These four posts (the box set) set out to try to define the energetics for a reasonable reaction path for the Willgerodt-Kindler reaction. The rate of this reaction corresponds approximately to a free energy barrier of ~30 kcal/mol.

Imperial College London

These four posts (the box set) set out to try to define the energetics for a reasonable reaction path for the Willgerodt-Kindler reaction. The rate of this reaction corresponds approximately to a free energy barrier of ~30 kcal/mol. Any pathway found to be &gt;10 kcal/mol at its highest point above this barrier was deemed less probable. The first three efforts at defining such pathways all gave such a result.

The Willgerodt-Kindler reaction. Completing the Box set.

White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.♣ The first Imperial department to move into […]

White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.

 ♣

The first Imperial department to move into the MSRH (Molecular Sciences Research Hub) building is chemistry.

The “White City Trio” – The formation of an amide from an acid and an amine in non-polar solution (updated).

Previously, I pondered about the strange N=N double bond in nitrosobenzene dimer as a follow up to commenting on the curly arrow mechanism of the dimerisation.

Previously, I pondered about the strange N=N double bond in nitrosobenzene dimer[1] as a follow up to commenting on the curly arrow mechanism of the dimerisation.[2] 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

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

The two previous  posts, 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 are shorter than normal (which is ~2.05Å for e.g. the S8 ring) by ~ 0.1Å and some […]

The two previous  posts[1],[2] 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 are shorter than normal (which is ~2.05Å for

 e.g.

the S

 8

ring) by ~ 0.1Å and some are longer by ~0.24Å. Here we extend this to the unknown molecule shown below.

5-Imino-5λ4-heptathiepane 3-oxide. More exuberent anomeric effects.

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 record is itself identified by a persistent identifier known as a DOI.

The secrets of FAIR Metadata: optimisation for Chemical Compounds.

Scientists are familiar with the term data, at least in a scientific or chemical context, but appreciating metadata (meaning "after", or "beyond") is slightly more subtle, in the sense of using it to mean data about data. The challenge lies in clarifying where the boundary between data and its metadata lies and in specifying and controlling the vocabulary used for these metadata descriptions.

Metametadata: data about data about (chemical) data.

Publishing embargoes seem a relatively new phenomenon, probably starting in areas of science when the data produced for a scientific article was considered more valuable than the narrative of that article. However, the concept of the embargo seems to be spreading to cover other aspects of publishing, and I came across one recently which appears to take such embargoes into new and uncharted territory.

Publishing embargoes.

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.

What’s a Journal For? This debate has been raging ever since preprint servers were introduced as far back as 1991!

Derek Lowe asks “What’s a Journal For?” – Knowledge graphs?

Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this.

Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this. In that instance, it involved recognising that a cyclic molecule which appeared to have the cyclohexatriene benzene-aromatic pattern

 1

was in fact a trimer of carbon dioxide.

Tunable aromaticity?  An unrecognized new aromatic molecule?

In an earlier post on this topic,‡ I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below.

In an earlier post on this topic,[1]

 ‡

I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below. The arrows in red can be described as firstly addition to the carbonyl group to form either a transient intermediate (a two-step process) or instead a formal transition state state as a concerted single-step mechanism.

More examples of “double-headed” curly arrows: S and C Nucleophiles attacking acetyl chloride

The term bispericyclic reaction was famously coined by Caramella et al in 2002 to describe the unusual features of the apparently innocuous dimerisation of cyclopentadiene.

The term bispericyclic reaction was famously coined by Caramella

 et a

l in 2002[1] to describe the unusual features of the apparently innocuous dimerisation of cyclopentadiene. It shows features of two paths for different pericyclic reactions, comprising a 2+4 cycloaddition in the early stages, but evolving into a (degenerate) pair of [3,3] sigmatropic reactions in the latter stages.

A new type of bispericyclic reaction: Cyclopropanone + butadiene.

The recently reported synthesis 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? Firstly, the crystal structure is shown below, albeit as a dimer rather than a periodic lattice (click on image to obtain 3D coordinates).

The recently reported synthesis[1] 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?

In previously asking what the largest angle subtended at four-coordinate carbon might be, I noted that as the angle increases beyond 180°, the carbon becomes inverted, or hemispherical (all four ligands in one hemisphere). So what does a search for this situation reveal in the CSD?

Examples of inverted or hemispherical carbon?

