bluuebunny/crossref_metadata_2025 huggingface dataset:
An exothermic E2 elimination: an unusual intrinsic reaction coordinate.
Authors: Rzepa Henry
Published: September 2023

The previous post explored why E2 elimination reactions occur with an

antiperiplanar

geometry for the transition state. Here I have tweaked the initial reactant to make the overall reaction

exothermic

rather than

endothermic

as it was before. The change is startling. The exothermicity is of course due to the aromatisation of the ring. The IRC is however quite different from before. IRC for E2 elimination.
Updating a worked problem in conformational analysis. Part 2: an answer.
Authors: Rzepa Henry
Published: September 2023

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.
Do marauding electrons go in packs?
Authors: Rzepa Henry
Published: September 2023

Is there a preferred pack size for electrons on the move? Or put less flamboyantly, is there an optimum, and a maximum number of arrows (electron pairs) that one might push in revealing the mechanism of a concerted reaction? A sort of village-instinct for electrons.
Hafnium and Niels Bohr
Authors: Rzepa Henry
Published: September 2023

In 1923, Coster and von Hevesy[cite]10.1038/111079a0[/cite] claimed discovery of the element

Hafnium

, atomic number

72

(latin Hafnia, meaning Copenhagen, where the authors worked) on the basis of six lines in its X-ray spectrum. The debate had long raged as to whether (undiscovered) element 72 belonged to the rare-earth group 3 of the periodic table below yttrium, or whether it should be placed
Science publishers (and authors) please take note.
Authors: Rzepa Henry
Published: September 2023

I have for perhaps the last 25 years been urging publishers to recognise how science publishing could and should change. My latest thoughts are published in an article entitled “

The past, present and future of Scientific discourse

” (DOI: 10.1186/1758-2946-3-46). Here I take two articles, one published 58 years ago and one published last year, and attempt to reinvent some aspects.
Beryllocene and Uranocene: The 8, 18 and 32-electron rules.
Authors: Rzepa Henry
Published: September 2023

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.
Secrets of a university tutor: dissection of a reaction mechanism. Part 2, the stereochemistry.
Authors: Rzepa Henry
Published: September 2023

In the previous post, I went over how a reaction can be stripped down to basic components. That exercise was essentially a flat one in two dimensions, establishing only what connections between atoms are made or broken. Here we look at the three dimensional arrangements. It all boils down to identifying what the stereochemistry of the bonds marked with a wavy line are. To make it simple, let us start with the molecule shown on the left.
What is the future of books?
Authors: Rzepa Henry
Published: September 2023

At a recent conference, I talked about what books might look like in the near future, with the focus on mobile devices such as the iPad. I ended by asserting that it is a very exciting time to be an aspiring book author, with one’s hands on (what matters),

the content

. Ways of expressing that content are currently undergoing an explosion of new metaphors, and we might even expect some of them to succeed!
Chemicalizing a blog.
Authors: Rzepa Henry
Published: September 2023

I am at the ACS meeting, attending a session on chemistry and the Internet. This post was inspired by Chemicalize, a service offered by ChemAxon, which scans a post like this one, and identifies molecules named. I had previously used generic post taggers, which frankly did not work well in identifying chemical content. So this is by way of an experiment.
From the colour blue to molecular wires
Authors: Rzepa Henry
Published: September 2023

In the previous post I pondered the colour of Monastral blue (copper phthalocyanine). Something did not quite fit, and so I speculated that perhaps some oxidation of the pigment might give a new species. This species (Cambridge code FEGJOQ) comprises two parts of copper phthalocyanine, 1 part of the corresponding cation, and 1 part of triodide anion.
Conformational restriction involving formyl CH…F hydrogen bonds.
Authors: Rzepa Henry
Published: September 2023

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.
Nobelocene: a (hypothetical) 32-electron shell molecule?
Authors: Rzepa Henry
Published: September 2023

The two previous posts have explored one of the oldest bonding rules (pre-dating quantum mechanics), which postulated that filled valence shells in atoms forming molecules follow the magic numbers 2, 8, 18 and 32. Of the 59,025,533 molecules documented at the instant I write this post, only one example is claimed for the 32-electron class.
Use case - how to get species occurrence data from GBIF for a genus
Authors: Chamberlain Scott
Published: September 2023

Real use cases from people using our software are awesome. They are important for many reasons: 1) They make the code more useable because we may change code to make the interace and output easier to understand; 2) They may highlight bugs in our code;
(re)Use of data from chemical journals.
Authors: Rzepa Henry
Published: September 2023

If you visit this blog you will see a scientific discourse in action.
Hunt the charge: the Cheshire cat of chemistry
Authors: Rzepa Henry
Published: September 2023

