Imperial College London

Henry Rzepa

Valence shell electron pair repulsion theory is a simple way of rationalising the shapes of many compounds in which a main group element is surrounded by ligands. ClF

 3

is a good illustration of this theory.

VSEPR Theory:   A closer look at chlorine trifluoride, ClF3.

Chemistry as the inspiration for art! The inspiration was the previous post. As for whether its art, you decide for yourself.

And now for something completely different: The art of molecular sculpture.

The Wikipedia page on hypervalent compounds reveals that the concept is almost as old as that of normally valent compounds.

Hypervalency: Is it real?

Lactide is a small molecule made from lactic acid, which is itself available in large quantities by harvesting plants rather than drilling for oil. Lactide can be turned into polymers with remarkable properties, which in turn degrade down easily back to lactic acid. A perfect bio-renewable material!

Bio-renewable green polymers:  Stereoinduction in poly(lactic acid)

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 reaction. It is also used to infer,

 via

valence bond or resonance theory, what the mechanistic implications of that reaction are.

The 100th Anniversary year of Curly Arrows.

A comment made on the previous post on the topic of hexa-coordinate carbon cited an article entitled “

 Observation of hypervalent CLi
 
 6
 
 by Knudsen-effusion mass spectrometry

“[cite]10.1038/355432a0[/cite] by Kudo as a amongst the earliest of evidence that such species can exist (in the gas phase). It was a spectacular vindication of the earlier theoretical

Is  CLi6 hypervalent?

I have been discussing some historical aspects of the absolute configuration of molecules and how it was connected to their optical rotations. The nomenclature for certain types of molecules such as sugars and less commonly amino acids includes the notation (+) to indicate that the specific optical rotation of the molecule has a positive (rather than a negative) value.

Sign inversions in optical rotation as a function of wavelength (ORD spectra)

Another post inspired by a comment on an earlier one; I had been discussing compounds of the type I.I

 n

(n=4,6) as possible candidates for hypervalency.

Hypervalent or not? A fluxional triselenide.

In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article[cite]10.1038/s41557-019-0398-3[/cite] on exploring the aromaticity of large 4n+2 cyclic rings. One of them had been induced into a “figure-eight” or lemniscular conformation, as shown below.

Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin.

In the previous two posts, a strategy for tuning the nature of the CS bond in the molecule HO-S≡C-H was developed, based largely on the lone pair of electrons identified on the carbon atom. By replacing the HO group by one with greater σ-electron withdrawing propensity, the stereo-electronic effect between the O-S bond and the carbon lone pair was enhanced, and in the process, the SC bond was strengthened.

The nature of the C≡S triple bond: part 3.

A previous post was triggered by Peter alerting me that interactive electronic supporting information (

 IESI

) we had submitted to a journal in 2005[cite]10.1021/ic0519988[/cite] appeared to be strangely missing from the article landing page. This set me off recollecting our journey, which had started around 1998, and to explore what the current state of these ancient

 IESI

s were in 2022.

Four stages in the evolution of interactive ESI as part of articles in chemistry journals.

Thus famously wrote Woodward and Hoffmann (WH) in their classic monograph about the conservation of orbital symmetry in pericyclic reactions.

Violations. There are none!

I occasionally spot an old blog that emerges, if only briefly, as “trending”. In this instance, only the second blog I ever wrote here, way back in 2009 as a follow up to this article.[cite]10.1021/ed084p1535[/cite] With something of that age, its always worth revisiting to see if any aspect needs updating or expanding, given the uptick in interest.

Trimerous pericyclic reactions.

Continuing an exploration of the mechanism of this reaction, an alternative new mechanism was suggested in 1989 (having been first submitted to the journal ten years earlier!).[cite]10.1002/jhet.5570260518[/cite] Here the key intermediate proposed is a thiirenium cation (labelled

 8

in the article) and labelled

 Int3

below.

The Willgerodt-Kindler Reaction: mechanistic reality check 2.

One of the most fascinating and important articles dealing with curly arrows I have seen is that by Klein and Knizia on the topic of C-H bond activations using an iron catalyst.[cite]10.1002/anie.201805511[/cite] These are so-called high spin systems with unpaired electrons and the mechanism of C-H activation involves both double headed (two electron) and fish-hook (single electron) movement.

Curly arrows in the 21st Century. Proton-coupled electron transfers.

