Category: Organic Chemistry Basics

Organic Chemistry Basics and key Concepts; Total Synthesis of Natural Products

  • Nucleophilic Aromatic Substitution Mechanism & Key Concepts

    Nucleophilic Aromatic Substitution Mechanism & Key Concepts

    summary of nucleophilic aromatic substitution reactions

    • 1. Mechanism: In the nucleophilic aromatic substitution, an electrophilic aromatic ring reacts with a nucleophile. Usually, addition-elimination replaces the C-LG with a C-Nuc bond. This process goes through a stabilized carbanion (‘Meisenheimer’ complex / int.).
    • 2. Leaving groups: Halides are most common, including fluoride despite it being a bad leaving group! Addition and not LG departure is the rate-determining step. Fluorine works well because its high EN makes carbon more electrophilic, accelerating initial addition.
    • 3. Substituents: Electron-withdrawing groups are critical to polarize the ring and stabilize the negative charge in the Meisenheimer complex.
    • 4. & 5. Alternative mechanisms: Rarely, the elimination occurs before addition. Strong bases can promote elimination-addition mechanisms (via benzynes) while diazonium compounds can undergo SN1-like substitutions (via carbocations).

    1. The SNAr Substitution Mechanism

    The nucleophilic aromatic substitution is a variation of a reaction we know well: the electrophilic aromatic substitution.

    Reaction scheme showing the mechanism of nucleophilic aromatic substitution

    They achieve similar goals but using the opposite reactivity!

    What’s the goal? Replacement or substitution of an existing group with a new one. In electrophilic substitutions, we are replacing C-H bonds (H departing as a proton or H+) with a new C-E bond by adding a reactive electrophile.
    In nucleophilic substitutions, we cannot do this as this would require H to act as a leaving group. Instead, we are replacing C-LG bonds – where LG is typically a electronegative group like a halogen – with C-Nuc bonds by adding a nucleophile.

    Why opposite reactivity? Nucleophilic aromatic substitution uses nucleophiles to attack electron-deficient, electrophilic aromatic rings. Simply put, the nucleophile is “the minus” and the ring is “the plus”.
    For electrophilic aromatic substitution, it’s the opposite: we use electron-rich aromatic rings (minus) that react with electrophiles (plus).

    We can construct an illustrative energy diagram based on the mechanism above. Similar to the electrophilic case, the first addition is the rate-determining step with the highest activation energy. This makes a lot of sense because the ring loses its aromaticity, so there is a considerable energy barrier.

    Energy diagram showing transition states and intermediate during nucleophilic aromatic substitution

    The ease of this addition (i.e., the energy of TS1) and the stability of the carbanion intermediate / Meisenheimer complex depends on the leaving group and ring substituents. Let’s review this in some additional detail.

    2. The Leaving Group in Nucleophilic aromatic substitution

    Nucleophilic aromatic substitutions can work with a broad set of leaving groups, but most common are halides like chloride of fluoride. Leaving groups have two roles:
    1. Obvious: They need to be able to depart after the initial addition because otherwise, it would not be a C-Nuc substitution of C-LG
    2. Less obvious: Similar to activating substituents, they accelerate the initial addition by increasing the electrophilicity of the carbon they are bound to.

    There are many cases in organic chemistry where two or more factors are at play. Fluoride is a rubbish leaving group in the second step but the best activator for the first step. Because the first step is the critical one (highest energy/ rate-determining), the pro outweighs the con.

    Electron withdrawing effect on lowering transition state energy

    Unsurprisingly, on the other end of the spectrum, iodide is a bad activator because the C-I bond is much less polarizes than the C-F bond. This explains why aryl iodides are much, much less reactive.

    Halides are special snowflakes. You will benefit greatly from understanding their EN, acidity (and leaving group quality) and bond strengths. Also, remember their role in SEAr reactions: they direct ortho and para but are deactivating overall.

    3. Substituent Effects in Nucleophilic aromatic substitutions

    For nucleophilic aromatic substitutions, any existing groups at the ring are even more important than in in electrophilic aromatic substitutions.

    Electron-rich rings are great for electrophilic reactions (these are more nucleophilic and can stabilize the intermediary cation) do not participate in nucleophilic aromatic substitutions. If the ring is ‘already negative’, why would it want another negative charge to come close to it?

    Conversely, electron-poor rings do not participate in electrophilic reactions but are great for nucleophilic substitutions (these rings are electrophilic and can stabilize the intermediary anion).

    The most potent activating groups are nitro, sulfone, nitriles and carbonyl groups. If they are ortho or para, we can draw stabilized resonance structures where the negative charge benefits from delocalization into the substituents’ π system.

    Pi-acceptor activation of aromatic ring in nucleophilic aromatic substitution

    Usually, we want at least one electron-withdrawing (activating) group on the ring. Rarely, ‘brute force’ reactions also happen in unactivated systems. One example is the old-school synthesis of phenol using the Dow process. The more activating groups, the easier and better the reaction.

    Reaction scheme of the Dow process which is hydrolysis of a chloro arene

    Wrapping up on SNAr (addition-elimination), remember the nitro group for its unique ability to bridge electrophilic and nucleophilic aromatic substitutions. Once introduced through electrophilic substitution, it acts deactivating for subsequent electrophilic reactions but acts activating for other, nucleophilic substitutions (if the starting material allows it by having a leaving group). Here’s an example. Nitro groups can convert to other functional groups (here: reduction to anilines) so they can be very handy.

    Reaction scheme showing aromatic nitration and nitro group activating effect

    4. Elimination-Addition Mechanism (Benzyne)

    Speaking of unactivated systems, there is a different way that these undergo substitutions. Using strongly basic nucleophiles can invert the sequence of steps: instead of addition-elimination, we see elimination-addition.