Charges in chemistry, like the grin on Lewis Carroll’s cat, can be mysterious creatures. Take for example the following structure, reported by Paul Lickiss and co-workers (DOI: 10.1039/b513203g). A silenium cation.
Mobile-friendly solutions for viewing (WordPress) Blogs with embedded 3D molecular coordinates.
Authors: Rzepa Henry
Published: September 2023

My very first post on this blog, in 2008, was to describe how Jmol could be used to illustrate chemical themes by adding 3D models to posts. Many of my subsequent efforts have indeed invoked Jmol. I thought I might review progress since then, with a particular focus on using the new generations of mobile device that have subsequently emerged.
Ferrocene
Authors: Rzepa Henry
Published: September 2023

The structure of ferrocene was famously analysed by Woodward and Wilkinson in 1952[cite]10.1021/ja01128a527[/cite],[cite]10.1016/S0022-328X(00)88947-0[/cite], symmetrically straddled in history by Pauling (1951) and Watson and Crick (1953). Quite a trio of Nobel-prize winning molecular structural analyses, all based on a large dose of intuition.
The peroxidation of alkynes: things are not always what they seem.
Authors: Rzepa Henry
Published: September 2023

The epoxidation of an

alkene

to give an oxirane is taught in introductory organic chemistry. Formulating an analogous mechanism for such reaction of an

alkyne

sounds straightforward, but one gradually realises that it requires raiding knowledge from several other areas of (perhaps slightly more advanced) chemistry to achieve a joined up approach to the problem.
Quadruple antarafacial delight.
Authors: Rzepa Henry
Published: September 2023

A feature of many a classic review article is that not only does it organise and rationalise existing literature, but it will predict new chemistry as well. I have already noted Woodward and Hoffmann’s (WH) review as achieving the former, and here I take a (sideways) look at one of their predictions.
Atropisomerism in Taxol. An apparently simple bond rotation?
Authors: Rzepa Henry
Published: September 2023

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.
The 2013 rOpenSci challenge
Authors: Ram Karthik
Published: September 2023

At rOpenSci we’re very passionate about engaging with our community and getting more people on board with open science and open data. There are many challenges to be overcome before this practice becomes mainstream. Even when researchers see the value in engaging more openly, the learning curve associated with various aspects of the workflow can seem daunting.
Shared space (in science).
Authors: Rzepa Henry
Published: September 2023

I thought I would launch the 2012 edition of this blog by writing about

shared space

. If you have not come across it before, it is (to quote Wikipedia), “an urban design concept aimed at integrated use of public spaces.” The BBC here in the UK ran a feature on it recently, and prominent in examples of shared space in the UK was Exhibition Road. I note this here on the blog since it is about 100m from my office.
Do electrons prefer to move in packs of 4, 6 or 8 during proton exchange in a calixarene?
Authors: Rzepa Henry
Published: September 2023

This story starts with a calixarene, a molecule (suitably adorned with substituents) frequently used as a host to entrap a guest and perchance make the guest do something interesting. Such a calixarene was at the heart of a recent story where an attempt was made to induce it to capture cyclobutadiene in its cavity.
Extreme chemical intimacy: the Xe2@C60 ion-pair.
Authors: Rzepa Henry
Published: September 2023

Unusual bonds are always intriguing, and the Xe-Xe bond is no exception.
Stereoselectivities of Proline-Catalyzed Asymmetric Intermolecular Aldol Reactions.
Authors: Rzepa Henry
Published: September 2023

Astronomers who discover an asteroid get to name it, mathematicians have theorems named after them. Synthetic chemists get to name molecules (Hector’s base and Meldrum’s acid spring to mind) and reactions between them. What do computational chemists get to name? Transition states! One of the most famous of recent years is the Houk-List.
The perception of stereochemistry. A challenging case.
Authors: Rzepa Henry
Published: September 2023

Most representational chemistry generated on a computer requires the viewer to achieve a remarkably subtle transformation in their mind from two to three dimensions (we are not quite yet in the era of the 3D iPad!). The Cahn-Ingold-Prelog convention was a masterwork (which won the Nobel prize). It is shown in action for the molecule on the left below.
Molecular illusions and deceptions. Ascending and Descending Penrose stairs.
Authors: Rzepa Henry
Published: September 2023

It is not often that an article on the topic of illusion and deception makes it into a chemical journal.
Spotting the unexpected. Anomeric effects involving alkenes?
Authors: Rzepa Henry
Published: September 2023

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.
Valentine chemistry
Authors: Rzepa Henry
Published: September 2023

The Möbius band is an experimental delight. In its original forms, it came flat-packed as below.
Secrets of a university tutor: dissection of a reaction mechanism.
Authors: Rzepa Henry
Published: September 2023