Way back in the late 1980s or so, research groups in chemistry started to replace the filing of their paper-based research data by storing it in an easily retrievable digital form. This required a computer database and initially these were accessible only on specific dedicated computers in the laboratory.

Data base or Data repository? – A brief and very selective history of data management in chemistry.

Here is another of the “large” molecules in the c&amp;e news shortlist for molecule-of-the-year, 2020.

Here is another of the “large” molecules in the c&amp;e news shortlist for molecule-of-the-year, 2020. This one is testing the Hückel 4n+2 rule out to a value never before seen (n = 40, or 162 π-electrons).[1] The take-home message is that this rule seems to behave well in predicting global aromaticity even at this sort of scale! The smallest and largest of the 34 examples for which coordinates are provided are shown below.

Global aromaticity at the nanoscale.

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.

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.[1] 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.

In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus “NU-1501-Al” can absorb 14 weight% of hydrogen.

In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus “NU-1501-Al” can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about 4-5 kg of hydrogen gas would be need to be stored and released safely.

A molecular sponge for hydrogen storage- the future for road transport?

All of the molecules in this year’s C&amp;EN list are fascinating in their very different ways. Here I take a look at the twisty tetracene (dodecaphenyltetracene) which is indeed very very twisty.

All of the molecules in this year’s C&amp;EN list are fascinating in their very different ways. Here I take a look at the twisty tetracene (dodecaphenyltetracene) which is indeed very very twisty.[1]   Click on image to view 3D model   Unfortunately, the authors point that the twisty-ness does not lead to a stable helical configuration at room temperatures and so separate enantiomers cannot be isolated.

Molecules of the year – 2019: twisty tetracene.

Having shown that carbon as a carbene centre, C: can act as a hydrogen bond acceptor, as seen from a search of crystal structures, I began to wonder if there is any chance that carbon as a radical centre, C• could do so as well. Definitely a subversive thought, since radical centres are supposed to abstract hydrogens […]

Having shown that carbon as a carbene centre, C

 :

can act as a hydrogen bond acceptor, as seen from a search of crystal structures, I began to wonder if there is any chance that carbon as a radical centre, C• could do so as well. Definitely a subversive thought, since radical centres are supposed to abstract hydrogens rather than to hydrogen bond to them.

Can a carbon radical act as a hydrogen bond acceptor?

In a previous post, I looked at the Findability of FAIR data in common chemistry journals. Here I move on to the next letter, the A = Accessible.

In a previous post, I looked at the Findability of FAIR data in common chemistry journals. Here I move on to the next letter, the A = Accessible. The attributes of A[1] include: (meta)data are retrievable by their identifier using a standardized communication protocol. the protocol is open, free and universally implementable.  the protocol allows for an authentication and authorization procedure.

The “Accessible” in FAIR (data).

For perhaps ten years now, the future of scientific publishing has been hotly debated. The traditional models are often thought to be badly broken, although convergence to a consensus of what a better model should be is not apparently close.

For perhaps ten years now, the future of scientific publishing has been hotly debated. The traditional models are often thought to be badly broken, although convergence to a consensus of what a better model should be is not apparently close. But to my mind, much of this debate seems to miss one important point, how to publish data.

Open Access journal publishing debates – the elephant in the room?

In the previous post, I investigated the mechanism of cyclopropanation of an enal using a benzylic chloride using a quantum chemistry based procedure. Here I take a look at the NMR spectra of the resulting cyclopropane products, with an evaluation of the original stereochemical assignments.

In the previous post, I investigated the mechanism of cyclopropanation of an enal using a benzylic chloride using a quantum chemistry based procedure. Here I take a look at the NMR spectra of the resulting cyclopropane products, with an evaluation of the original stereochemical assignments.[1] Three products were identified,

 4a-c

(aryl=2,4-dinitro) with a fourth diastereomer undetected.

Organocatalytic cyclopropanation of an enal: (computational) product stereochemical assignments.

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.

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.

Crystallography meets DFT Quantum modelling.

The annual “molecule of the year” results for 2021 are now available … and the winner is Infinitene., This is a benzocirculene in the form of a figure eight loop (the infinity symbol), a shape which is also called a lemniscate after the mathematical (2D) function due to Bernoulli.

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;

Molecule of the year 2021: Infinitene.

You might have noticed if you have read any of my posts here is that many of them have been accompanied since 2006 by supporting calculations, normally based on density functional theory (DFT) and these calculations are accompanied by a persistent identifier pointer‡ to a data repository publication.