My momentum of describing early attempts to use optical rotation to correlate absolute configuration of small molecules such as glyceraldehyde and lactic acid with their optical rotations has carried me to

 L-Malic acid

(below labelled as (

 S

)-Malic acid). The measured optical rotatory dispersion curve at low wavelengths is shown below (dashed line for Malic acid, solid line for Lactic acid). A sign inversion

L-Malic acid: An exercise in conformational analysis impacting upon optical rotatory dispersion (ORD).

In 2012, I wrote a story of the first ever reaction curly arrows, attributed to Robert Robinson in 1924. At the time there was a great rivalry between him and another UK chemist, Christopher Ingold, with the latter also asserting his claim for their use.

Early &#8220;curly&#8221; (reaction) arrows. Those of Ingold in 1926.

This editorial from Nature[cite]10.1038/d41586-023-01612-x[/cite] is a timely reminder of the importance of data.

&#8220;For chemists, the AI revolution has yet to happen&#8221;.

The recently reported synthesis[cite]10.1126/science.abq0516[/cite] of octafluorocubane established a sublimation point as 168.1–177.1°C (a melting point was not observed). In contrast, the heavier perfluoro-octane has an m.p. of -25°C. Why the difference?

Why does octafluorocubane have such a high sublimation point?

Chloroform, often in the deuterated form CDCl

 3

, is a very common solvent for NMR and other types of spectroscopy. Quantum mechanics is increasingly used to calculate such spectra to aid assignment and the solvent is here normally simulated as a continuum rather than by explicit inclusion of one or more chloroform molecules. But what are the features of the hydrogen bonds that form from chloroform to other acceptors?

Hydrogen bonding to chloroform.

In the previous post, I discussed the structure of the free base form of tetrodotoxin, often represented as originally suggested by Woodward[cite]10.1351/pac196409010049[/cite] below in an ionic form:      Quantum calculations suggested that this form was higher in energy than neutral forms devoid of the zwitterionic charge separation in a relatively non polar solvent such as chloroform. For this, a so-called continuum solvation model was used.

The Structure of Tetrodotoxin as a free base &#8211; with a better solvation model.

At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. I tell its story (or a part of it) here. But to start, try the following experiment. Find a Word document of .docx type on your hard drive Remove the .docx suffix and replace it with a .zip suffix. Expand as if it is an archive (it is!). A folder is created and this itself contains four further folders.

Research data: Managing spectroscopy-NMR.

Recollect this earlier post on the topic of the Baeyer-Villiger reaction. In 1999 natural abundance kinetic isotope effects were reported[cite]10.1021/ja992016z[/cite] and I set out to calculate the values predicted for a particular model constructed using Quantum mechanics. This comparison of measurement and calculation is nowadays a standard verification of both experiment and theory.

Reproducibility in science:  calculated kinetic isotope effects for the Baeyer-Villiger reaction.

I don’t normally write about the pharmaceutical industry, but I was intrigued by several posts by Derek Lowe (who does cover this area) on the topic of creating new drugs by deuterating existing ones. Thus he covered the first deuterated drug receiving FDA approval last year, having first reviewed the concept back in 2009. So when someone introduced me to

 sila-haloperidol

, I checked to see if Derek had written about it.

Silicon drug analogues.

This is another in the occasional series of “what a neat molecule”. In this case, more of a “what a neat idea”. The s-triazine below, when coordinated to eg ZnI

 2

, forms what is called a metal-organic-framework, or MOF.

X-ray analysis and absolute configuration determination using porous complexes.

Its a bit like a jigsaw puzzle in reverse, finding out to disassemble a chemical reaction into the pieces it is made from, and learning the rules that such reaction jigsaws follow. The following takes about 45-50 minutes to follow through with a group of students.

Secrets of a university tutor: dissection of a reaction mechanism.

In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.

 ‡

Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed. The original report in 2016[cite]10.1103/PhysRevLett.116.061102[/cite] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.

FAIR Research data: Gravitational waves as an example from the astrophysics community.

We tend to think of simple hydrocarbons as relatively inert and un-interesting molecules. However, a recent article[cite]10.1002/anie.201202894[/cite], which was in fact highlighted by Steve Bachrach on his blog , asks what “

 The Last Globally Stable Extended Alkane

” might be. In other words, at what stage does a straight-chain hydrocarbon fold back upon itself, and no significant population of the linear form remain?