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.
cis-Butene: a reaction coordinate dissected and methyl flags.
Authors: Rzepa Henry
Published: September 2023

In two previous posts, I have looked at why

cis

-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H…H “

topological

” bond, rather than attraction between the H…H region to form a weak chemical “

bond

”. Here I take a look at what happens when that central C=C bond is gradually removed.
Combichem: an introductory example of the complexity of chemistry
Authors: Rzepa Henry
Published: September 2023

Chemistry gets complex very rapidly. Consider the formula CH

3

NO as the topic for a tutorial in introductory chemistry. I challenge my group (of about 8 students) to draw as many different molecules as they can using exactly those atoms. I imply that perhaps each of them might find a different structure; this normally brings disbelieving expressions to their faces.
Following one’s nose: a quadruple bond to carbon. Surely I must be joking!
Authors: Rzepa Henry
Published: September 2023

Do you fancy a story going from simplicity to complexity, if not absurdity, in three easy steps? Read on! The following problem appears in one of our (past) examination questions in introductory organic chemistry. From relatively mundane beginnings, one can rapidly find oneself in very unexpected territory. How would one make 3-nitrobenzonitrile?
The Dieneone-phenol controversies.
Authors: Rzepa Henry
Published: September 2023

During the 1960s, a holy grail of synthetic chemists was to devise an efficient route to steroids. R. B. Woodward was one the chemists who undertook this challenge, starting from compounds known as dienones (

e.g.

1

) and their mysterious conversion to phenols (

e.g.

2

or

3

) under acidic conditions.
Monastral: the colour of blue
Authors: Rzepa Henry
Published: September 2023

The story of Monastral is not about a character in the Magic flute, but is a classic of chemical serendipity, collaboration between industry and university, theoretical influence, and of much else.
The handedness of DNA: an unheralded connection.
Authors: Rzepa Henry
Published: September 2023

Science is about making connections. Plenty are on show in Watson and Crick’s famous 1953 article on the structure of DNA[cite]10.1038/171737a0[/cite] but often with the tersest of explanations. Take for example their statement “

Both chains follow right-handed helices

”. Where did that come from?
Triple metal delight
Authors: Rzepa Henry
Published: September 2023

Much like chocolate, some of us metallaholics cannot get enough. So WUQXIP proved an irresistible frolic (DOI: 10.1021/om020789h). Let us start with benzene.  It can have metals added in two ways, whilst preserving its essential aromaticity. Triple metal delight. Making a metal sandwich is of course very well known, ferrocene being the first example where the bonding was identified.
Anatomy of an arrow-pushing tutorial: reducing a carboxylic acid.
Authors: Rzepa Henry
Published: September 2023

Arrow pushing (why never pulling?) is a technique learnt by all students of organic chemistry (inorganic chemistry seems exempt!). The rules are easily learnt (supposedly) and it can be used across a broad spectrum of mechanism. But, as one both becomes more experienced, and in time teaches the techniques oneself as a tutor, its subtle and nuanced character starts to dawn.
An orbital analysis of the stereochemistry of the E2 elimination reaction
Authors: Rzepa Henry
Published: September 2023

The so-called

E2 elimination

mechanism is another one of those mainstays of organic chemistry. It is important because it introduces the principle that anti-periplanarity of the reacting atoms is favoured over other orientations such as the syn-periplanar form; Barton used this principle to great effect in developing the theory of conformational analysis. Here I explore its origins.
Janus mechanisms (the past and the future): Reactions of the diazonium cation.
Authors: Rzepa Henry
Published: September 2023

Janus was the mythological Roman god depicted as having two heads facing opposite directions, looking simultaneously into the past and the future. Some of the most ancient (

i.e.

19th century) known reactions can be considered part of a chemical mythology; perhaps it is time for a Janus-like look into their future. Reaction of the diazonium cation with cyanide.
Computers 1967-2011: a personal perspective. Part 2. 1985-1989.
Authors: Rzepa Henry
Published: September 2023

As a personal retrospective of my use of computers (in chemistry), the Macintosh plays a subtle role. 1985: In the previous part, I noted how the Corvus Concept computer introduced a network hard drive (these still being too expensive for any one individual to afford one); the same principle applied to the 1985 Macintosh but now relating to the remarkable introduction of the laser printer.
Molecular gymnastics in 2+2 cycloadditions. Two different moves compared.
Authors: Rzepa Henry
Published: September 2023

The previous post showed how the 2+2 cycloaddition of an alkene could occur by a sort of sideways insinuation of the bonds. I have also shown how the same reaction can occur with a dramatic rotation of one of the double bonds. This post compares the two moves side by side. 0.0 5.3 kcal/mol The forbidden dance The allowed dance. As is sometimes the case in real life, the forbidden option has the lower activation barrier!
Some fun with no-go areas of chemistry: cyclobutadiene.
Authors: Rzepa Henry
Published: September 2023

