Making Molecules

@makingmolecules

Making molecules - trying to explain chemistry one page at a time. One page summaries and more wordy descriptions found at:

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Making Molecules@makingmolecules· 13d

The next #ChemEd #Chemistry #ChemSky 1-page intro covers common [3,3]-sigmatropic rearrangements. Lovely reactions that are a nice way to form C-C bonds with good control of stereochemistry from readily formed precursors. As always, it's just an intro, no orbitals & no Woodward-Hoffmann. Enjoy.

This one-page summary looks at [3,3]-sigmatropic rearrangements. It starts by giving a quick run down of the naming convention (where the [3,3] or [i,j] nomenclature comes from. There is then an attempt to have one diagram cover all the common [3,3]-sigmatropic rearrangements such as the Cope, anionic oxy-Cope, Claisen and a host of modified Claisen rearrangements. This also gives a quick look at the chance of controlling the stereochmistry. Then there are examples of the anionic oxy-Cope rearrangement, the Johnson-Claisen and the Ireland-Claisen rearrangement. Hope you all like it.

Making Molecules@makingmolecules· Jul 14

This #ChemEd #Chemistry #ChemSky summary introduces 1,3-dipolar cycloadditions. It builds on the Diels-Alder 1 pagers & is another [4+2] cycloaddition but gives 5-membered rings. It is only an intro. More details will be on makingmolecules.com as soon as I've typed up my notes. Enjoy!

A one page summary of 1,3-dipolar cycloadditions. It starts with an introduction covering the general reaction and classifying 1,3-dipoles as either linear or bent. There are then four examples; nitrile oxide-alkene cycloadditions, nitrone-alkene cycloadditions, azide-alkyne cycloadditions and azomethine ylide cycloadditions (my favourite). The discussion of the azide reaction mentions the original pericyclic reaction and the catalysed variant that won the Nobel Prize.

Making Molecules@makingmolecules· Jun 16

#ChemEd #Chemistry #ChemSky summary looks at modifications of the Diels-Alder reaction. It includes IMDA (tie the ends together), HDA (swap one (or more) carbons out) & IEDDA. It mentions the old explanation for LA catalysis (the more modern explanation is at makingmolecules.com/blog/da-like...)

A summary of modified Diels-Alder reactions. It starts with the general reaction scheme showing the control of relative stereochemistry and the normal electronics. There is then a quick look at how you can alter the electronics (frontier molecular orbitals) to change the reaction (acceleration or inverse demand). Then there are four examples: a Lewis acid accelerated reaction with improved regioselectivity; an intramolecular Diels-Alder reaction (IMDA) where the two reactants have been tied together; a hetero-Diels-Alder reaction (HDA) where one carbon has been replaced by an oxygen atom; a bonus intramolecular hetero-Diels-Alder reaction just to show you string these things together and then an inverse electron demand Diels-Alder (IEDDA) where the dienophile is electron rich and the diene electron poor. More information can be found at https://www.makingmolecules.com/blog/da-like-reactions

Making Molecules@makingmolecules· Jun 2

My 1st #Chemistry #ChemEd #ChemSky summary on pericyclic reactions (more to follow) & it is on the Diels-Alder reaction. This is a fantastic reaction but I only cover the basics. Bond formation, regioselectivity (very simplistically) & a comment on exo vs endo. No Woodward-Hoffmann rules. Enjoy.

A one page summary of the Diels-Alder reaction. This is just the basics and only covers a general reaction showing which bonds are made. Then gives a superficial explanation of regiochemistry followed by comments on endo vs exo selectivity.
For more details see https://www.making molecules.com

Making Molecules@makingmolecules· May 12

As promised, a #ChemEd #Chemistry #ChemSky summary introducing enamines as enolate equivalents. It's only an intro so covers formation + 3 reactions. No regio- or stereoselectivity even though they're fun. I did include the catalytic cycle from enamine organocatalysis as people expect it. Enjoy.

A summary covering the simple alkylation of enamines (or enamines acting as enolate equivalents).
It shows the general reaction along with the mechanism for the formation of enamines and then the mechanism for their alkylation. There is a summary of three reactions, alkylation, Michael or conjugate addition and the aldol reaction. The mechanism for enamine organocatalysis is also included as I'd be daft not to these days.