You might have noticed if you have read any of my posts here is that many of them have been accompanied since 2006 by supporting calculations, normally based on density functional theory (DFT) and these calculations are accompanied by a persistent identifier pointer

 ‡

to a data repository publication.

HPC Access and Metadata Portal (CHAMP).

Introductory chemistry will tell us that a triple bond between say two carbon atoms comprises just one bond of σ-axial symmetry and two of π-symmetry. Increasingly mentioned nowadays is the possibility of a quadruple bond between carbon and either itself or a transition metal, as discussed in the previous post.

Introductory chemistry will tell us that a triple bond between say two carbon atoms comprises just one bond of σ-axial symmetry and two of π-symmetry. Increasingly mentioned nowadays is the possibility of a quadruple bond between carbon and either itself or a transition metal, as discussed in the previous post. Such a bond comprises TWO bonds of σ-axial symmetry.

What does a double σ-bond along a bond axis look like?

Here I investigate a recent report of a new generation of polyesters with the intrinsic properties of high crystallinity and chemical recyclability. The latter point is key, since many current plastics cannot be easily recycled to a form which can be used to regenerate the original polymer with high yield.

Here I investigate a recent report[1] of a new generation of polyesters with the intrinsic properties of high crystallinity and chemical recyclability. The latter point is key, since many current plastics

 cannot

be easily recycled to a form which can be used to regenerate the original polymer with high yield. Here I show some aspects of this fascinating new type of polymer.

High-performance polythioesters with high chemical recyclability.

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.

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. Metadata

 vs

Data.

Metadata. Why?

There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity. The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy.

There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity.[1] The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy. Here I explore some crystal structures containing this motif for possible insights.

Dispersion-induced triplet aromatisation?

A Theoretical Method for Distinguishing X‐H Bond Activation Mechanisms.

An article with the title shown above in part recently appeared. Given the apparent similarity of HF1- to CH3F1- and CH3F2-, the latter of which I introduced on this blog previously, I thought it of interest to apply my analysis to HF1-.

An article with the title shown above in part recently appeared.[1] Given the apparent similarity of HF

 1-

to CH

 3

F

 1-

and CH

 3

F

 2-

, the latter of which I introduced on this blog previously, I thought it of interest to apply my analysis to HF

 1-

. The authors[1] conclude that “

 the F atom of HF
 
 −
 
 is negative and hypervalent and the bonding is more covalent than

Identification of a simplest hypervalent hydrogen fluoride anion.

For around 16 years, Floyd Romesberg’s group has been exploring un-natural alternatives (UBPs) to the Watson-Crick base pairs (C-G and A-T) that form part of the genetic code in DNA.

A form of life that can stably store genetic information using a six-letter, three-base-pair alphabet?

At the moment, the bond slam is something of a home from home for this blog and since much of my activity is happening there rather than here, I thought I might give you pointers to some of the topics, which are evolving, so to speak, before our very eyes.

At the moment, the bond slam is something of a

 home from home

for this blog and since much of my activity is happening there rather than here, I thought I might give you pointers to some of the topics, which are evolving, so to speak, before our very eyes.

The Bond Slam – a second peek inside.

I noted in my WATOC conference report a presentation describing the use of calculated reaction barriers (and derived rate constants) as mechanistic reality checks. Computations, it was claimed, have now reached a level of accuracy whereby a barrier calculated as being 6 kcal/mol too high can start ringing mechanistic alarm bells.

Dyotropic Ring Expansion: more mechanistic reality checks.

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.

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.

About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings.

About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å[1]. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings. Now a new report[2] and commented upon by Steve Bachrach, claims a similar distance for hydrogens attached to carbon,

 i.e.

C-H…H-C, but without the ring compression.

Dispersion “bonds”: a new example with an ultra-short H…H distance.

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 has an SI which is paginated at 907;

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[1] has an SI which is paginated at 907;

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

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.

In a comment appended to an earlier post, I mused about the magnitude of the force constant relating to the interconversion between a classical and a non-classical structure for the norbornyl cation.

In a comment appended to an earlier post, I mused about the magnitude of the force constant relating to the interconversion between a classical and a non-classical structure for the norbornyl cation. Most calculations indicate the force constant for an “isolated” symmetrical cation is +ve, which means it is a true minimum and not a transition state for a [1,2] shift.

