubstituted molecule." No explanation was offered, although they note that similar effects have been observed in S8O, S7I+ and S7O. The S7 molecule was yesterday brought to my attention (thanks Derek!) over a pub lunch and in the time honoured manner of scientists, sketched out on a napkin (with a pen obtained from the waitress!).

Back in early 2012, I pondered about the relationships between a science-based blog post and a science-based journal article10.59350/3pbz1-vcd67. This was in part induced by my discovering a blog plugin called Kcite, which allow a journal articles to be appended to the blog in the form of a numbered reference list. The only required input for Kcite was the DOI of the article (as you can see earlier in this paragraph).

X-ray crystallography is the technique of using the diffraction of x-rays by the electrons in a molecule to determine the positions of all the atoms in that molecule. Quantum theory teaches us that the electrons are to be found in shells around the atomic nuclei. There are two broad types, the outermost shell (also called the valence shell) and all the inner or core shells.

Starting around 2016, journal publishers started including mandatory "Data Availability" statements as part of research articles; a typical (dated) example is linked here, including guidelines for how to cite the data itself. I wrote about these aspects last year in a blog post for the RSC journal Digital Discovery10.26434/chemrxiv-2024-dz2dv and here I follow up with more news. In a recently published article about Direct Amidation Reactions10.1039/D4SC07744J, the following version of a data availability statement appears: …

Derek Lowe tells the story of "carbyne", a potential further allotrope of carbon, comprising linear chains of carbon atoms, C-C≡C-C≡C-C. Whether such a molecule can exist on its own has long been the the topic of speculation. Now a report has appeared of a "pseudocarbyne", stabilised by gold atoms.10.1038/s41598-024-80359-5 The now thankfully almost ubiquitous data availability statement includes the DOI: …

I can remember a time when journal articles carried selected data within their body as e.g. Tables, Figures or Experimental procedures, with the rest consigned to a box of paper deposited (for UK jour...

Chemists now use the term “curly arrows” as a language to describe the electronic rearrangements that occur when a (predominately organic) molecule transforms to another – the so called chemical react...

In the previous post, I looked[cite]10.59350/xp5a3-zsa24[/cite] at the recently reported[cite]10.1021/ja02261a002[/cite] hexa-arylethane containing a carbon-carbon one-electron bond, its structure hav...

More than 100 years ago, before the quantum mechanical treatment of molecules had been formulated, G. N. Lewis proposed[cite]10.1021/ja02261a002[/cite] a simple model for chemical bonding that is stil...

Michael in a comment here on the mechanism of the Masamune-Bergman reaction notes that when it occurs as part of the Calicheamicin (an antibody-drug conjugate or ADC) version of this mechanism, a pre-...

The idea of so-called FAIR (Findable, Accessible, Interoperable and Reusable) data is that each object has an associated metadata record which serves to enable the four aspects of FAIR. Each such reco...

Each year C&E News publishes a list of candidates for the Molecule of the Year. For 2024 the list is (in order of votes cast for each) Mirror-image cyclodextrin [cite]10.1038/s44160-024-00495-8[/cite]...

This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box 10.1002/anie.202318829 Mirror-image cyclodextrin 10.1038/s44160-024-00495-8 Molecular shuttle in a box 10.1002/anie.202318829 Rule-bending strained alkene 10.1126/science.adq3519 First soluble promethium complex 10.1038/s41586-024-07267-6 Single-electron carbon-carbon bond 10.1038/s41586-024-07965-1 Hot MOF for capturing carbon10.1126/science.adk5697 The molecule shown below inside the cavity is coronene. A free energy barrier of ~13 kcal/mol was determined using NMR peak coalescence temperatures, and inferred to correspond to the energy required to move the coronene from one end of the cavity to the other.