The strangely attractive conformation of C17H36.

Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated

 “supporting information

” rather than the (often page limited) article itself. For example, this article[cite]10.1021/jacs.6b13229[/cite] has an SI which is paginated at 907;

Supporting information: chemical graveyard or invaluable resource for chemical structures.

Birch reduction of benzene itself results in 1,4-cyclohexadiene rather than the more stable (conjugated) 1,3-cyclohexadiene. Why is this?

The mechanism of the Birch reduction. Part 3: reduction of benzene

Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[cite]10.1039/C39920001323[/cite]. That was then. This is now.

More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.

Text books (is this a misnomer, much like “papers” are in journals?) in a higher-educational chemistry environment, I feel, are at a cross-roads. What happens next? Faced with the ever-increasing costs of course texts, the department where I teach introduced a book-bundle about five years ago. The bundle included all the recommended texts for an appreciable discount over individual purchase.

&#8220;Text&#8221; Books in a  (higher) education environment.

In the preceding post, I described a fascinating experiment and calculation by Bogle and Singleton, in which the trajectory distribution of molecules emerging from a

 single

transition state was used to rationalise the formation of two isomeric products

 2

and

 3.

In the present post, I explore possible consequences of including a sodium cation (X=Na

 +

below) in the

Dynamic effects in nucleophilic substitution at trigonal carbon (with Na+).

The Baldwin rules for ring closure follow the earlier ones by Bürgi and Dunitz in stating the preferred angles of nucleophilic (and electrophilic) attack in bond forming reactions, and are as famous for the interest in their exceptions as for their adherence. Both sets of rules fundamentally explore the geometry of the transition states involved in the reaction, as reflected in the activation free energies.

Transition state models for Baldwin&#8217;s rules of ring closure.

WATOC 2020 was just held in 2022 in Vancouver Canada, over one week. With many lectures held in parallel, it is not possible for one person to cover anything like the topics presented, so this is a personal view of some of those talks that I attended. As happens with many such events, common themes gradually emerge and here I highlight just two that struck me as important for the future of computational chemistry.

Personal Impressions from WATOC 2020 &#8211; Dispersion and non Born-Oppenheimer models.

The properties of electrons are studied by both chemists and physicists. At the boundaries of these two disciplines, sometimes interesting differences in interpretation emerge. One of the most controversial is that due to Bader (for a recent review, see DOI: 10.1021/jp102748b) a physicist who brought the mathematical rigor of electronic topology to bear upon molecules.

Are close H&#8230;H contacts bonds?

Organic chemistry has some no-go areas, where few molecules dare venture. One of them is described by a concept known as anti-aromaticity. Whereas aromatic molecules are favoured species, their anti-equivalent is avoided. I previously illustrated this (Hückel rule) with cyclopropenium anion.

Some fun with no-go areas of chemistry: cyclobutadiene.

The mechanism of ester hydrolysis is a staple of examination questions in organic chemistry. To get a good grade, one might have to reproduce something like the below. Here, I subject that answer to a reality check.

A sideways look at the mechanism of ester hydrolysis.

I mentioned in the last post that one can try to predict the outcome of electrophilic aromatic substitution by approximating the properties of the transition state from those of either the reactant or the (presumed Wheland) intermediate by invoking Hammond’s postulate[cite]10.1021/ja01607a027[/cite]. A third option is readily available nowadays; calculate the transition state directly. Here are the results of exploring this third variation.

Kinetic vs Thermodynamic control. Subversive thoughts for electrophilic substitution of Indole.

My last comment as appended to the previous post promised to analyse two so-called extended porphyrins for their topological descriptors. I start with the Cãlugãreanu/Fuller theorem

Linking numbers, and twist and writhe components for two extended porphyrins.

I noted in an earlier blog, a potential (if difficult) experimental test of the properties of the singlet state of dicarbon, C

 2

. Now, just a few days ago, a ChemRxiv article has been published suggesting another (probably much more realistic) test.[cite]10.26434/chemrxiv.11446224.v1[/cite] This looks at the so-called

 7

Σ open shell state of the molecule where three electrons from one σ and two π orbitals are excited

Comment on &#8220;Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces&#8221;: The 7Σ heptet excited states for related molecules.