What is the (calculated) structure of a norbornyl cation anion-pair in water?

This, the fourth candidate provided by C&amp;EN for a vote for the molecule of the year as discussed here, lays claim to the World’s most polar neutral molecule (system 1 shown below). Here I explore a strategy for extending that record.

This, the fourth candidate provided by C&amp;EN for a vote for the molecule of the year as discussed here, lays claim to the World’s most polar neutral molecule (system

 1

shown below).[1] Here I explore a strategy for extending that record. The claim for

 1

(

 3

in [1]) is on the basis of its measured dipole moment which is 14.1± 0.7D in THF.

Molecules of the year? The most polar neutral compound synthesized…

Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news and known as HMTD (hexamethylene triperoxide diamine). The crystal structure was reported some time ago and the article included an inspection of the computed wavefunction.

Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news and known as HMTD (hexamethylene triperoxide diamine). The crystal structure was reported some time ago[1] and the article included an inspection of the computed wavefunction.

More stereoelectronics galore: hexamethylene triperoxide diamine.

The first conference devoted to scientific uses of Wikipedia has just finished; there was lots of fascinating stuff but here I concentrate on one report that I thought was especially interesting. To introduce it, I need first to introduce WikiData. This is part of the WikiMedia ecosystem, and one of the newest.

The first conference devoted to scientific uses of Wikipedia has just finished; there was lots of fascinating stuff but here I concentrate on one report that I thought was especially interesting. To introduce it, I need first to introduce WikiData. This is part of the WikiMedia ecosystem, and one of the newest. The basic concept is really simple. It is a repository for data objects; 14,757,419 of them as I write this to be precise.

A sea-change in science citation? The Wikipedia Science conference.

Peter Edwards has just given the 2015 Hofmann lecture here at Imperial on the topic of solvated electrons. An organic chemist knows this species as “e–” and it occurs in ionic compounds known as electrides; chloride = the negative anion of a chlorine atom, hence electride = the negative anion of an electron.

Peter Edwards has just given the 2015 Hofmann lecture here at Imperial on the topic of

 solvated electrons

. An organic chemist knows this species as “

 e
 
 –
 

” and it occurs in ionic compounds known as

 electrides

; chloride = the negative anion of a chlorine atom, hence

 electride

= the negative anion of an electron.

Electrides (aka solvated electrons).

Previously on this blog: modelling the reduction of cinnamaldehyde using one molecule of lithal shows easy reduction of the carbonyl but a high barrier at the next stage, the reduction of the double bond.

A better model for the mechanism of Lithal (LAH) reduction of cinnamaldehyde?

Steganone
 

is an unusual natural product, known for about 40 years now. The assignment of its absolute configurations makes for an interesting, on occasion rather confusing, and perhaps not entirely atypical story. I will start with the modern accepted stereochemical structure of this molecule, which comes in the form of two separately isolable atropisomers.

Chiroptical spectroscopy of the natural product Steganone.

The element silicon best represents the digital era of the mid 20th century to the present;

The element

 silicon

best represents the digital era of the mid 20th century to the present; without its crystalline form, there would be no computers (or this blog). Although it was first prepared in pure amorphous (powder) form around 1823[1] by Berzelius, it was not until 1854 that Henri Sainte-Claire Deville made it in crystalline form, using metallic aluminium to isolate it. He described it [1] as having a “metallic luster”.

The world ash tree of the computer hardware industry… crystalline silicon from 1854.

Homoaromaticity is a special case of aromaticity in which π-conjugation is interrupted by a single sp3 hybridized carbon atom (it is sometimes referred to as a suspended π-bond with no underlying σ-foundation). But consider the carbene shown below. This example comes from a recently published article which was highlighted on Steve Bachrach’s blog.

Homoaromaticity is a special case of aromaticity in which π-conjugation is interrupted by a single sp

 3

hybridized carbon atom (it is sometimes referred to as a suspended π-bond with no underlying σ-foundation). But consider the carbene shown below. This example comes from a recently published article[1] which was highlighted on Steve Bachrach’s blog.

Six vs ten aromatic electrons?

Here is another example gleaned from that Woodward essay of 1967 (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249), where all might not be what it seems.

Here is another example gleaned from that Woodward essay of 1967 (

 Chem. Soc. Special Publications

(Aromaticity),

 1967

,

 21

, 217-249), where all might not be what it seems. Woodward notes that the reaction between the (highly reactive)

 1

does not occur.