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.
Buses (and dyotropic rearrangements) always come in threes.
Authors: Rzepa Henry
Published: September 2023

The last two posts have played a game of find the electrons. We saw how the dyotropic rearrangement of ethane borrowed electrons from the C-C bond, and how 1,2,dibromoethane went ionic on us. How about this mixed system, in which a hydrogen and a BH

2

swap their positions? Dyotropic rearrangement involving boron and hydrogen. It is yet again different.
The formation of cyanohydrins: re-writing the text books. ! or ?
Authors: Rzepa Henry
Published: September 2023

Nucleophilic addition of cyanide to a ketone or aldehyde is a standard reaction for introductory organic chemistry. But is all as it seems? The reaction is often represented as below, and this seems simple enough. Cyanohydrin formation. But attention to detail suggests that, HCN being a weak acid, there will be only a very small concentration of cyanide anion in the presence of HCl.
A modern take on pericyclic cycloaddition. Dimerisation of cis-butene
Authors: Rzepa Henry
Published: September 2023

The π2 + π2 cyclodimerisation of cis-butene is the simplest cycloaddition reaction with stereochemical implications. I here give it the same treatment as I did previously for electrocyclic pericyclic reactions.
Shorter is higher: the strange case of diberyllium.
Authors: Rzepa Henry
Published: September 2023

Much of chemistry is about bonds, but sometimes it can also be about anti-bonds. It is also true that the simplest of molecules can have quite subtle properties. Thus most undergraduate courses in chemistry deal with how to describe the bonding in the diatomics of the first row of the periodic table.
Perbromate. A riddle, wrapped in a mystery, inside an enigma; but perhaps there is a key.
Authors: Rzepa Henry
Published: September 2023

Chemists love a mystery as much as anyone. And gaps in patterns can be mysterious. Mendeleev’s period table had famous gaps which led to new discovery. And so from the 1890s onwards, chemists searched for the perbromate anion, BrO

4

–

. It represented a gap between perchlorate and periodate, both of which had long been known. As the failure to turn up perbromate persisted, the riddle deepened.
Scholarly metadata in R
Authors: Chamberlain Scott
Published: September 2023

Scholarly metadata - the meta-information surrounding articles - can be super useful. Although metadata does not contain the full content of articles, it contains a lot of useful information, including title, authors, abstract, URL to the article, etc. One of the largest sources of metadata is provided via the Open Archives Initiative Protocol for Metadata Harvesting or OAI-PMH.
A stable borylene. An exercise in lateral thinking.
Authors: Rzepa Henry
Published: September 2023

I have often heard the question posed “

how much of chemistry has been discovered?

” Another might be “

has most of chemistry, like low-hanging fruit, already been picked?

”. Well, time and time again, one comes across examples which are only a simple diagram or so away from what might be found in any introductory chemistry text, and which would tend to indicate the answers to these questions is a
A short history of molecular modelling: 1860-1890.
Authors: Rzepa Henry
Published: September 2023

In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century.
The stereochemistry of [8+2] pericyclic cycloadditions.
Authors: Rzepa Henry
Published: September 2023

Steve Bachrach has blogged on the reaction shown below. If it were a pericyclic cycloaddition, both new bonds would form simultaneously, as shown with the indicated arrow pushing. Ten electrons would be involved, and in theory, the transition state would have 4n+2 aromaticity.
Facilitating Open Science with Python
Authors: Moss Steve
Published: September 2023

A guest blog post by Steve Moss

Why Python? A little background! I started using Python in the summer of 2010. I had applied for the Master of Research postgraduate degree in Computational Biology at the University of York. They teach the programming portion of their course using Python. I thought it might be useful to learn it, before starting, to give me a bit of a head start.
The inner secrets of an ion-pair: Isobornyl chloride rearrangements.
Authors: Rzepa Henry
Published: September 2023

Observation of the slow racemization of isobornyl chloride in a polar solvent in 1923-24 by Meerwein led to the recognition that mechanistic interpretation is the key to understanding chemical reactivity. The hypothesis of ion pairs in which a

chloride anion

is partnered by a

carbocation

long ago entered the standard textbooks (see DOI 10.1021/ed800058c and 10.1021/jo100920e for background reading).
Updating a worked problem in conformational analysis. Part 1: the question.
Authors: Rzepa Henry
Published: September 2023

Conformational analysis comes from the classical renaissance of physical organic chemistry in the 1950s and 60s. The following problem is taken from E. D. Hughes and J. Wilby

J. Chem. Soc.

, 1960, 4094-4101, DOI: 10.1039/JR9600004094, the essence of which is that Hofmann elimination of a neomenthyl derivative (C below) was observed as

anomalously

faster than its menthyl analogue.
Gravitational fields and asymmetric synthesis
Authors: Rzepa Henry
Published: September 2023