One frequently has to confront the question: will a hydrogen bond form between a suitable donor (lone pair or π) and an acceptor? One of the factors to be taken into consideration for hydrogen bonds which are part of a cycle is the ring size. Here I explore one way of quantifying the effect for the series below, n=1-5 (4-8 membered rings).      I will use the NBO approach.

Hydrogen bond strength as a function of ring size.

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&amp;E News for my opinion.

ChemRxiv. Why?

Cavities promote reactions, and they can also trap the products of reactions. Such (supramolecular) chemistry is used to provide models for how enzymes work, but it also allows

 un-natural

reactions to be undertaken.

Reactions in supramolecular cavities &#8211; trapping a cyclobutadiene: ! or ?

The conventional procedures for reporting analysis or new results in science is to compose an “article”, augment that perhaps with “supporting information” or “SI”, submit to a journal which undertakes peer review, with revision as necessary for acceptance and finally publication. If errors in the original are later identified, a separate corrigendum can be submitted to the same journal, although this is relatively rare.

Questions about the (metadata) components of a scientific article.

In the previous two posts, I noted the recent suggestion of how a stable frozen S

 N

2 transition state might be made. This is characterised by a central carbon with five coordinated ligands.

It&#8217;s penta-coordinate carbon Spock- but not as we know it!

The iconic diagram below represents a cornerstone of organic chemistry.

Longer is stronger.

The traditional structure of the research article has been honed and perfected for over 350 years by its custodians, the publishers of scientific journals. Nowadays, for some journals at least, it might be viewed as much as a profit centre as the perfected mechanism for scientific communication. Here I take a look at the components of such articles to try to envisage its future, with the focus on molecules and chemistry.

Re-inventing the anatomy of a research article.

Five years back, I speculated about the mechanism of the epoxidation of ethene by a peracid, concluding that kinetic isotope effects provided interesting evidence that this mechanism is highly asynchronous and involves a so-called “hidden intermediate”. Here I revisit this reaction in which a small change is applied to the atoms involved. Below are two representations of the mechanism.

Epoxidation of ethene: a new substituent twist.

Every introductory course or text on aromatic electrophilic substitution contains an explanation along the lines of the resonance diagram shown below. With an

 o

/

 p

directing group such as NH

 2

, it is argued that negative charge accumulates in those positions as a result of the resonance structures shown. MEP for PhNH2. Click for 3D.The opposite occurs for electron withdrawing groups.

Aromatic electrophilic substitution: a different way of predicting regiospecificity

There is much focus at the moment on how to ensure experimental replicability in

 e.g.

the molecular sciences. An important aspect of that is having access to

 FAIR

data; data which is findable, accessible, inter-operable and re-usable. One of the “gold standards” in chemistry is the data associated with crystal structures.

Accessing (raw) chemical data: a peek into the CIF format.

Following on from my re-investigation of close hydrogen bonding contacts to the π-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469/hpc/2478) is similar to the previous one:   QA is any of N,O,F,Cl. X is any atom, including metals and non-metals.

π-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach?

Singleton and co-workers have produced some wonderful work showing how dynamic effects and not just transition states can control the outcome of reactions. Steve Bachrach’s blog contains many examples, including this recent one. This shows that tolyl thiolate (X=Na) reacts with the dichlorobutenone to give two substitution products in a 81:19 ratio.

Dynamic effects in nucleophilic substitution at trigonal carbon.

Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions.

Ten years on: Jmol and WordPress.

Previously, I looked at autocatalytic mechanisms where the carboxyl group of an oxetane-carboxylic acid could catalyse its transformation to a lactone, finding that a chain of two such groups were required to achieve the result. Here I look at an alternative mode where the oxetane-carboxylate itself acts as the transfer chain, via a H-bonded dimer shown below.

Unexpected Isomerization of Oxetane-Carboxylic Acids – an alternative autocatalytic mechanism evaluated.

The previous post set out a problem in conformational analysis. Here is my take, which includes an NCI (non-covalent interaction) display as discussed in another post. The lowest energies of the four diastereomers

 A-D

, each in two conformations (

 1/2

) were calculated at the ωB97D/6-311G(d,p)/SCRF=ethanol level, and are shown here relative to

 A1

(kcal/mol) as free energies.

Updating a worked problem in conformational analysis. Part 2: an answer.

C&amp;EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is.    I went about finding out as follows: The article DOI for all seven candidates was linked to the C&amp;EN site.

