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Making Molecules @makingmolecules.com · 2d

More electrophilic aromatic substitution. Last week was the general reaction, today covers (de)activation & directing effects.
It is a #UG simplification so no discussion of inductive effect vs hyperconjugation etc (or the transannular effect). Enjoy #ChemEd #Chemistry #ChemSky

A one page summary of activating and directing effects in electrophilic aromatic substitution. There are 6 boxes. 1 - introduces naming relative to the initial substituent (ortho, meta and para). 2 - then looks at strong activating groups (EDG) & the fact that they are ortho para directing. 3 - introduces weak activators like alkyl groups (and we can argue whether I should use inductive effects or hyperconjugation as the reason). These are mostly ortho directing electronically but para directing due to steric. 4 - deactivating groups due to electron withdrawing groups (EWG) that are meta directing (or rather not orthodox and para directing). 5 - states that halides are deactivating but ortho para directing then 6 gives an example of using these effects.

Making Molecules @makingmolecules.com · 9d

Here's a #ChemEd #Chemistry #ChemSky summary of electrophilic aromatic substitution. As an ex-[2.2]paracyclophane chemist, this is a reaction dear to my heart.
Here is just the basic mechanism aimed at UG (the mechanisms for electrophile activation are www.makingmolecules.com/blog/electro...).
Enjoy

A summary of electrophilic aromatic substitution. There are six boxes. The first gives the general reaction and why it is different to addition to an alkene. The second gives the general curly arrow mechanism. After that it is a look at specific examples: bromination, nitration, sulfonation, Friedel-Crafts alkylation and Friedel-Crafts acylation. If you want more detail of the mechanisms of activation of the electrophiles read https://www.makingmolecules.com/blog/electrophilic-aromatic-substitution

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Making Molecules @makingmolecules.com · 16d

These #ChemEd #Chemistry #ChemSky summaries target early UG & the basics. Except when they don't. Here is a follow-up to anti-Markovnikov addition summary & a look at asymmetric hydroboration. It's still a summary. Only substrate control & pinene reagents. www.makingmolecules.com/blog/asymhyd...

A summary of asymmetric hydroboration under either substrate control or pinene reagent control. The first box shows simple hydroboration. The second box shows an example of stereoselective hydroboration of a chiral cyclic molecule or substrate control. Then there is a look at stereoselective hydroboration of acyclic alkenes with an allylic stereocentre. Finally, there is reagent controlled hydroboration using pinene derived reagents to control the enantioselectivity of hydroboration.

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Making Molecules @makingmolecules.com · 22d

No MakingMolecules #ChemEd summary today as NZ_Molecules is in Singapore with the wonderful folk at Gerstel (& only being a tiny bit jealous of their kit).

I feel a summary of sensory directed analysis coming at some point as it is simply fascinating (& a powerful technique to help at work).

Making Molecules @makingmolecules.com · Sep 9

A #ChemEd #Chemistry #ChemSky summary of anti-Markovnikov addition to alkenes using radical hydrobromination or hydroboration/oxidation. It's classic UG material introducing regioselectivity/stabilising intermediates. It's a simplification, more at www.makingmolecules.com/blog/antimar...

A graphical summary of anti-Markovnikov addition to alkenes. It starts by showing the different products possible by hydrobromination and how the choice of reagent and control the regiochemistry. The second box contains the radical chain mechanism that explains anti-Markovnikov addition of HBr. The second half of the summary looks at hydroboration-oxidation and its mechanism.

Making Molecules @makingmolecules.com · Sep 2

No new #ChemEd #Chemistry #ChemSky summary today, just an attempt to summarise the alkene chemistry that has been covered in the last couple of infographics. It also acts as a spoiler for next week's look at anti-Markovnikov addition.
Hopefully it still has some use.

A summary of common electrophilic addition to alkenes including bromination, bromohydrin formation, hydration, epoxidation, hydrogenation, dihydroxylation, and radical reactions.