Our understanding of science mostly advances in small incremental and nuanced steps (which can nevertheless be controversial) but sometimes the steps can be much larger jumps into the unknown, and hence potentially more controversial as well. More accurately, it might be

e.g.

relatively unexplored territory for say a chemist, but more familiar stomping ground for say a physicist.
The mechanism of the Baeyer-Villiger rearrangement.
Authors: Rzepa Henry
Published: September 2023

The Baeyer-Villiger rearrangement was named after its discoverers, who in 1899 described the transformation of menthone into the corresponding lactone using Caro’s acid (peroxysulfuric acid). The mechanism is described in all text books of organic chemistry as involving an alkyl migration.
The melting points from benzene to cyclohexane: a prime example of dispersion forces in action?
Authors: Rzepa Henry
Published: September 2023

One of the delights of wandering around an undergraduate chemistry laboratory is discussing the unexpected, if not the outright impossible, with students. The >100% yield in a reaction is an example. This is sometimes encountered (albeit only briefly) when students attempt to recrystallise a product from cyclohexane, and get an abundant crop of crystals when they put their solution into an ice-bath to induce the crystallisation.
The inner secrets of the DNA structure.
Authors: Rzepa Henry
Published: September 2023

In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets. A fragment of a single chain of DNA, taken from a Z-helix.
Validating the chemical literature heritage. Eudesma-1,3-dien-6,13-olide.
Authors: Rzepa Henry
Published: September 2023

Previously, I had noted that Corey reported in 1963/65 the total synthesis of the sesquiterpene dihydrocostunolide. Compound

16

, known as

Eudesma-1,3-dien-6,13-olide

was represented as shown below in black; the hydrogen shown in red was implicit in Corey’s representation, as was its stereochemistry. As of this instant, this compound is just one of 64,688,893 molecules recorded by Chemical Abstracts.
is.invasive()
Authors: Bartomeus Ignasi
Published: September 2023

The following was a guest post from Ignasi Bartomeus, originally posted on his blog on 26 Nov, 2012. Check out a related blog post here. Note the functionality discussed in this post is now in our taxize package under the function gisd_isinvasive. We hacked out a quick Shiny app so you can play around with the below function in taxize on the web to get invasive status and plot it on a phylogeny.
Chemistry in an attosecond.
Authors: Rzepa Henry
Published: September 2023

An attosecond is 10

-18

s. The chemistry that takes place on this timescale is called electron dynamics. For example, it is the time taken for an electron to traverse the 1s orbit in a hydrogen atom. And chemists are starting to manipulate electrons (and hence chemistry) on this timescale; for example a recent article (DOI: 10.1021/ja206193t) describes how to control the electrons in benzene using attosecond laser pulses.
Data-round-tripping: moving chemical data around.
Authors: Rzepa Henry
Published: September 2023

For those of us who were around in 1985, an important chemical IT innovation occurred. We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the

clipboard

, paste it into a word processor (it was called a Macintosh). Perchance even print the result on a laserprinter.
Mechanistic morphemes. Perisolvolysis of a cyclopropyl chloride.
Authors: Rzepa Henry
Published: September 2023

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.
Mindless chemistry or creative science?
Authors: Rzepa Henry
Published: September 2023

The (hopefully tongue-in-cheek) title

Mindless chemistry

was given to an article reporting[cite]10.1021/jp057107z[/cite] an automated stochastic search procedure for locating all possible minima with a given composition using high-level quantum mechanical calculations. “Many new structures, often with nonintuitive geometries, were found”. Well, another approach is to follow unexpected hunches.
Are close H…H contacts bonds? The dénouement!
Authors: Rzepa Henry
Published: September 2023

I wrote earlier about the strangely close contact between two hydrogen atoms in

cis

-butene. The topology of the electron density showed characteristics of a bond, but is it a consensual union?
The chemistry behind a molecular motor. The four wheels?
Authors: Rzepa Henry
Published: September 2023

In the previous post, I wrote about the processes that

might

be involved in a molecular wheel rotating. A nano car has four wheels, and surely the most amazing thing is how the wheels manage to move in synchrony. This is one hell of a tough problem, and I do not attempt an answer here, but simply record an odd observation.
Hexavalent carbon revisited (and undecavalent boron thrown in).
Authors: Rzepa Henry
Published: September 2023

A little while ago, I speculated (blogs are good for that sort of thing) about hexavalent carbon, and noted how one often needs to make (retrospectively) obvious connections between two different areas of chemistry. That post has attracted a number of comments in the two years its been up, along the lines:

what about carboranes?