How FAIR are the data associated with the 2017 Molecules-of-the-Year?

A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells.

What are the highest bond indices for main group and transition group elements?

A little while ago I pondered allotropic bromine, or Br(Br)

 3

. But this is a far wackier report[cite]10.1126/science.aao7293[/cite] of

 a molecule of light.

The preparation and detection of dimer and trimer bound photon states is pure physics; probably considered by the physicists themselves as NOT chemistry. It is certainly true, as a chemist,  that I understood only a little of the article.

Is  (hν)3 an allotrope of light?

Fascination with nano-objects, molecules which resemble every day devices, is increasing. Thus the world’s smallest car has just been built[cite]10.1038/nature10587[/cite]. The mechanics of such a device can often be understood in terms of chemical concepts taught to most students. So I thought I would have a go at this one!

Driving the smallest car ever made: a chemical perspective.

This week the ACS announced its intention to establish a “

 ChemRxiv preprint server to promote early research sharing

“. This was first tried quite a few years ago, following the example of especially the physicists. As I recollect the experiment lasted about a year, attracted few submissions and even fewer of high quality.

Chemistry preprint servers (revisited).

Kinetic isotope effects have become something of a lost art when it comes to exploring reaction mechanisms. But in their heyday they were absolutely critical for establishing the mechanism of the benzidine rearrangement[cite]10.1021/ja00373a028[/cite]. This classic mechanism proceeds

 via


 bis

protonation of diphenyl hydrazine, but what happens next was the crux.

The  Benzidine rearrangement. Computed kinetic isotope effects.

The interface between physics, chemistry (and materials science) can be a fascinating one. Here I show a carbon nanotorus, devised by physicists[cite]10.1103/PhysRevLett.88.217206[/cite] a few years ago. It is a theoretical species, and was predicted to have a

 colossal paramagnetic moment

. Carbon nanotorus.

Metallic carbon nanotori

As the title hints, I have been here before. The S

 N

1 solvolysis mechanism of t-butyl chloride was central to the flourishing of physical organic chemistry from the 1920s onwards, and it appears early on in most introductory lecture courses and text books. There we teach that it is a two-stage mechanism.

The SN1 Mechanism for a third time. Exploration of the intrinsic reaction coordinate.

The title of this post paraphrases E. J. Corey’s article in 1997 (DOI: 10.1016/S0040-4039(96)02248-4) which probed the origins of conformation restriction in aldehydes. The proposal was of (then) unusual hydrogen bonding between the O=C-H…F-B groups. Here I explore whether the NCI (non-covalent-interaction) method can be used to cast light on this famous example of how unusual interactions might mediate selectivity in organic reactions.

Conformational restriction involving formyl CH&#8230;F hydrogen bonds.

A fascinating re-examination has appeared[cite]10.1002/anie.201505482[/cite] of a reaction first published[cite]10.1002/ange.19600721210[/cite] in 1960 by Wittig and then[cite]10.1002/jlac.19646790106[/cite] repudiated by him in 1964 since it could not be replicated by a later student.

Yes, no, yes. Computational mechanistic exploration of (nickel-catalysed) cyclopropanation using tetramethylammonium triflate.

Nitrogen tri-iodide, or more accurately the complex between it and ammonia ranks amongst the oldest known molecules (1812). I became familiar with it around the age of 12-13, in an era long gone when boys (and very possibly girls too) were allowed to make such substances in their parent’s back gardens

 ‡

and in fact in the school science laboratory,

 †

an experiment which earned me a personal request to visit the head teacher.

Halogen bonds 3: &#8220;Nitrogen tri-iodide&#8221;

Conferences can be intense, and this one is no exception. After five days, saturation is in danger of setting in. But before it does, I include two more (very) brief things I have learnt. Sason Shaik introduced a theme he first investigated years ago, but for which no experiment had been devised for verification. He revived his theme when a journalist contacted him last year to report exactly such an observation, which I now recount.

One more WATOC 2017 Report.

I have several times used arrow pushing on these blogs. But since the rules for this convention appear to be largely informal, and there appears to be no definitive statement of them, I thought I would try to produce this for our students. This effort is here shared on my blog. It is what I refer to as the standard version; an advanced version is in preparation. Such formality might come as a surprise to some;

A curly-arrow pushing manual

If you search

 e.g.