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Making Molecules @makingmolecules.com · Aug 26

A #ChemEd #Chemistry #ChemSky intro to the frontier molecular orbital view of electrophilic addition to alkenes. It is a companion to the last one (bsky.app/profile/maki...). It is an oversimplification but useful at #UG level (I hope).
It shows the limitations of curly arrow mechanisms.
Enjoy.

The frontier molecular orbital (valence bond) view of electrophilic addition to alkenes employed by organic chemists at undergraduate level. The summary shows the orbitals involved in hydrohalogenation, bromination, epoxidation and some of the factors influencing reactivity. It is a companion to last week's curly arrow summary.

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Making Molecules @makingmolecules.com · Aug 19

The 1st in a series of #ChemEd #Chemistry #ChemSky summaries on the reactions of alkenes. I'm starting with nucleophilic alkenes & the common UG reactions of the addition of HX, Br2, epoxidation etc. It's a bit crowded but hopefully it is useful. More details & reactions over the coming weeks.

A summary of the reactions of alkenes behaving as nucleophiles. This covers the common examples such as the addition of HX, bromination, bromhydrin formation, epoxidation with peracids and syn dihydroxylation. In each case, I've given the curly arrow mechanism and a brief explanation of any regioselectivity. There is also a quick overview of carbocation stability (again, to help with the explanation of regioselectivity).

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Making Molecules @makingmolecules.com · Aug 12

A #ChemEd #Chemistry #ChemSky summary of acyl substitution. There is one mechanism repeated multiple times (with variations). It is addition & elimination. Acylation is possibly the most important reaction (along with proton transfer) for non-chemists taking chemistry. Hope this is useful. Enjoy.

A summary on nucleophilic acyl substitution. It starts with the loathsome chart of carboxylic acid derivative reactivity (with the addition of pKa just to highlight the important of leaving group on reactivity as well as the normal discussion of electrophilicity). Then there is the mechanism for the formation of acyl chlorides. Important for chemists, not so important for those interested in biology/biochemistry. Then there are three general mechanisms that can be applied to a host of reactions. The first is the attack of an anionic nucleophile. The second is acyl substitution with a neutral nucleophile and finally we have acid-catalysed acyl substitution. Hopefully these can be applied to the vasty majority of reactions that UG will encounter.

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Making Molecules @makingmolecules.com · Aug 5

More nucleophilic addition to aldehydes/ketones, this #ChemEd #Chemistry #ChemSky summary covers condensation & the formation/hydrolysis of acetals, imines & enamines. The mechanism is the same each time, but understanding why they deliver different products is important. Enjoy

A summary of the condensation reactions of aldehydes/ketones. This is nucleophilic addition to the carbonyl with substitution of the oxygen atom. There are six sections. The first shows the formation of an acetal or addition of two equivalents of alcohol across an aldehyde or ketone. The second shows the reverse reaction, the addition of water across an acetal to give an aldehyde or ketone. The third box shows the mechanism of acetal formation and discusses how to make the reaction irreversible. The fourth section is imine formation and the addition of a primary amine to an aldehyde/ketone. It includes the mechanism. The fifth box is enamine formation by using a secondary amine. And finally there is summary about the differences between the addition of alcohols, primary or secondary amines.

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Making Molecules @makingmolecules.com · Jul 29

A #ChemEd #Chemistry #ChemSky intro to models for explaining diastereoselectivity of nuc addition to C=O with an α stereocentre. It is a huge simplification. A tease for a fascinating subject. Other models exist but these are the ones often found at UG. Enjoy www.makingmolecules.com/blog/diaster...

A summary of the simple models for diastereoselective addition to aldehydes/ketones. The summary is divided into seven sections. 1. An introduction showing a nucleophile attacking an aldehyde with an α stereocenter. 2. An assumption that the nucleophile approaches along the Bürgi-Dunitz angle. 3. The nucleophile will be assumed to be a bare anion (this box shows that this is rarely true). 4. Felkin-Anh model. 5. Polar Felkin-Anh model. 6. Modified Cornforth model. 7. Cram chelation model.