    This process is rather strange and unintuitive. In absence of any other acidic protons, the base deprotonates a proton ortho to the leaving group. The base needs to be strong because the resulting carbanion is not stable at all. It’s not too happy and continues to react further by kicking out the leaving group. In these reactions aryl fluorides perform way worse than bromides or chlorides because of the weak leaving group quality of fluoride.

    This forms our second intermediate, a so-called benzyne – a benzene ring with a triple bond. Alkynes usually strive to be fully linear but embedding it in a ring makes this impossible. Accordingly, benzyne is rather strained but it can exist as a fleeting intermediate.

    Benzyne as an intermediate in nucleophilic aromatic substitutions

    Now that we covered the elimination of the C-LG group, let’s get to the addition. These reactions use an excess of base / nucleophile, so even after deprotonation, we have a lot of reactant available. Nucleophilic attack to the weak triple bond creates the C-Nuc bond, giving a final intermediate that looks similar to the anion formed in the first deprotonation.

    Elimination-addition mechanism for nucleophilic aromatic substitutions going through benzyne intermediate

    Reactions of substituted aryl halides can lead to mixtures of regioisomers. This is a major difference to the SNAr mechanism, where one starting material can only give one product (Nuc ends up on the same carbon as the LG was attached to).
    These details deserve a separate discussion. Electronic and steric factors can introduce regioselectivity of the addition. If the substituent is a simple alkyl group like shown here, the addition is not really regioselective (1:1 mixture of isomers).

    5. SN1 mechanism for nucleophilic aromatic substitution

    A final exceptional mechanism is observed for diazonium compounds. Similar to the elimination-addition, this step does not require the activating substituents that we’ve discussed for the normal SNAr (addition-elimination) mechanism.

    It’s totally different from the other two mechanisms which had anionic intermediates (Meisenheimer complex and benzene anions, respectively) – it features a cationic intermediate!

    Nucleophilic aromatic substitution of diazonium salt

    Why does this work? When warmed, diazonium salts release nitrogen gas, the best of all leaving groups. With this energy gain, the aromatic ring gladly temporarily turns into an aryl cation. This should remind you of the unimolecular substitution mechanism where the LG departs first, followed by addition of the nucleophile.

    The Balz–Schiemann reaction is a name reaction using this SN1-like pathway to create aryl fluorides. This means we can use nucleophilic aromatic substitution to make … starting materials for more nucleophilic aromatic substitution!
    Today I learned: Both German chemists Balz and Schiemann had the first name Günther (now this is what I call valuable information).

    Balz-Schiemann reaction converting a diazo salt to an aryl fluoride

    Beware, not all aryl diazonium derivatizations go through cationic intermediates. Instead of being polar, the well-known Sandmeyer reaction is a radical process.

    I might explain both of these in future – in the mean time, just search them on Google to make the connection.

    nucleophilic aromatic substitution Examples

    Study exercises for nucleophilic aromatic substitution

    Here are some additional examples of aromatic substitutions. Two reactions differ from the rest from a mechanistic perspective. Which?

    To minimize the spoilers and add some more space between the questions and the solutions – thanks for reading this article!
    Feel free to check out my page or my videos if you’re bored / looking for content!

    Solutions for nucleophilic aromatic substitution exercises
  • Electrophilic Aromatic Substitution Mechanism & Key Concepts

    Electrophilic Aromatic Substitution Mechanism & Key Concepts

    Summary of electrophilic aromatic substitution reactions

    • 1. Mechanism: A nucleophilic aromatic ring attacks the electrophile E+, giving a cation, and loses H+ to regain its aromaticity. This substitutes C-H for C-E.
    • 2. Key reactions: Bromination, chlorination, Friedel-Crafts alkylation (R) & acylation (C(O)R). nitration (NO2), sulfonation (SO3H). Most reactions utilize acid or Lewis acids to create reactive electrophiles.
    • 3. Substituents – Activation: Electron-donating groups at a ring increase nucleophilicity and reactivity. Electron-withdrawing groups work the opposite.
    • 4. Substituent – Regioselectivity: Activators lead to ortho and para products. Deactivating groups direct meta (excl. halogens).
    • 5. Examples: TNT synthesis nicely exemplifies ring activation. Pharmaceuticals use electrophilic aromatic substitution – sometimes with heterocycles!
    • 6. Orbitals: Addition is fastest where overlap of donor (HOMO) and acceptor (LUMO) is best. However, orbital models do not explain the full story!
    • Common mistakes and reaction examples at the end!

    1. mechanism of electrophilic aromatic substitution

    So what is electrophilic aromatic substitution?
    Substitution as it replaces a C-H bond at an aromatic ring with a new C-E bond.
    Electrophilic because our new E group was introduced as an electrophile.

    Because our new group is an electrophile, the double bond of the aromatic ring has to be the nucleophile (just like in electrophilic additions)! Here’s how to identify nucleophiles vs electrophiles.
    Note that the electrophile can be a neutral molecule that’s positively polarized, it does not have to be positively charged.

    Reaction mechanism of electrophilic aromatic substitution

    Note: The order is ‘form C-E, then break C-H’. While the other way around can work, it requires different reaction conditions (very strong base to deprotonate C-H) and is not as broadly applicable.

    Let’s see what we can learn from this energy diagram.
    1. One of the double bonds attacks the electrophile (here: NO2+). Because this breaks the aromaticity of the starting material, the step requires quite a bit of activation energy (the molecule has to have energy to climb the hill of TS1).

    Reaction coordinate for electrophilic aromatic substitution showing the transition states and carbocation intermediate, also called the Wheland intermediate


    2. The addition product is a carbocation (the double bond was ‘invested’ by one carbon to form the bond with E+, the other carbon has one electron less in its proximity and is now a non-aromatic carbocation). The positive charge sits next to the other double bonds , so it is somewhat stabilized and delocalized. This is a real intermediate whereas the transition states are just “snapshots at maximum energy”. This is also called Wheland intermediate or sigma complex.