Scifinder for N,O-diphenyl hydroxylamine (RN 24928-98-1) there is just one literature citation, to a 1962 patent. Nothing else;

Why is N,O-diphenyl hydroxylamine (PhNHOPh) unknown?

The

 1

H NMR spectrum of an aromatic molecule such as benzene is iconic; one learns that the unusual chemical shift of the protons (~δ 7-8 ppm) is due to their deshielding by a

 diatropic

ring current resulting from the circulation of six aromatic π-electrons following the Hückel 4n+2 rule.

The NMR spectra of methano[10]annulene and its dianion. The diatropic/paratropic inversion.

Zosurabalbin[cite]10.1038/s41586-023-06873-0[/cite],[cite]10.1093/ofid/ofad500.1754[/cite], is receiving a great deal of attention as a new class of antibiotic which can target infections for which current treatment options are inadequate.

Macrocyclic peptide antibiotics &#8211; now Zosurabalpin &#8211; then  antibacterial  agents based on cyclic D,L-α-peptide architectures.

The Science education unit at the ACS publication C&amp;EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year’s batch.

Molecules of the year: 2023

It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key.

Conference report: an example of collaborative open science (reaction IRCs).

Amides with an H-N group are a component of the peptide linkage (O=C-NH). Here I ask what the conformation (it could also be called a configuration) about the C-N bond is. A search of the following type can be defined:     	   	The dihedral shown is for H-N-C=O (but this is equivalent to the C-C-N-C dihedral, which is also often called the dihedral angle associated with the peptide group). I have also added a distance, from a C-H

The conformational preference of s-cis amides.

This is a venerable organic reaction, which curiously I have not previously covered here. First described in 1859, its nature was only properly elucidated in 1873. It is a member of a class of reaction I have previously named “solvolytically assisted pericyclic”, or “perisolvolytic“. Here I explore some of the subtle stereoelectronic effects observed for this apparently simple reaction.      It applies to a class of molecule known as 1,2-diols.

The Pinacol rearrangement.

In discussing ferrocene in the previous post, I mentioned Irving Langmuir’s 1921 postulate that filled valence shells in what he called

 complete

molecules would have magic numbers of 2, 8, 18 or 32 electrons (deriving from the sum of terms in 2[1+3+5+7]). The first two dominate organic chemistry of course, whilst the third is illustrated by the transition series, ferrocene being an example of such.

Beryllocene and Uranocene: The 8, 18 and 32-electron rules.

The previous post described the fascinating 170-year history of a crystalline compound known as Herapathite and its connection to the mechanism of the Finkelstein reaction

 via

the complex of Na

 +

I

 2


 –

(or Na

 2


 2+

I

 4


 2-

). Both compounds exhibit (approximately) linear chains of iodine atoms in their crystal structures, a connection which was discovered serendipitously.

More examples of crystal structures containing embedded linear chains of iodines.

The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it yourself.

On the importance of  Digital repositories in Chemistry

The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures.

A periodic table for anomeric centres, this time with quantified interactions.

In this earlier post, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)

 2

and d(ATAT)

 2,

an undertaking which has taken about two months of computer time!

The thermodynamic energies of left and right handed DNA.

The number of repositories which accept research data across a wide spectrum of disciplines is on the up. Here I report the results of conducting an experiment in which chemical modelling data was deposited in six such repositories and comparing the richness of the metadata describing the essential properties of the six depositions. The repositories are as follows:

 Figshare

as a repository dates from 2012.

A comparison of descriptive metadata across different data repositories.

The recent release of the DataCite Data Citation corpus, which has the stated aim of providing “a trusted central aggregate of all data citations to further our understanding of data usage and advance meaningful data metrics” made me want to investigate what the current state of citing data in the area of chemistry might be. Chemistry is known to be a “data rich” science (as most of the physical sciences are) and  here on this very blog I

Data Citation &#8211; a snapshot of the chemical landscape.

The science journal is generally acknowledged as first appearing around 1665 with the Philosophical Transactions of the Royal Society in London and (simultaneously) the French Academy of Sciences in Paris. By the turn of the millennium, around 10,000 science and medical journals were estimated to exist.

(Hyper)activating the chemistry  journal.

I should start by saying that the server on which this blog is posted was set up in June 1993. Although the physical object has been replaced a few times, and had been “virtualised” about 15 years ago, a small number of the underlying software base components may well date way back, perhaps even to 1993.