So here I have decided to explore that portal into boron chemistry.
The hydroboration-oxidation mechanism: An updated look.
Authors: Rzepa Henry
Published: September 2023

One thing almost always leads to another in chemistry. In the last post, I described how an antiperiplanar migration could compete with an antiperiplanar elimination. This leads to the hydroboration-oxidation mechanism, the discovery of which resulted in Herbert C. Brown (at least in part) being awarded the Nobel prize in 1979. This reaction represents a fairly steep learning curve for new students of organic chemistry.
Henry Armstrong: almost an electronic theory of chemistry!
Authors: Rzepa Henry
Published: September 2023

Henry Armstrong studied at the Royal College of Chemistry from 1865-7 and spent his subsequent career as an organic chemist at the Central College of the Imperial college of Science and technology until he retired in 1912.
Mechanism of the reduction of a carboxylic acid by borane: revisited and revised.
Authors: Rzepa Henry
Published: September 2023

I asked a while back whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I suggested a possible mechanism.
The colour of purple
Authors: Rzepa Henry
Published: September 2023

One of my chemical heroes is William Perkin, who in 1856 famously (and accidentally) made the dye mauveine as an 18 year old whilst a student of August von Hofmann, the founder of the Royal College of Chemistry (at what is now  Imperial College London). Perkin went on to found the British synthetic dyestuffs and perfumeries industries.
Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?
Authors: Rzepa Henry
Published: September 2023

On 8th August this year, I posted on a fascinating article that had just appeared in Science[cite]10.1126/science.1188002[/cite] in which the crystal structure was reported of two small molecules, 1,3-dimethyl cyclobutadiene and carbon dioxide, entrapped together inside a calixarene cavity.
Reductive ozonolysis: the interesting step.
Authors: Rzepa Henry
Published: September 2023

The mechanism of the reaction of alkenes known as ozonolysis was first set out in its modern form by Criegee. The crucial steps, (a), (b) and (d), are all pericyclic cycloaddition/eliminations.
More is more: the dyotropic rearrangement of 1,2-dibromoethane.
Authors: Rzepa Henry
Published: September 2023

In the previous post,  I discussed what we could learn from ethane by forcing it into a pericyclic dyotropic rearrangement. We saw how it voraciously scavenged two electrons from the  C-C bond to achieve this. What if we give it more electrons? Thus 1,2-dibromoethane undergoing the same reaction. Dyotropic rearrangement of 1,2-dibromoethane.
Metallic carbon nanotori
Authors: Rzepa Henry
Published: September 2023

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.
Bonds.
Authors: Rzepa Henry
Published: September 2023

Bonds are a good example of something all chemists think they can recognise when they see them. But they are also remarkably dependent on context. We are running a molecular modelling course at the moment, and I found myself explaining to someone how very context-sensitive they can be. I thought it might be useful to collect my thoughts here.
Déjà vu all over again. Are H…H interactions attractive or repulsive?
Authors: Rzepa Henry
Published: September 2023

The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF

3

). The previous post on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in the Cambridge data base, and focus on another interesting example. 9-anthranyl derivatives. Click for Pirkle with normalised C-H lengths.
Embedding molecules in blogs: ChemDoodle, WebGL and SVG
Authors: Rzepa Henry
Published: September 2023

If you get a small rotatable molecule below, then ChemDoodle/HTML5/WebGL is working. Why might this be important? Well, the future is mobile, in other words, devices that rely on batteries or other sources of built-in power. This means the power guzzling GPU cards of the past (some reach ~400 Watts!) cannot be used.
Anatomy of a simple reaction: the hydration of an alkene.
Authors: Rzepa Henry
Published: September 2023

The hydration of an alkene by an acid is one of those fundamental reactions, taught early on in most chemistry courses. What can quantum mechanics teach us about the mechanism of the reaction? The hydration of ethene by a hydronium cation.
Computers 1967-2011: a personal perspective. Part 4. Moore’s Law and Molecules.
Authors: Rzepa Henry
Published: September 2023

Moore’s law

describes a long-term trend in the evolution of computing hardware, and it is often interpreted in terms of processing speed. Here I chart this rise in terms of the size of computable molecules. By computable I mean specifically how long it takes to predict the geometry of a given molecule using a quantum mechanical procedure. LSD, the 1975 benchmark for computable molecules.
Data-round-tripping: wherein the future?
Authors: Rzepa Henry
Published: September 2023

Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists.
Less is more: the dyotropic rearrangement of ethane
Authors: Rzepa Henry
Published: September 2023

In a time when large (molecules) are considered beautiful (or the corollary that beauty must be big), it is good to reflect that small molecules may teach us something as well. Take ethane. Is there anything left which has not been said about it already? Well, consider the reaction below, in which two hydrogen atoms mutually hop from one carbon to the other. The dyotropic reaction of ethane.
The thermodynamic energies of left and right handed DNA.
Authors: Rzepa Henry
Published: September 2023