    3. The deprotonation occurs quite easily (the hill to TS2 is lower than the first one) and gives the stable substituted aromatic product. By the way, you don’t need to add base (e.g., KOH) for this step; the proton will get lost to other molecules present in the reaction or solvent. If the final product is lower in energy vs. starting material (more specifically, “enthalpy”), the reaction is exothermic.

    But benzene is very simple and boring. In sections 2-4, we cover:
    2. What types of electrophiles we can add and how we generate them
    3. How other ring substituents can accelerate or slow down this reaction (activation)
    4. How other ring substituents influence where the reaction occurs (regioselecitvity)

    By the way, this is an old reaction! Pioneering work came from the Brit Armstrong in the 1880s already, and the American George Wheland in the 20th century.

    Source: J. Chem. Soc., Trans., 1887, 51, 258

    From our videos, we know that the early days of chemistry were was a bit crazy. Even simple benzene was disputed (left: Armstrong’s “centroid formula”). We can’t blame these OG chemists as our modern knowledge evolved out of the many dubious theories.

    2. Key electrophilic aromatic substitution reactions

    These reactions have the same fundamental mechanism… but they differ in how they generate their reactive electrophile. They all use some sort of reagent (green/purple boxes) to get to the true electrophilic species that is attacked by the aromatic ring.

    Overview of key electrophilic aromatic substitution reactions: Bromination, Friedel Crafts alkylation and acylation, Nitration and Sulfonation

    Bromination, chlorination and Friedel-Crafts reactions use a Lewis acid (=electrophilic metal compounds that things with electron pairs can coordinate to). This makes the Br, Cl, R or C(O)R centers more positively polarized, so they are more reactive with the double bond.

    Nitration and sulfonation use a ‘normal’ acid (e.g., sulfuric acid) to protonate the reactants and activate them into more electrophilic species. Nitration is a particularly useful reaction as the group can converted to amino or hydroxyl groups.

    After initial electrophile generation, all reactions follow the same steps and experience the same substituent effects (Sections 3. and 4. below). For full clarity, I might explain the nuances of each reaction in more detail in future posts.

    There are two important points I want to point out on the halogenation reactions above: bromination and chlorination.

    1) The typical conditions are bromine or chlorine + Lewis acid, but students will see in more advanced classes that there are other sources of electrophilic bromine or chlorine, like NBS or NCS (N-bromo/chloro-succinimide). I’ll probably explain these reagents more in separate posts.

    In organic chemistry, there are always multiple ways of achieving a certain reaction or generating a certain reactive species, e.g., an electrophile.

    2) Chemistry class syllabus usually ignores the other two cousins in the halogen family: iodine and fluorine. But that doesn’t mean that they cannot participate in these reactions! The point is more that these reactions are less common and straightforward, so they are usually not discussed.
    If you can somehow generate activated/ polarized electrophiles (I+ or F+), they will also react with electron-rich aromatic rings just like Cl+ or Br+ shown above. While there are several options for iodination (using I2 and additional reactants like acids), fluorination is more challenging and requires special reagents (not F2). Aryl fluorides are thus usually made with nucleophilic aromatic substitution reactions like the Balz-Schiemann reaction.

    3. Activating and deactivating groups

    Recall: Our aromatic ring is a nucleophile, attracted to positive charge or polarization (which are electrophiles) because it has a decent amount of electron density.

    The higher the electron-density in a ring, the more nucleophilic and more reactive it will be. This accelerates aromatic electrophilic substitution (higher reaction rate).

    The electron-density of aromatic systems is influenced by the ring substituents. For example, nitrobenzene does not undergo normal Friedel-Crafts acylations.

    Here are the key groups, (directional) strength and primary drivers.
    Activators tend to be π donors (they push/ delocalize their electron pair into the ring) while deactivators tend to be π acceptors (they accept delocalized electrons, acting as an electron sink). If this doesn’t make sense, please read up on resonance.

    Activating and deactivating groups for electrophilic aromatic substitution

    Note the key counterintuitive example: halogens deactivate rings more strongly (due to their negative inductive σ effect, think high electronegativity) than they activate them (due to their mesomeric π effect, they have a free electron pair).

    Another way to think about these groups is to revisit our energy diagram. The TS1 is partially positively charged and the intermediate is fully positively charged. Obviously, this positive charge will be very comfortable if there is a lot of electron density in the ring (charges like to be spread across and stabilized across atoms). Inversely, deactivators would make the intermediate unhappy. It’s like robbing someone who’s already very poor – not the best look.

    Electron-donating effect lowers transition state energy during electrophilic aromatic substitutions

    The stabilizing effects for activating groups mean that TS1 requires a lower activation energy (because the ring is more nucleophilic) and our carbocation intermediate is also lower in energy (the charge is better stabilized by the electron-rich ring).

    Note: It’s critical that these groups are directly attached. If there is an “alkyl spacer” between the ring and a strong (de)activator, the effect will vanish. The donor or acceptor groups need to be conjugated with the ring! The substituents here would be more like σ donors.

    Donor and acceptor groups conjugated with the aromatic ring

    4. Regioselectivity of aromatic electrophilic substitutions (Directing Effects)

    This regioselectivity can be rationalized by looking at the delocalization/ stabilization of the carbocation intermediate. Ortho and para additions favor carbocations where the positive charge sits next to the R group (either directly in case of ortho or after delocalization in the case of para).
    If R can stabilize this positive charge as a σ or π electron donor, it will lower the energy of the carbocation and prefer these pathways over the meta addition.

    Regioselective electrophilic aromatic substitution based on inductive and mesomeric stabilization

    Well if R is an electron-withdrawing group, the positive charge will absolutely hate being next to it (electron-sink next to something that already doesn’t have enough electrons). Thus, deactivating groups avoid ortho and para substitution and show meta selectivity.

