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Making Molecules
@makingmolecules.com
950 followers 780 following 110 posts
Making molecules - trying to explain chemistry one page at a time.

One page summaries and more wordy descriptions found at:
https://www.makingmolecules.com
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After 2 months of aromatic chem, here is something a little different (but not that different) & a #Chemistry #ChemSky #ChemEd summary on conjugate or 1,4- or Michael additions.
To sound like a stuck record, it is aimed at UG with only the general mechanism & brief notes on regioselectivity.
Enjoy.
A one page summary of conjugate additions. It is split into four sections. The first is the overall transformation with a list of the general structures that can participate in conjugate additions. The second section is a general formula. It covers the main steps but is a little vague on the proton transfers (like most organic chemists). Next there is a brief look at regioselectivity and what factors influence 1,2-addition versus 1,4-addition. It is not in depth but gives pointers. Finally, there are some examples.
November 25, 2025 at 7:22 AM
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The last nucleophilic aromatic substitution #Chemistry #ChemEd #ChemSky summary is a summary of the previous summaries. It shows 4 mechanisms of nucleophilic aromatic substitution including classic substitution, aryne intermediates, ionic & radical substitution of diazonium salts. Hope it helps.
A summary of the different methods for nucleophilic aromatic substitution. This includes the displacement of an activate leaving group (such as a fluoro derivative), the substitution of a halide through the formation of an aryne intermediate, and two mechanisms for the substitution of diazonium salts; either through an ionic mechanism or a metal mediated radical substitution.
November 18, 2025 at 7:38 AM
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With stunning originality & a certain amount of flare, I give you Nucleophilic Aromatic Substitution 3. A #ChemEd #Chemistry #ChemSky summary discussing substitution via aryne intermediates. It is pitched at #UG. More detail/references at www.makingmolecules.com/blog/benzyne
Hope it is useful
Enjoy
Another summary on nucleophilic aromatic substitution. In the first box, it shows that elimination can form an aryne that allows addition to occur. Overall, this results in substitution. The second box gives the mechanism and shows that two products can be formed depending on which end of the aryne the nucleophile adds. The third box shows a crude/simplified view of aryne structure while the final box shows one way of explaining regioselectivity (a more modern approach exists and there is a link to the appropriate paper).
November 11, 2025 at 7:45 AM
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The second #ChemEd #Chemistry #ChemSky summary on nucleophilic aromatic substitution. This time it covers the formation & use of diazonium salts. The substitution mechanism is either ionic or radical depending on the nucleophile.

Good(ish) with paracyclophane (honest)!

Hope this is useful.
Enjoy
A summary of nucleophilic aromatic substitution using diazonium salts. There is a summary of the most common transformations (phenols, halides, nitriles and a reduction). There is a curly arrow mechanism of diazonium salt formation. Finally, there is the mechanism of ionic substitution and the radical substitution.
November 4, 2025 at 7:23 AM
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After 3 #Chemistry #ChemSky #ChemEd summaries on electrophilic aromatic substitution, we move to the nucleophilic variant SNAr (surprise).
Not as common (due to structural limitations), but equally useful. Next week, the same reaction but with diazonium salts.
Hopefully no silly mistakes this time!
A one page summary of nucleophilic aromatic substitution. The first box introduces the transformation. The second is the general addition-elimination mechanism. The third looks at the importance of substitution patterns and the last box gives potential useful substituents and reagents.
October 21, 2025 at 6:53 AM
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Anyone for a summary of a summary?
After two weeks of #ChemEd #ChemSky #Chemistry summaries on electrophilic aromatic substitution here, by popular demand, is one chart that covers just the basics.
Enjoy.
A summary of electrophilic aromatic substitution. This really is the barebones - all it covers is the general mechanism, examples of the most common reactions and activation & directing effects. This is basically a revision sheet.
October 14, 2025 at 7:02 AM
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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.
October 7, 2025 at 7:37 AM
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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
September 30, 2025 at 7:27 AM
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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.
September 23, 2025 at 7:21 AM
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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).
September 16, 2025 at 2:10 PM
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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.
September 9, 2025 at 8:52 AM
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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.
September 2, 2025 at 8:16 AM
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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.
August 26, 2025 at 8:58 AM
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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).
August 19, 2025 at 8:23 AM
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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.
August 12, 2025 at 8:19 AM
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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.
August 5, 2025 at 8:14 AM
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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.
July 29, 2025 at 8:02 AM
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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.
July 22, 2025 at 8:00 AM
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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.
July 15, 2025 at 8:50 AM
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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.
June 19, 2025 at 8:25 AM
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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.
June 10, 2025 at 7:59 AM
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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.
May 20, 2025 at 9:35 AM
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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.
May 6, 2025 at 8:13 AM
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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.
April 29, 2025 at 8:17 AM
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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.
April 22, 2025 at 8:33 AM