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Making Molecules @makingmolecules.com · Jul 22

This #ChemEd #Chemistry #ChemSky summary is an intro to nucleophilic addition to aldehydes/ketones. It's the 1st of many as I think carbonyl addition is far more useful than the traditional Sn1/Sn2 approach for teaching the basics (& more examples in biology). Hopefully it's useful. Enjoy.

Nucleophilic addition to aldehydes and ketones. This is an introduction to this vital reaction. It just covers simple addition and some guidelines to whether the reaction is reversible or irreversible. Hopefully, it acts as the foundations to more discussion about specific examples. There are 5 boxes. 1. Shows why the carbonyl group is electrophilic. 2. looks at the general reaction mechanism of addition and then protonation (and I am aware that this can be reversed but you've got to stat somewhere). 3. Is irreversible addition and protonation. 4. Is reversible addition with either a nitrile or alcohol. 5. Finally shows the orbitals but is really just a teaser.

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Making Molecules @makingmolecules.com · Jul 15

There haven’t been any updates to MakingMolecules, as I was preparing a workshop on #SciCommun for MESA www.linkedin.com/company/macd...
These slides (alt text for an explanation) give a flavour of the day.
It was a fun day with a great bunch of scientists.
MakingMolecules will return soon(ish).

Two slides from a science communication workshop given to MESA students. The first slide is the title and says "Tips on Science Communication" and "Gareth Rowlands"
Second slide was a summary that covers the four key concepts: 1. Have one big idea, 2. Know your audience, 3. Present a story, 4. Refine, edit and practice.

Two more slides. The first shows pictures I made using PowerPoint - one is of a small extracellular vesicles and the other is of a membrane used in TRPS for counting particles.
The second slide shows how you can use the three act model to introduce a story to the communication. It is based around the AND, BUT, THEREFORE method of story telling.

Making Molecules @makingmolecules.com · Jun 19

It has become tradition for MakingMolecules to post a chemistry-related celebration of Matariki & the Māori New Year. This year I've added Puanga (Rigel) as it is more visible in the Manawatū. By luck, I have celebrated the 200 anniversary of benzene as well! www.chemistryworld.com/opinion/benz...

A chemistry themed celebration of Matariki and Puanga. The text is Mānawatia a Matariki mā Puanga that hopefully means welcome/celebrate Matariki and Puanga.

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Making Molecules @makingmolecules.com · Jun 10

The previous #ChemEd #Chemistry #ChemSky summaries provided the background to org rcts (except the acid/base 1 which is THE most important org rct). Here are curly arrows, the last thing I need before starting reactions! It's a summary, more details elsewhere www.makingmolecules.com/blog/curlyar...

A summary covering the basics of an organic reaction mechanism and the curly arrow (aka the greatest invention ever).
There are six sections to this summary. The first tries to explain what a reaction mechanism is. The second then introduces the curly arrow and its colleague, the curly fishhook. Third is a list of some of the more common nucleophiles and electrophiles. Fourth is one way of approaching writing a reaction mechanism (there are other approaches. This may not even be my favourite approach as I have taught a number but it seemed to work well in this context). Fifth is the three common 'types' of curly arrow (they aren't different, so type might be the wrong word. Basically, students will commonly encounter three combinations of source and acceptor). Finally, there are some common reaction patterns that you see in many reactions.

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Making Molecules @makingmolecules.com · May 20

A #ChemEd #Chemistry #ChemSky summary on my favourite subject (after dairy chem of course), chirality. I love that a small change (reflection) makes a big difference. Students seem to hate chirality so here is a simple intro (more stereochem: www.makingmolecules.com/blog/tpyjoy3...)

A summary of chirality and chemistry. Introduces the idea that mirror images do not have to be the same, that they can have different properties. Tries to do it at a very simple level with not discussion of point groups or symmetry.

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Making Molecules @makingmolecules.com · May 6

Following the pKa scales, here is a #ChemEd #Chemistry #ChemSky intro to predicting relative acidity based on stability of the conjugate base. It's a simple #UG look at a complex subject. Far too simple in retrospect. Here is a blog (www.makingmolecules.com/blog/predict...) that gives more context.