    Halogens are again sneaky. Regarding ring activation, their negative inductive effect (electron-withdrawal) overrides their positive mesomeric effect (electron pair donation). Regarding regioselectivity, the mesomeric effect is more important (deal with it). Outside of this special case, all groups follow the same rules.

    5. Examples: Tnt & pHARMACEUTICALS

    Our first example is 2,4,6-trinitrotoluene or TNT. One of many ways of synthesizing TNT is exactly what you think: take toluene and nitrate the heck out of it.
    The issue? Substituent effects!
    You see, while toluene is decently nucleophilic (it’s slightly activated through the methyl group), it becomes less and less reactive the more nitro groups are attached.

    Synthesis of TNT through electrophilic aromatic substitutions

    The first addition gives a mix of ortho and para substituted products. final nitration only occurs at high temperatures and use of fuming sulfuric acid, a particularly reactive form of sulfuric acid containing additional sulfur trioxide. There are easier and more clever ways to make TNT, but that shouldn’t be our focus.

    You also see that just because TNT is deactivated towards electrophilic aromatic substitution, it still likes to explode violently. Reactivity is always relative. This is because detonation does not depend on the nucleophilicity of the aromatic ring 🙂

    Most pharmaceuticals contain aromatic rings so we can find these reactions in their syntheses. One example is the drug lifitegrast. Its synthesis uses an intramolecular Friedel-Crafts alkylation to create the bicyclic core.

    Intramolecular Friedel-Crafts alkylation

    Final lesson: Heterocycles can also be nucleophiles! (aromatic ring with heteroatom)

    The synthesis of the antibiotic metronidazole is very simple. The first step is nitration of the ring with carbon as the nucleophile. In the second step, the nitrogen acts as the nucleophile and undergoes a SN2 reaction with the alkyl chloride.

    Nitration of an imidazole ring

    The five-membered rings pyrrole (heteroatom: N) and furan (heteroatom: O) are very electron-rich so we also often see them engage in electrophilic substitution reactions.

    Bromination of furan and pyrrole

    This is because the electron pair can stabilize the positive charge during the reaction mechanism. It’s like having an activating substituent effect within the ring!

    6. Orbitals in aromatic substitutions

    You probably shouldn’t read this section if you’re just learning about aromatic substitutions.
    Drawing resonance structures is useful for us mortal humans. However, they are just tools and don’t correspond to reality. After all, we’re taught that “real structure” of a molecule is a mix of all “good” resonance structures. Advanced readers might ask themselves if orbitals can be useful predictors for aromatic reactions?

    We won’t go through orbital theory here, but in short: When atoms form bonds in a molecule, their atomic orbitals combine to molecular orbitals. These can be filled with electrons or empty (or half-empty, if it’s a radical). The highest-energy filled orbital (HOMO, occupied) influences nucleophilic behavior and the lowest-energy empty orbital (LUMO, unoccupied) influences electrophilic behavior.

    Looking at orbitals can be partially insightful. Here’s a 3D visualization of the early days of an electrophilic aromatic nitration. The HOMO of chlorobenzene (nucleophile) is getting close to the LUMO of the nitronium cation (electrophile). How will they add?

    You can see that on the ring, para and (to a slightly lesser degree) ortho positions have high contributions, while there is “almost no orbital” on meta. Any electrophilic attack at meta would thus be disfavored (low orbital overlap).
    Our nitronium electrophile has a slightly higher LUMO localization at the central nitrogen, meaning the nitrogen is more electrophilic than the oxygens!

    So, it looks like molecular orbitals can nicely predict the regioselectivity that we observe for chlorobenzene. So why don’t people talk about orbitals in the same fashion as they do e.g., for the Diels-Alder reaction?

    1. Aromatic substitutions are one of the first reactions students, so going into orbitals would be an overkill that makes everyone hate chemistry even more.
    2. More importantly, they don’t always give the full picture. Consider the HOMO of nitrobenzene below. This aromatic ring is deactivated and should attack meta.

    We do see that the para position is not contributing to the HOMO at all, but the orbital structure does not tell us why there is no substitution at ortho! In this case, our resonance structure analysis is actually more helpful because it tells us that the ortho-position of nitro groups is particularly electron-poor.

    There are other ways to analyse this, e.g., by computing charge density. Below you can find an atomic charge analysis for benzene, aniline and nitrobenzene. Ignore the method or units – simply put, a more negative number equals more electron-density at a given atom. More electron-density means more nucleophilic and more reactive towards electrophiles.

    Electron density in substituted aromatic rings

    Source: Phys. Chem. Chem. Phys., 2016, 18, 11624

    Here are some thoughts:

    1. Benzene: Obviously, hydrogens are more electropositive than carbons (they have a positive charge number). The molecule is symmetrical.
    2. Aniline: Electron-density is higher at ortho and para relative to meta, explaining the directing effect. Relative to benzene, ortho and para have higher electron density, i.e., the aniline ring is more activated and reactive .
      Note that there is a lot of electron density on the amine as well! (Aniline can also react as a N-nucleophile! See common mistakes)
    3. Nitrobenzene: Electron-density is highest at meta relative to ortho and para, explaining the directing effect. Now, the carbons all have lower electron density, in line with deactivation / lowering of reactivity due to the nitro group.
      Sidenote: The nitro group’s electron-withdrawing effect further polarizes the C-H hydrogens as they are more electron-poor in nitrobenzene.

    So, orbital theory is sometimes more, and sometimes less useful. Generally, combining multiple models and perspectives gives us a better appreciation. For now, you can happily ignore orbitals for these reactions (but not for others!).

    Common Mistakes in Electrophilic Aromatic Substitutions

    Students can feel overwhelmed trying to remember effects or specific aromatic substitutions. This can lead to common mistakes or errors, including:

    Mixing up ortho, para and meta: This is the first hurdle for new students. If you’re struggling with this, try remembering it this way: Meta is in the middle between the other two. The letter o comes before p in the alphabet, so ortho is closer to R.