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!
Violations. There are none! Part 2.
Authors: Rzepa Henry
Published: September 2023

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.
A historical detective story: 120 year old crystals
Authors: Rzepa Henry
Published: September 2023

In 1890, chemists had to work hard to find out what the structures of their molecules were, given they had no access to the plethora of modern techniques we are used to in 2010. For example, how could they be sure what the structure of naphthalene was? Well, two such chemists, William Henry Armstrong (1847-1937) and his student William Palmer Wynne (1861-1950;
Spotting the unexpected. The trifluoromeric effect in the hydration of the carbonyl group.
Authors: Rzepa Henry
Published: September 2023

The equilibrium for the hydration of a ketone to form a gem-diol hydrate is known to be highly sensitive to substituents. Consider the two equilibria: For propanone, it lies almost entirely on the left, whereas for the hexafluoro derivative it is almost entirely on the right. The standard answer to this is that electron-withdrawing substituents destabilize the carbonyl compound more than the hydrate.
Breast Cancer Forecasting Using Machine Learning Algorithms
Authors: A.Thilaka  , E.Sundaravalli
Published: September 2023

Some of the most prevalent and significant causes for malignancies in women is breast cancer. It is presently a widespread health problem, and it has recently become more frequent. The greatest method for managing breast cancer symptoms is early identification. The only kind of cancer that primarily affects women globally is breast cancer, which has the potential to be a major cause of mortality. Early detection of breast cancer is crucial in order to properly treat it and save many lives. This paper covers the results and analyses of several machine learning algorithms for identifying breast cancer. Several machine learning models used the information once it was analyzed. In this paper the Random forests and SVC algorithms were applied and compare the performance of these algorithms. The dataset was taken from UCI repository. Analyze and compare the classifiers' performance in terms of accuracy, precision, and f1-Score in addition. For implementing the ML algorithms, the dataset was split among training and testing phases. The notebook application Jupyter was used to implement these models. When compared to the other two models, it was successfully proven that the SVC model offers the best results. SVC's accuracy of 93% is greater than the method described earlier in that regard. The method used by this model, which will classify cancer into benign and malignant categories, yields the best results.
Machine Learning Techniques for Lung Cancer Risk Prediction using Text Dataset
Authors: Kumar Mohan  , Bhraguram Thayyil
Published: September 2023

The early symptoms of lung cancer, a serious threat to human health, are comparable to those of the common cold and bronchitis. Clinical professionals can use machine learning techniques to customize screening and prevention strategies to the unique needs of each patient, potentially saving lives and enhancing patient care. Researchers must identify linked clinical and demographic variables from patient records and further pre-process and prepare the dataset for training a machine-learning model in order to properly predict the development of lung cancer. The goal of the study is to develop a precise and understandable machine learning (ML) model for early lung cancer prediction utilizing demographic and clinical variables, as well as to contribute to the growing field of medical research ML application that may improve healthcare outcomes. In order to create the most effective and precise predictive model, machine learning techniques like Logistic Regression, Decision Tree, Random Forest, Support Vector Machine, K-Nearest Neighbor (KNN), and Naive Bayes were utilized in this article.
Enhancing Performance of Hybrid Electric Vehicle using Optimized Energy Management Methodology
Authors: Prabhdeep Singh
Published: September 2023

The fuel consumption and the fuel management strategy (PMS) of the hybrid electric vehicle are closely linked (HEV). In this study, a hybrid power management technique and an adaptive neuro-fuzzy inference (ANFIS) method are established. Artificial intelligence represents a huge improvement in electricity management across different energy sources (AI). The main energy source of the hybrid power supply is a proton exchange membrane fuel cell (PEMFC), while its electrical storage devices are a battery bank and an ultracapacitor. The hybrid electric vehicle's power management strategy (PMS) and fuel consumption are closely related (HEV). In this paper, an adaptive neuro-fuzzy inference and hybrid power management strategy (ANFIS) approach is developed. A significant advance in electricity management across multiple energy sources is artificial intelligence (AI). The proton exchange membrane fuel cell (PEMFC) serves as the primary energy source of the hybrid power supply, and the ultracapacitor and battery bank serve as its electrical storage components.
Analysis Role of ML and Big Data Play in Driving Digital Marketing's Paradigm Shift
Authors: Ashish Kumar Pandey
Published: September 2023