Making Molecules@makingmolecules· Apr 28

After enols & enolates, here's a #ChemEd #Chemistry #ChemSky on enolate equivalents. These allow control of selectivity & permit stereoselective enolate chemistry (something I love & will eventually write a summary on). Here is formation & aldol-like reaction. Enamines will get their own summary.

A summary covering some simple enolate equivalents. It looks at the formation of lithium enolates with LDA and shows the use of this reagent in the aldol reaction. Then there are the silyl enol ethers and their use in a Lewis acid activated aldol-like reaction. Finally, there are the wonderful boron enolates. And, you guessed it, their use in an aldol reaction. Next summary will have enamines.

Making Molecules@makingmolecules· Apr 22

No #ChemEd #Chemistry summary this week as the Analytical Science team was unleashed for a night of science, chemistry and fun. Big thanks to Brad and Daisy.

One very cold flower about to meet its doom

Daisy, Brad and my good self before all the fun starts

Making Molecules@makingmolecules· Apr 14

Breaking radio silence with 2x #ChemEd #Chemistry #ChemSky summaries of aldol-like rcts. These are just lists of reactions without the explanation of the last couple of summaries. One tries to include mechanisms. More a stop gap than anything else. Hopefully, someone will find them useful. Enjoy.

A summary of aldol-like reactions, listing the most common examples found in many UG courses. There is an attempt to add some mechanisms to this, but not much. Not much in the way of explanation either. It is just a list!

A summary of aldol-like reactions, listing the most common examples found in many UG courses. It is purely a list and not very exciting. Might be a revision aid. Might not (it was a stop gap as I was too busy to put together proper summary!).

Making Molecules@makingmolecules· Mar 24

This was stolen from @bagphos.bsky.social and says the same thing more amusingly.A

Making Molecules@makingmolecules· Mar 24

Having introduced the aldol, here is a #ChemEd #Chemistry #ChemSky summary of the more common named variants. They're all the same reaction (just the electrophile/nucleophile changes; see reply). The mechanism is the same. Don't let the names mislead you. Hopefully it is useful to some.

Aldol-like reactions. All of these involve a stabilised anion adding to an electrophile, either a carbonyl group or an iminium ion.
It covers the general mechanism and then gives examples of the Claisen & Dieckmann condensations (enolate adding to an ester. Only difference is if they are attached to each other). The Mannich reaction (enol adding to iminium species) and the Henry reaction (or nitro-aldol. A nitro stabilised anion adding to an aldehyde)... wow autocorrect hates chemistry after all these years and many additions to the user dictionary. I almost understand why some students switch it off.

Making Molecules@makingmolecules· Mar 10

The obvious next post after looking at enols/enolates is the aldol reaction. The aldol reaction is an impressive beast used by both nature and chemists. This #ChemEd #Chemistry #ChemSky summary is just the intro. There will be more over the coming weeks. I hope UG enjoy this!

A summary or introduction to the aldol reaction. It shows the general reaction with both the aldol addition and the aldol condensation. This is followed by the curly arrow mechanism for the base-promoted aldol addition and the base-promoted aldol condensation. After that, there is, of course, the acid-catalysed version.
Finally, I mention the crossed or mixed aldol and allude to the fact that selectivity can become an issue.

Making Molecules@makingmolecules· Feb 24

Enolates (& their equivalents) are one of the cornerstones of many a good synthesis. So here is a #Chemistry #ChemEd #ChemSky intro to their formation & general reaction. More details on the aldol reaction & enolate equivalents will be in subsequent summaries. Enjoy.

A one page summary covering the formation and a couple of basic reactions of enolates (more reactions, like the aldol reaction will come in subsequent summaries). This is divided into three boxes. 1) Formation by deportation, including a brief discussion of regiochemistry in non-symmetric ketones. 2) A cartoon of the general reaction of enolates (reaction at the alpha position). 3) some useful examples of reactions that don't totally follow my generalisation.