    Thinking too superficially: Although electrophilic substitution is the most common reaction of aromatic compounds you’ll see, don’t jump to conclusions too quickly. In this example, an acyl chloride (electrophile) would lead to O-acylation instead of electrophilic aromatic substitution. The benzene ring is deactivated and thus not nucleophilic enough.

    Trick question for electrophilic aromatic substitution

    Along the same lines: In section 6. Orbitals, we saw that charge analysis suggests high electron density at the nitrogen of aniline. Again, under many conditions, anilines can react as N nucleophiles instead of C nucleophiles (e.g., alkylation at nitrogen instead of at carbon).

    Electrophilic or nucleophilic?: Get your terms right. Nucleophilic aromatic substitution reaction does not substitute C-H but rather C-X, where X is a good leaving group. This is the opposite of what saw for the electrophilic substitution: our aromatic ring is the electrophile here. This reaction is explained here.

    Misunderstanding substituent effects: Abbreviations can be confusing, and we might wrongly believe a specific atom or an abbreviated group to be activating or deactivating. Before you go with it, double-check why a substituent would be an electron-donating group or an electron-withdrawing group. E.g., can you really find an electron-pair that is driving a positive mesomeric effect?

    Remember to consider if a newly introduced functional group is more or less activating. Reactions often use an excess of reagents (more moles of reagent than starting material). Adding one activating group? The ring might add more (e.g., polyalkylation in Friedel-Crafts alkylations). Want to add more than one deactivating group? This might be challenging (remember our TNT example)!

    Electrophilic Aromatic Substitution Examples

    Practice questions for electrophilic aromatic substitutions

    Here are additional questions to test your knowledge of the reaction mechanism and directing effects of substituents.

    The first exercise is pretty straight-forward, with the fluoro-substituted ring being less activated (thus, bromination occurs on the other one, para to the aryl-aryl bond).
    The same idea applies to the question on the right, where we expect the inductive acceptor effect of the trifluoromethyl group to deactivate the ring towards sulfonation.
    The Friedel-Crafts acylation is pretty obvious (para to the electron-donating ether group).
    Last, we have a Friedel-Crafts like C-C bond formation. Instead of a alkyl halide and Lewis acid, we generate our carbon electrophile by protonation of the double bond with sulfuric acid.

    Solutions for electrophilic aromatic substitutions

    Hope this summary helped you get a good overview of this class of aromatic reactions.
    Feel free to check out my page or my videos for more learning and fun content!

  • 🧠 Is Organic Chemistry Hard? (Spoiler: Kinda)

    🧠 Is Organic Chemistry Hard? (Spoiler: Kinda)

    “Why do they call it organic chemistry? Nothing about this feels natural.”

    A student, somewhere out there

    Organic chemistry is often perceived as one of the most challenging subjects for students. Unfortunately, this creates a lot of anxiety and misconceptions about its complexity and requirements, particularly for students in adjacent fields like medicine, pharmacy or biology.

    But why the bad reputation?

    1. Concepts: Yes, organic chemistry is complex! After all, it deals with the literal wizardry of transforming living matter. The complexity (and bad teaching) can make many students feel overwhelmed – amplified by cumulative learning: missing foundational concepts makes it difficult to understand advanced ones.
    2. Representation: Organic chemistry requires abstract thinking and relies on molecular drawings that are often not intuitive or tangible. After all, we are drawing 3D things on 2D paper. Fischer projections anyone?! (I hated these)
      (how to change: look at 3D model, simulate it online, practice practice)
    3. Process: Teachers rush through content without explaining it properly, leading students to fall behind completely and/or rely on memorization to stay afloat (how to change: try to maximize the support at your uni with open doors, ask more senior students – if no support environment, look online and try to understand the why, write as many things out as you can to build your mental muscle…)

    But do not despair – organic chemistry can be more accessible than you might think. Here are some ways to help you address these issues.

    1. Organic Chemistry Concepts

    Build the foundation: Whatever level of class you are taking, first go back to your older materials. For introductory organic chemistry lectures this means understanding basic models like the atomic model (electrons, protons, neutrons) and orbitals and hybridization (if relevant in your class). Why do molecules inherently repel each other, and why do reactions occur nevertheless? What is a chemical reaction? Then, revisit concepts like electronegativity, nucleophilicity and electrophilicity (link), …
    I might work on a full list of concepts in future.

    Understand the functional groups (link): Learn the structures of the most common functional groups in organic chemistry. Sorry, but there is some memorization involved. It’s just like learning a new language: you need to memorize at least new words! For this, you have to understand what a skeletal formula is, and how it differs to normal molecular drawings (next section).
    Again, I will go into more details in future but here are two easy exercises:
    => Get a list of the 15-20 most common functional groups and draw their structures in skeletal formulas. Can’t remember a particular one, like the nitro group and its partial charges? Well, simply draw it 5 times for 2-3 days. You will know all of them in no time.
    Then, look at them and think about their similarities: For example, a thiol group is like a hydroxyl group (or an alcohol), just that the oxygen is replaced by sulfur which is in the same “group” in the periodic system. An ester is similar to a tertiary amide, just that the -OR group bound to the central carbonyl carbon is replaced by a -NR2 group. Tertiary amides are similar to secondary and primary amides, just that the number of alkyl rests versus hydrogens bound to nitrogen differ.
    => Google “pharmaceuticals” and check out their structures on Google images. Pick a random pharmaceutical – what functional groups can you identify? Which groups are ones you do not know yet? Do they look similar to any which you know already?