Marketing strategies are being revolutionized by the development of user data and the expanding usability of Machine Learning (ML) as well as Big Data approaches. The wide variety of options that ML and Big Data applications provide in building and sustaining a competitive corporate edge are not fully understood by researchers and marketers. Based on a thorough analysis of academic and commercial literature, we offer a classification of ML and Big Data use cases in marketing in this article. In order to effectively employ ML and Big Data in marketing, we have discovered 11 recurrent use cases that are grouped into 4 homogenous families. These families are: fundamentals of the consumer, the consumer experience, decision-making, and financial impact. We go over the taxonomy's repeating patterns and offer a conceptual framework for understanding and extending it, emphasizing the practical ramifications for marketers and academics.
Clinical Prediction on ML based Internet of Things for E-Health Care System
Authors: Shivi Chaturvedi
Published: September 2023

Machine learning (ML) is a powerful method for uncovering hidden patterns in data from the Internet of Things (IoT). These hybrid solutions intelligently improve decision-making in a variety of fields, including education, security, business, and healthcare. IoT uses machine learning to uncover hidden patterns in bulk data, allowing for better forecasting and referral systems. IoT and machine learning have been embraced in healthcare so that automated computers may generate medical records, anticipate diagnoses, and, most critically, monitor patients in real time. On different databases, different ML algorithms work differently. The overall outcomes may be influenced by the variance in anticipated results. In the clinical decision-making process, there is a lot of variation in prognostic results. As a result, it's critical to comprehend the various machine learning methods utilised to handle IoT data in the healthcare industry. Machine learning of adaptive neuro fuzzy inference system (ANFIS) algorithms is being used to monitor human health in this suggested effort. The UCI database is used for initial training and validation of machine learning systems. Using the IoT system, the test phase collects the person's heart rate, blood pressure, and temperature. The test stage assesses if the sensor data obtained by the IoT framework can predict any irregularities in the health state. To evaluate the accuracy of the forecast %, statistical analysis is performed on cloud data acquired from the IoT. Other routines are derived from K-neighbour results.
Do-It-Yourself, Low-Cost Pop-Up Usability Labs for Learning Experience Designers
Authors: Schmidt Matthew , Earnshaw Yvonne
Published: September 2023

This article introduces the concept of pop-up usability labs as a practical and cost-effective solution for conducting usability testing in real-world learning experience design (LXD) contexts. Various configurations of pop-up usability labs are presented, including budget-friendly, portable, semi-permanent, and mobile setups, along with recommendations for hardware and software requirements. The importance of selecting appropriate software packages for usability data analysis is emphasized, with suggestions for low-cost, no-cost, and open-source options for quantitative and qualitative data analyses. Pop-up usability labs offer numerous advantages, such as accommodating limited funding and reaching participants in rural areas. However, they also present challenges that require LXD professionals to become familiar with the equipment and data analysis methods. Despite these limitations, pop-up usability labs provide a viable, resource-efficient approach for LXD professionals to conduct usability testing in real-world settings, identify and address design flaws related to usability, and embrace more human-centered design practices in the development of educational and learning technology products, systems, or services.
What’s the Difference Between Learning Experience Design and Instructional Design?
Authors: Reigeluth Charles , An Yunjo
Published: September 2023

Some proponents of learning experience design (LXD) have set it apart as an alternative to instructional design (ID). This article explores the similarities and differences between LXD and ID and whether the two are really in conflict. It begins by defining learning experience (LX). Then it contrasts LX with what instruction should be like. Next, it focuses on defining LXD and contrasting it with ID. It explores some issues that influence the view of LXD as an evolution of ID or as a new discipline or field. Finally, it offers some suggestions for advancing knowledge in this important area.
Designing and Evaluating a 3D Virtual World Game for English Language Learning: A Learning Experience Design Approach
Authors: Huang Rui
Published: September 2023

This study took an iterative multi-phase learning experience design (LXD) approach to design and evaluate a 3D virtual world game focusing on English language learning. Multiple LXD methods were conducted including empathy interview, heuristic evaluation, cognitive walkthrough, and concurrent think-aloud usability testing, in order to identify usability problems and how learners rated the usability of the intervention. A total of 137 usability problems were identified. Learners rated the game with high overall perceived usability. This study provided evidence for the multi-dimensional usability framework proposed by Jahnke and colleagues and its application at a micro level.
Learning Experience Design in the Light of Design Knowledge and Philosophy
Authors: Gray Colin , Boling Elizabeth
Published: September 2023

Instructional design has been dominated by a philosophy focused on efficiency, effectiveness, and appeal. Learning Experience Design (LXD), emerging recently, offers a different set of values with the potential to enhance and evolve the practice of design for teaching and learning. Using the concepts of knowledge and philosophy from the literature on design theory, we challenge the notion that LXD is a discrete new field separate from instructional design and instead identify LXD as an alternate philosophy of design. We conclude with the opportunity to recognize additional philosophies in the field and consider the impacts of philosophy on knowledge-building practices.