Making Molecules@makingmolecules· Feb 10

The 1st of a few #ChemEd #Chemistry #ChemSky summaries related to enols/enolates/etc. This one covers keto-enol tautomerization and two reactions of enols. As always, it is just meant to cover the basics. It is a summary to refresh/support students' memories. As such, I hope it is of some use.

A summary of the formation of enols or keto-enol tautomerization and then two reactions of enols. There are four boxes of information. The first shows the curly arrow mechanism for both the acid and base catalysed formation of enols. The second box looks at the stability of the enol. Then we turn our attention to the bromination and nitrosation of an enol. THe mechanism is the same for both and hopefully reinforces some basic principles.

Making Molecules@makingmolecules· Jan 27

The obligatory summary of a summary and a table of E1 vs E2 vs Sn1 vs Sn2. Hopefully, this is of use to some, but if I'm brutally honest, it was just a quick stop gap while I work on more fun #ChemEd #Chemistry #ChemSky summaries (currently writing ones on cycloadditions and rearrangements). Cheers

The classic table of E1 vs E2 vs SN1 vs SN2. Hopefully it is useful in giving UG students an idea of what mechanism might be in operative and answering some of those annoying exam questions (reality sucks, and it is highly likely that multiple mechanisms will be operating at the same time!).

Making Molecules@makingmolecules· Jan 20

The obvious follow-up to SN1/SN2 substitution is a #ChemEd #Chemistry #ChemSky summary on E1/E2 elimination. This summary only looks at E1/E2 & not fun like E1cB. More detail is www.makingmolecules.com/blog/elimina.... Enjoy (& yes a summary of which mechanism operates is coming next week). Enjoy

Making Molecules@makingmolecules· Jan 13

Today's #Chemistry #ChemEd #ChemSky summary is SN1/SN2 substitution. I waited until 46th summary to cover this as I don't think it's as important as the chemistry of the carbonyl group (but is invariably introduced 1st in textbooks 🤷‍♂️go figure). More info www.makingmolecules.com/blog/substit... enjoy

Making Molecules@makingmolecules· Jan 6

A contentious #ChemEd #Chemistry #ChemSky summary covering rates of reaction. It is the textbook version & is wrong if you understand kinetics ;) I'll add references showing why as a reply. It's here as most UG still learn it. Hopefully it is useful & doesn't cause too many misconceptions

A summary of the rates of reaction as found in textbooks (another way of saying, it is a gross simplification that is incorrect). Useful (hopefully) at the beginning of a student's study of mechanisms.

Making Molecules@makingmolecules· Dec 2

The last MakingMolecules #Chemistry #ChemEd #ChemSky of the year, but what a post, an org chemist introducing rates of reaction with collision theory! The pool analogy is shaky/orientation is important than direction/frequency not numbers). It's a vital topic but find a physical chemist for details.

A rough introduction to collision theory. Simplistically, collision theory treats molecules as hard spheres and says they will react if they hit each other with sufficient energy and in the correct orientation. The energy is required to overcome activation barrier. There is an analogy to pool and that you can think about trying to pot a ball. Needs two balls to hit, needs to have the correct energy and need them to be orientate correctly so that the ball goes in the pocket (but I'm avoiding saying direction as that is incorrect and causes confusion). TO accelerate a reaction you can increase the concentration as this increases the frequency of reactions. You can heat them up, the more they move the higher the frequency of collisions. The hotter the molecules, the more energy and the more chance of having sufficient energy. Or you could add a catalyst and this lowers the amount of energy the molecules require by changing rhetorical reaction pathway.

Making Molecules@makingmolecules· Nov 25

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.

Making Molecules@makingmolecules· Nov 18

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.

Making Molecules@makingmolecules· Nov 11

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).

Making Molecules@makingmolecules· Nov 4

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.

Making Molecules@makingmolecules· Oct 21

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.

Making Molecules@makingmolecules· Oct 14

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.

Making Molecules@makingmolecules· Oct 7

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· Sep 30

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

Making Molecules@makingmolecules· Sep 23

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.

Making Molecules@makingmolecules· 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· 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.

Making Molecules@makingmolecules· 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.