    Work your way up the complexity of reactions:
    😔 The bad news : There are a literal TON of reactions in organic chemistry.
    😊 The good news: Thankfully, you don’t have to know all of them, and many of them share the same logic and concepts. Here you should again start easy and build up.
    => Before trying to understand SN1 reactions or more difficult name reactions, first review acid-base reactions and oxidations/reductions. Then, get into additions. Then, substitutions and eliminations (SN2 and E2 first because they are just one step – then, SN1 and E1). After these, you can start to look at name reactions and complex transformations. For example, if you have are discussing electrophilic aromatic substitutions in class, you need to know how much simpler additions and substitutions work!

    Focus on conceptual understanding: It’s normal to memorize things at the start, but really strive to understand the “why” behind reactions and mechanisms. For example: Why does a molecule X react in a substitution – where is its nucleophilic group? Why is the reagent Y an oxidant – which atom has a high oxidation number and gets reduced? Why does the reaction occur regioselectively at this position of the aromatic ring – are there electron-donating or electron-withdrawing substituents somewhere?

    Create mind maps: Look at all the reactions you have studies in your class, and try to connect them based on their similarities. Or, connect different concepts: resonance impacts many other factors like acidity of a molecule. How? Electronegativity impacts intermolecular forces like hydrogen bonds and dipole effects. How? Diastereoisomerism impacts melting and boiling points. Why

    Create analogies: Whenever you find a concept confusing or can’t remember it, create an analogy. For example, nucleophiles and electrophiles can correspond to rich and broke people, respectively. Electrophiles would like to borrow the electrons of the nucleophiles, creating a strong attraction. The process of the rich lending money to the poor is the nucleophile giving its electrons to the electrophile.

    2. Representation

    Master skeletal formulas: Organic chemistry relies on skeletal formulas which omit the explicit indication of carbon and most hydrogen atoms. Remember, each “bend” or end of a line represents a carbon atom, and hydrogen atoms are implied to fill the carbon’s required bonds.

    Change your perspective: Molecules can be represented in various ways: Lewis structures, skeletal structures, Newman projections, Fischer projections… Each emphasizes different aspects of a molecule (e.g., stereochemistry). Practice switching between them to strengthen your spatial awareness.
    => Practice converting between full structures and skeletal formulas until it’s your second nature. Make sure you understand where electron pairs are present!
    => Convert between Newman projections and skeletal formulas. Are your Fischer projections your enemy? Well, go and solve literally 20 different problems. You will get the hang of it.

    Use molecular models to visualize stereochemistry: Stereochemistry is a tricky topic because because it involves 3D thinking. Physical or digital 3D models of molecules can help you see how atoms are arranged in space.
    => Use online resources like MolView to visualize molecules. Struggling with chirality, enantiomers, and diastereomers? Go to town on the visualization. Rotate, inspect and understand the structures! If you have an university ChemDraw license, use Chem3D!

    Practice electron pushing: Organic reactions are governed by electron movement. Curved arrows indicate this electron flow. Whenever you’re learning a new reaction, focus on understanding the arrows, which show how bonds are made and broken. If you can follow the electrons, you’ll have a better grasp on the mechanics of reactions. The same applies to resonance. Pick any molecule of your choice and draw all the different resonance structures. Why resonance structure is the most stable? How does resonance impact the reactivity of the molecule?

    Color code drawings for clarity: Use different colors if that helps you. For example, always use red to indicate movement of electrons. Does the reaction involve partial charges? Color code them!

    “Play chess” – think several moves ahead: At the beginning, you should write out every single step in a reaction. Once you are at the intermediate level (when you get to practicing retrosynthesis), try visualizing several transformations at once. How would my final product look like if I oxidize the alcohol in the molecule to the aldehyde and perform a Wittig reaction?

    3. How to learn organic chemistry

    Stay consistent with daily practice: We’ve all been guilty of cramming at some point. However, organic chemistry is best learned through regular practice. Even if you only have 15 minutes, do something related to the course every day—whether it’s reviewing notes, drawing mechanisms, or solving practice problems. The more often you engage with the material, the more familiar it becomes.
    => Every day, read about one new molecule of your choice. Think drugs against neurodegeneration are cool? Research the structures of Alzheimer’s drugs. What are their functional groups? How are they synthesized? Maybe you are into doing sports? Look at the different types of steroids and performance-enhancing drugs that there are! (Do NOT take them, just read about them…)

    Activate your little brain cells: Look, we all are guilty of passively consuming information and entertainment. But instead of just reading textbooks or watching videos, actively engage with the content. Draw out mechanisms as you learn them, explain concepts in your own words, or quiz yourself on reaction types and mechanisms. Basically, anything you are not writing down or creating yourself, you will probably not remember!

    Test yourself with practice problems: Organic chemistry is problem-solving heavy, so doing lots of practice problems is essential. Don’t be discouraged by mistakes or getting stuck – this is part of the learning process. The rate-limiting step (see what I did there?) might be how many good problems you can find – you know, ones with proper explanations. The quality of your problems will depend on your luck and teacher.
    I’m working on a problem book for chemistry myself – but yeah, go to town on Google and YouTube.

    Emphasize understanding over memorization: I mentioned this one already – but given we are talking about the learning process here, I wanted to reiterate.

    Create your own study materials: Summarize concepts, reactions, and mechanisms in your own words. Create summary sheets, mind maps (see above), or flashcards tailored to your learning style. Experiment and see what works for you! For the things that you will need to memorize (e.g., functional groups, pKa values, named reactions…), you should have a clear approach.

    Team up: Organic chemistry is almost always more manageable when tackled with peers. Explain concepts to each other, discuss exercises together, and discuss tricky mechanisms. Your classmates are ahead of you? Great, you can suck out their insights and ask questions. You are ahead of your classmates? Great, help them and in doing so, you will further elevate your capabilities. Are you in university and not against earning an extra buck? Tutor students that are 1-2 years below your level.