Another Woodward pericyclic example dissected: all is not what it seems.

A few posts back, I explored the “benzidine rearrangement” of diphenyl hydrazine. This reaction requires diprotonation to proceed readily, but we then discovered that replacing one NH by an O as in N,O-diphenyl hydroxylamine required only monoprotonation to undergo an equivalent facile rearrangement.

A few posts back, I explored the “benzidine rearrangement” of diphenyl hydrazine. This reaction requires diprotonation to proceed readily, but we then discovered that replacing one NH by an O as in N,O-diphenyl hydroxylamine required only monoprotonation to undergo an equivalent facile rearrangement. So replacing both NHs by O to form diphenyl peroxide (Ph-O-O-Ph) completes this homologous series.

Why diphenyl peroxide does not exist.

I recently got an email from a student asking about the best way of rationalising epoxide ring opening using some form of molecule orbitals. This reminded me of the famous experiment involving propene epoxide.

I recently got an email from a student asking about the best way of rationalising epoxide ring opening using some form of molecule orbitals.

How to predict the regioselectivity of epoxide ring opening.

A quartet of articles has recently appeared on the topic of cyclobutadiene.,,,. You will find a great deal discussed there, but I can boil it down to this essence.

A quartet of articles has recently appeared on the topic of cyclobutadiene.[1],[2],[3],[4]. You will find a great deal discussed there, but I can boil it down to this essence.

To be cyclobutadiene, or not to be, that is the question?  You decide.

My last comment as appended to the previous post promised to analyse two so-called extended porphyrins for their topological descriptors.

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.

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:

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.

Although have dealt with the π-complex formed by protonation of PhNHOPh in several posts, there was one aspect that I had not really answered; what is the most appropriate description of its electronic nature? Here I do not so much provide an answer, as try to show how difficult getting an accurate answer might be.

Although have dealt with the π-complex formed by protonation of PhNHOPh in several posts, there was one aspect that I had not really answered; what is the most appropriate description of its electronic nature?

How does one describe the wavefunction for the π-complex formed from PhNHOPh?

We tend to think of simple hydrocarbons as relatively inert and un-interesting molecules.

We tend to think of simple hydrocarbons as relatively inert and un-interesting molecules. However, a recent article[1], 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.

tpap
 

[1], as it is affectionately known, is a ruthenium-based oxidant of primary alcohols to aldehydes discovered by Griffith and Ley.

How to tame an oxidant: the mysteries of “tpap” (tetra-n-propylammonium perruthenate).

I have written earlier about dihydrocostunolide, and how in 1963 Corey missed spotting the electronic origins of a key step in its synthesis.. A nice juxtaposition to this failed opportunity relates to Woodward’s project at around the same time to synthesize vitamin B12.

I have written earlier about dihydrocostunolide, and how in 1963 Corey missed spotting the electronic origins of a key step in its synthesis.[1]. A nice juxtaposition to this failed opportunity relates to Woodward’s project at around the same time to synthesize vitamin B12. The step in the synthesis that caused him to ponder is shown below.

Vitamin  B12 and the  genesis of a new theory of chemistry.

Part one on this topic showed how a quantum mechanical model employing just one titanium centre was not successful in predicting the stereochemical outcome of the Sharpless asymmetric epoxidation.

Why the Sharpless epoxidation is enantioselective!

Sharpless epoxidation converts a prochiral allylic alcohol into the corresponding chiral epoxide with &gt; 90% enantiomeric excess,. Here is the first step in trying to explain how this magic is achieved.

Sharpless epoxidation converts a prochiral allylic alcohol into the corresponding chiral epoxide with &gt; 90% enantiomeric excess[1],[2]. Here is the first step in trying to explain how this magic is achieved. The scheme above shows how (achiral) prop-2-enol is converted using the asymmetric catalyst (R,R)-diethyl tartrate  and

 t

-butyl hydroperoxide as oxidant into the (S)-chiral epoxide.

Why is the Sharpless epoxidation enantioselective? Part 1: a simple model.

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

Following on from our first mechanistic reality check, we now need to verify how product A might arise in the mechanism shown below, starting from B.

Following on from our first mechanistic reality check, we now need to verify how product

 A

might arise in the mechanism shown below, starting from

 B

. This pathway backtracks the original one in reversing the final arrow of that process (shown in red in previous post and in magenta here for the arrow in reverse), to go uphill in energy to reach the secondary (unstabilised) carbocation.