A one page summary introducing the idea of predicting relative acidity (which compound will be the more acidic) based on the stability of the conjugate base, the anion. There are six boxes. The first introduces the idea of comparing acidity, the second looks at the effect of the atom on the stability of a charge. The third looks at the effect of delocalisation, then in the fourth we have the inductive effect. The fifth has hybridisation and the last is an example.

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Making Molecules @makingmolecules.com · Apr 29

The pKa of some org mols in MeCN. Like the earlier scales (H2O bsky.app/profile/maki... & DMSO bsky.app/profile/maki...), the data isn't mine (refs on sheet). This is an attempt to visualize the data differently.

Some will like it, some won't.

More #ChemEd #Chemistry summaries next week.

Enjoy

A visualisation of the pKa scale of some common organic molecules in acetonitrile. Original values taken from Leito & colleagues but all mistakes are my own. Landscape version.

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Making Molecules @makingmolecules.com · Apr 22

Occasionally, I take #ChemEd #ChemSky requests & after the pKa scale in H2O, I was asked for DMSO & MeCN versions. Here it is for DMSO. As before, it's nothing new. Values are taken from Reich/Bordwell (ref at bottom of scale) & I've just tried to make them more visual. I like pictures not tables.

A visualisation of the pKa scale of some common organic molecules in DMSO. Original values taken from Hans Reich & Bordwell but all mistakes are my own. Landscape version.

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Making Molecules @makingmolecules.com · Apr 9

Yup, definitely more than one way to do this & I've tried a few in my time! No idea if this one was better/worse than the others. Just fun/different to try & the feedback might help a new version (if there is another version...(A) writing something new more fun & (B) I left academia)

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Making Molecules @makingmolecules.com · Apr 8

Re-inventing the wheel. Instead of a #ChemEd #Chemistry #ChemSky summary here is my version of a pKa (in H2O) scale. Values are taken from the wonderful Evans/Ripin & Hans Reich resources. If you want a table, I recommend these.

This was an attempt at a more visual representation of the data

Enjoy

A visualisation of the pKa scale of some common organic molecules in water. Original values taken from Dave Evans, DH Ripin & Hans Reich but all mistakes are my own. The landscape version

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Making Molecules @makingmolecules.com · Apr 1

The last 2 summaries looked at equilibria in preparation for this #ChemEd #Chemistry #ChemSky summary on acids/bases. Protonation (hydronation for the pedantic) & proton (does anyone call H+ a hydron?) transfers are probably the most important reaction in org chem.

Enjoy this intro (more to come)

A summary of acids and bases. Six boxes including the general reaction, the classic pH scale, a definition of strong and weak acids, a discussion of the direction of the reaction. The use of pKa and a cut down pKa scale. There will be a more complete pKa scale (using Evans and Reich values) at a later stage.

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Making Molecules @makingmolecules.com · Mar 27

Congrats...well deserved and I know a lot of students (& staff) that love your graphics

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Making Molecules @makingmolecules.com · Mar 25

Seems I missed world frog day (bsky.app/profile/comp...) but here are some random posters I made when I was learning to use Affinity Designer. More than a little inspired by the records/designers I like, such as the Designers Republic ... there are lots more but they're all a little rubbish

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Making Molecules @makingmolecules.com · Mar 25

The follow up to last week's #ChemEd #Chemistry #ChemSky summary on equilibria, this one looks at Le Chatelier's Principle & outlines the effect of common stresses on equilibria.
Inspired either by Roy Lichtenstein or Damien Hirst, there are lots of dots (it's a joke ... Lichtenstein not Hirst)

A visual summary of Le Chatelier's Principle and the effect of stresses on equilibrium reactions. There are just three boxes. The first paraphrases Le Chatelier's principle (if you disturb an equilibrium it will respond by shifting in the direction that counteracts the change). The second box shows the effect of adding more starting material, changing the pressure or heating a reaction in a cartoon style using dots to represent molecules. It is not accurate but the principle is what matters. The final box shows all the different effects of stresses on a simple exothermic reaction.

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