    Use office hours and ask for help early: If something doesn’t make sense, ask for help right away. Afraid of looking like a moron? Well, the odds are at least half of your class is feeling like morons as well, so don’t feel bad! Visit your professor or teaching assistant during office hours to clarify any misunderstandings. Addressing confusion early prevents small gaps in knowledge from turning into major issues later.

    Use multiple resources: Don’t rely solely on one textbook or lecture notes. Different resources may explain the same concept in slightly different ways, and sometimes a different perspective makes things click. Use videos, alternative textbooks, online platforms, and forums to diversify your learning. No access to textbooks? Go to town on LibGen (google it).

    Prioritize your effort: As mentioned, building the foundation is key. But once you get into intermediate territory, there are SO many things you could theoretically read about. In the best case, your textbook and/or teacher might have clear objectives or checklists of topics to know. Assess on what you need to work on most, and then go hard.

    Is Organic Chemistry Hard?

    So, is organic chemistry hard? Honestly – yes, it’s hard.

    Is it as hard or terrifying as people make it out to be? No, not really. The great thing is that at some point, every new concept or reaction will be based on something you know already. After enough effort, there will be almost no cases where you really have absolutely no clue of how to approach a problem.

    Is it the hardest subject you will study? Maybe, maybe not. Depending on your area of focus, it might come least naturally to you, versus other subjects. If you dislike chemistry and math, physical chemistry will haunt you even more.

    To end on a positive: I loved organic chemistry more than any other subject but even I had been struggling with it initially.
    Resonance? Confusing as hell. Fischer projections? I couldn’t draw a single one correctly. The abbreviation of -Me for a methyl group (-CH3)? I thought it stood for “a generic metal” (lol).
    I asked A LOT of stupid “questions” (or in many cases did not ask them, which slowed down my progress). What had been a guessing game and brain-dead memorization, became almost second nature.

    Whatever your journey in organic chemistry, I hope you can figure out how to make it a bit more bearable and more successful – however you define it: just passing, improving your grade, or really going beyond the class and mastering it.

    I’m working on materials to help students unlock and practice organic chemistry. So if you are just getting started, stay tuned!

  • Functional Groups in Organic Chemistry: Introduction

    Functional Groups in Organic Chemistry: Introduction

    Functional groups are the foundation of organic chemistry as they define the structure, reactivity, and properties of organic compounds. Here, we explain what functional groups are (by looking at – wait for it – fruit salad), and introduce the most common functional groups.
    Did you know that functional groups were at the root of dispute and friendship of two chemistry legends? Let’s get into it!

    What are Functional Groups in Organic Chemistry?

    Instead of blindly memorizing a long list of functional groups, let us try to understand three key ideas first.

    1. Many functional groups are related to each other. For instance, by putting a C=O double bond next to an amine, we get an amide. Others are variants of each other. For example, a sulfur atom instead of an oxygen turns an ether group (R-O-R) into a thioether (R-S-R). When learning these groups, try to find the similarities and differences between them.
    There are different sub-families of functional groups. For instance, everything with a C=O double bond can be called a carbonyl. Aldehydes, ketones, amides, esters… are all relatives of the carbonyl family! Similarly, primary amines, secondary amines and tertiary amines are all amines!

    Carbonyl functional group in organic chemistry

    2. Properties of functional groups are largely independent of the molecule’s broader environment. The hydroxyl group in ethanol behaves the same way as in octanol (even though the latter is much bigger!).

    Hydroxyl functional group in organic chemistry

    3. Connected to the above, functional groups have an inherent polarity and thus, nucleophilicity or electrophilicity (link). For example, aldehydes are electrophilic on carbon but nucleophilic on oxygen. This baseline polarity of each functional group actually already explains most of the organic chemistry reactions that you will encounter. Interconversion of functional groups can change this natural polarity. For instance, enol forms of carbonyls are not electrophilic at the central carbon anymore, and are nucleophilic at the alpha-carbon!

    Enol functional group

    What are Functional Groups – SIMPLY EXPLAINED?

    Functional groups are just like different fruits in a fruit salad. Let’s see how the points above match to this analogy.

    1. Some fruits are related, like lemons and oranges as they are both citrus fruits. We mentioned carbonyls and ethers above. Another example are primary amines and tertiary amines very similar but not identical!

    2. Whether you catch a strawberry in one fruit salad or another one (these are different molecules in our analogy), they basically taste the same.

    3. Lemons are inherently acidic. Well, carboxylic acids are also always acidic. (Sometimes more, sometimes less – due to things like inductive and mesomeric effects.) Just like fruits have characteristic taste, functional groups have characteristic properties.
    This also nicely illustrates the keto-enol interconversion or even the advanced idea of Umpolung. Here, chemists invert the natural reactivity of the original functional group. The key example is conversion of aldehydes to dithianes which can be nucleophilic at the carbon (instead of electrophilic)!
    Using our fruit analogy, by cooking and caramelizing lemons (Umpolung), we can make them more sweet instead of bitter.

    Dithiane functional group in organic chemistry

    History of Functional Groups in Organic Chemistry

    Here’s some random background (if you know my content, you will realize I like this type of stuff):
    As the backbone of organic chemistry, functional groups as a concept have their origin in the early 19th century. At that point, elemental analysis had allowed chemists to determine the molecular formula of most inorganic compounds. These lack carbon-hydrogen bonds and are thus not organic (shocker!). The widespread theory of vitalism suggested that only living organisms can produce organic substances.

    Many students know that the German chemist Friedrich Wöhler overthrew this theory by synthesizing urea from inorganic ammonium cyanate in 1828. Less known is the controversy between Wöhler and Justus Liebig:
    Both of them were doing experiments on inorganic salts that they believed had the molecular formula “AgCNO“. However, Liebig’s salt was a powerful explosive while Wöhler’s was not.