Secrets of a university tutor. An exercise in mechanistic logic: second dénouement.

An obvious issue to follow-up my last post on the (solvated) intrinisic reaction coordinate for the Sn2 reaction is how variation of the halogen (X) impacts upon the nature of the potential.

The Sn2 reaction: followed up.

Whilst clusters of carbon atoms are well-known, my eye was caught by a recent article describing the detection of a cluster of boron atoms, B

 40

to be specific.[cite]10.1038/nchem.1999[/cite] My interest was in how the σ and π-electrons were partitioned. In a C

 40

, one can reliably predict that each carbon would contribute precisely one π-electron. But boron, being more electropositive, does not always play like that.

Data nightmares: B40 and counting its π-electrons

I blogged about this two years ago and thought a brief update might be in order now. To support the discussions here, I often perform calculations, and most of these are then deposited into a DSpace digital repository, along with metadata.

I blogged about this two years ago and thought a brief update might be in order now. To support the discussions here, I often perform calculations, and most of these are then deposited into a DSpace digital repository, along with metadata. Anyone wishing to have the full details of any calculation can retrieve these from the repository. Now in 2012, such repositories are more important than ever.

Digital repositories. An update.

I was first taught curly arrow pushing in 1968, and have myself taught it to many a generation of student since. But the other day, I learnt something new.

The first ever curly arrows.

I left the story of the molecule below on the precipice of a cliff. I had shaved off the four benzo groups (blue) in the time honoured computational tradition of clearing away distractions.

I left the story of the molecule below on the precipice of a cliff. I had shaved off the four benzo groups (blue) in the time honoured computational tradition of clearing away distractions. Unfortunately, it became clear as the story unfolded that the benzo groups had a distractingly critical role to play, and so its time to start adding them back again, but in stages.

Violations. There are none!  Part 2.

There are many treasures in Woodward and Hoffmann’s (WH) classic monograph.

There are many treasures in Woodward and Hoffmann’s (WH) classic monograph. One such is acetolysis of  the

 endo

chloride (green), which is much much faster than that of the

 exo

isomer (red). The explanation given in their article (p 805) confines itself to succinctly stating that only loss of the

 endo

halogen can be concerted with a required disrotatory ring opening of the cyclopropane.

Mechanistic morphemes. Perisolvolysis of a cyclopropyl chloride.

Another common type of pericyclic reaction is the migration of hydrogen or carbon along a conjugated chain, as in the [1,3] migration of a carbon as shown below. As before, I explore the stereochemistry of the thermal and photochemical reactions.

A modern take on pericyclic sigmatropic migrations.

How one might go about answering the question: do alkenes promote anomeric effects?

How one might go about answering the question: do alkenes promote anomeric effects? A search of chemical abstracts does not appear to cite any examples (I may have missed them of course, since it depends very much on the terminology you use, and new effects may not yet have any agreed terminology) and a recent excellent review of hyperconjugation does not mention it. Here I show how one might provide an answer.

Spotting the unexpected. Anomeric effects involving alkenes?

My previous post introduced the interesting guts of taxol. Two different isomers can exist, and these are called atropisomers; one has the carbonyl group pointing up, the other down.

My previous post introduced the interesting guts of taxol. Two different isomers can exist, and these are called atropisomers; one has the carbonyl group pointing up, the other down. The barrier to their interconversion in this case is generated by a rotation about the two single bonds connecting the carbonyl group to the rest of the molecule.

Atropisomerism in Taxol. An apparently simple bond rotation?

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

A

 scalemic

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

Scalemic molecules: a cheminformatics challenge!

It is not often that an article on the topic of illusion and deception makes it into a chemical journal. Such is addressed (DOI: 10.1002/anie.201102210) in no less an eminent journal than Angew Chemie.

It is not often that an article on the topic of illusion and deception makes it into a chemical journal.

Molecular illusions and deceptions. Ascending and Descending Penrose stairs.

Most scientific theories emerge slowly, over decades, but others emerge fully formed virtually overnight as it were (think Einstein in 1905). A third category is the supernova type, burning brightly for a short while, but then vanishing (almost) without trace shortly thereafter.

Henry Rzepa's Blog

Pericyclic assistance for SN-1 solvolysis

A Disrotatory 4n+2 electron anti-aromatic Möbius transition state for a thermal electrocyclic reaction.

Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog

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