A peak behind the (hosting) scenes of this blog.

In 2023, we very much take for granted that everyone and pretty much everything is online. But it was not always so and when I came across an old plan indicating how the chemistry department at Imperial College was connected in 1989, I was struck by how much has happened in the 34 years since. Nowadays all the infrastructures needed are effectively “built in” to the building when it is constructed and few are even aware of them.

A trip down memory lane: An online departmental connection map from 1989.

The title here is from an article on metalenses[cite]10.1021/acs.nanolett.6b01897[/cite] which caught my eye. Metalenses are planar and optically thin layers which can be manufactured using a single-step lithographic process. This contrasts with traditional lenses that are not flat and where the optical properties result from very accurately engineered curvatures, which in turn are expensive to manufacture.

Multispectral Chiral Imaging with a Metalens.

In this previous blog post I wrote about one way in which we have enhanced the journal article. Associated with that enhancement, and also sprinkled liberally throughout this blog, are links to a Digital Repository (if you want to read all about it, see DOI: 10.1021/ci7004737). It is a fairly specific repository for chemistry, with about 5000 entries.

A Digital chemical repository &#8211; is it being used?

C

 2

(dicarbon) is certainly interesting from a theoretical point of view. Whether or not it can be described as having a

 quadruple bond

has induced much passionate discussion[cite]10.1038/nchem.1263[/cite],[cite]10.1002/anie.201208206[/cite],[cite]10.1002/anie.201301485[/cite],[cite]10.1002/anie.201302350[/cite]. Its occurrence in space and in flames is also well-known.

Is dicarbon (C2) a molecule of chemical interest?

More inspiration from tutorials. In a lecture on organic aromaticity, the 4n+2/4n Hückel rule was introduced (in fact, neither rule appears to have actually been coined in this form by Hückel himself!). The simplest examples are respectively the cyclopropenyl cation and anion. The former has 2 π-electrons exhibiting cyclic delocalisation, and the 4n+2 (n=0) rule predicts aromaticity.

(anti)aromaticity avoided: a tutorial example

In the previous post, I showed that carbon can act as a hydrogen bond acceptor (of a proton) to form strong hydrogen bond complexes. Which brings me to a conceptual connection: can singlet dicarbon form such a hydrogen bond?  Dicarbon can be variously represented as above. The first form shows it as a bis-carbene, with an unbonded lone pair of electrons at each end of a carbon double bond.

Carbon as a hydrogen bond acceptor: can dicarbon (C2) act in this manner?

An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures?  The Conquest search query is very simple (no disorder, no errors).  When applied to the Cambridge structure database (CSD) the following two distributions are obtained.

Elongating an N-B single bond  is much easier than stretching a C-C single bond.

Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[cite]10.1039/P29940000703[/cite] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (&lt;80,000 structures; it’s now ten times larger) and the search software less powerful.

π-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?

Research data (and its management) is rapidly emerging as a focal point for the development of research dissemination practices.

The challenges in curating research data: one case study.

This is a spin-off from the table I constructed here for further chemical examples of the classical/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane

 via

a square planar geometry as compared with

 e.g.

NiH

 4

for which the square planar motif is its minimum.

How does methane invert (its configuration)?

In the previous post, I noted that a chemistry publisher is about to repeat an earlier experiment in serving pre-prints of journal articles. It would be fair to suggest that following the first great period of journal innovation, the boom in rapid publication “camera-ready” articles in the 1960s, the next period of rapid innovation started around 1994 driven by the uptake of the World-Wide-Web.

Journal innovations &#8211; the next step is augmented reality?

In the previous post, I introduced three of a new generation of search engines specialising in the discovery of data. Data has some special features which make its properties slightly different from the conceptual (or natural language) searches we are used to performing for general information and so a search engine specifically for data is invariably going to reflect this.

A cascading tutorial in finding rich NMR data using the Datacite datasearch engine.

The electrophilic substitution of indoles is a staple of any course on organic chemistry.

Understanding the electrophilic aromatic substitution of indole.

This is one of those posts of a molecule whose very structure is interesting enough to merit a picture and a 3D model. The study[cite]10.1126/science.aal1619[/cite] reports a molecular knot with the remarkable number of eight crossings.

Braiding a molecular knot with eight crossings.

A

 scalemic

molecule is the term used by Eliel to describe any non-racemic chiral compound.

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