    The obvious conclusion was that one of the analyses must be wrong, and one of the chemists must be a poor analyst! Liebig, pushed by his aggressive character, rapidly accused Wöhler of erroneous results. But Liebig analyzed a sample of the silver cyanate supplied by Wöhler and verified that they were correct. At this point, Liebig openly admitted that he had made a mistake in his initial accusation. And curiously this was the starting point of a friendship and even a scientific collaboration between the two scientists.”

    S. Esteban in J. Chem. Educ. 2008, 85, 9, 1201
    Constitutional isomers silver cyanate and fulminate

    The legendary Swedish chemist Berzelius (Wöhler’s professor) explained this controversy by proposing the concept of isomers. The realization that constitution of molecules can be different despite having the same atoms paved the way for discovery of all the functional groups we know today.

    Common functional groups

    Here are the most common functional groups. The bold ones are particularly important as they are invoked to explain some of the basic reactions in organic chemistry, such as nucleophilic substitutions (alkyl halides) or electrophilic additions.

    Overview of all important functional groups

    Instead of belabouring basic information you can find everywhere already, I want to draw your attention to two themes:

    1. Functional group relationships:
      What makes functional groups (in a certain row or across rows) similar?
      For instance, the first row are C-H hydrocarbon functional groups.
      Which functional groups are based on combinations of simpler functional groups?
      For example, an enone is an alkene that is connected to a ketone.
      Which functional groups are oxidized/ reduced versions of each other, and which have the same oxidation state?
      For instance, carboxylic acids are more oxidized versions of aldehydes and ketones, and have the same oxidation state as nitriles. This means nitriles can be converted to acids without reductants or oxidants!
    2. Functional group polarity:
      What do the red and blue colored atoms correspond to? How does the polarity and reactivity differ across related functional groups?
      For example, why is the central carbonyl carbon blue in aldehydes and ketones, but not blue anymore in carboxylic acids?
      Why is the hydrogen of the O-H bond of the carboxylic acid blue but not blue for the C-H in the aldehyde?
      Should the carbons of alkenes and arenes be marked red or rather blue? What does this depend on?

    3. Advanced: Functional group geometry: Can you rationalize all bond angles (e.g., alkynes vs. alkenes) and geometries of functional groups? Which parts of them are flat/ in one plane, and which ones are not?
      For example, why are in esters both the C=O and C-O-R bonds in the same plane? Why do esters prefer the Z-conformer where both C=O and C-O-R bond are facing the same side?
    Planarity of esters and Z-conformer

    In other posts, we will deep dive into individual functional groups and families to explain properties and most common reactions in more detail. Functional groups clearly also form the basis of protecting groups and their reactivity.

    Some final advice: Instead of learning a bunch of facts about 30 functional groups by heart in a brain dead manner, try to work first identify the commonalities and differences from a high level. The names might seem random at first but many of them will make sense once you take a look at what atoms or combinations of functional groups are present!

  • How to Identify Nucleophile vs Electrophile (Summary & Detailed)

    How to Identify Nucleophile vs Electrophile (Summary & Detailed)

    Ever struggle with how to identify if a group is a nucleophile vs. electrophile?
    If you are in a rush and don’t care about learning chemistry (bruh), the first sections got you. I recommend you try to truly understand the concept as it’s arguably the most important skill in organic chemistry.

    Nucleophile vs electrophile: Summary

    Nucleophiles and electrophiles are complementary, they react with each other. You will never see a reaction where two groups react with each other as nucleophiles!

    Level 0: Chemical bonds are like … financial transactions?

    If you’re a student, you’re likely broke (you are in need of, and easily accept money => you are electrophilic).
    You go to your parents to borrow some money for a dinner (they can donate money => they are nucleophilic).
    By getting money and the food, you get happier (you are energetically stable). Your parents are also stoked they can spend some time with their favorite child (they are also energetically stabilized).

    electrophile and nucleophile curved arrow direction

    This explains how we draw curly arrows, representing electron movement: There are no electrons at the electrophile (it is broke). Instead, the electron donation arrow starts at the nucleophile and points to the acceptor, the electrophile.

    Level 1: Nucleophile vs electrophile

    You have two options on how to remember which is which:
    1. Not recommended: You force-memorize some analogy like above with no brain cell activation, setting you up for nice failures in organic chemistry exams

    NucleophileElectrophileP*d*phile
    What it hasHas more than
    enough electrons
    Has some sort of
    positive polarization
    Problems, chocolate
    & puppies
    What it wantsWants to share
    its electrons

    (likes positive charges)
    Wants to accept
    other electrons

    (likes electrons)
    Kids
    ChargeNeutral or negativeNeutral or positivePrison sentence
    OrbitalsHigh-energy occupied Low-energy unoccupiedOrbits around kids
    and playground
    Acid or baseLewis baseLewis acidPuts them in his base(ment)

    The electrons that a nucleophile donates form the new bond with the electrophile. A simple example is the protonation of water. Which is the nucleophile vs electrophile?

    water as an nucleophile

    Reviewing the more complex mechanism for the hydration of formaldehyde, you will realize that:
    1. Specific atoms or also bonds can have nucleophilic or electrophilic behavior
    For example, in the first step, the carbonyl pi-bond is the electrophile. In the second step, the proton H+ is the electrophile.

    2. For reactions with multiple mechanistic steps, there can be many different nucleophiles and electrophiles
    For example, after the first addition to the carbonyl, the previously nucleophilic water molecule turns into a cationic intermediate which is now electrophilic (which is why it reacts with another nucleophilic water in a deprotonation)

    nucleophile vs electrophile in hydration of aldehydes

    Level 2: Types of nucleophiles

    How do we identify electron donors and electron acceptors? There are three categories for both. It’s easier for nucleophiles, so let’s start there.

    types of nucleophiles

    1A) Lone electron pairs, e.g., water H2O or ammonia NH3 (neutral nucleophile)
    Reaction example: Protonation of neutral bases
    1B) Negative charges (also electron pairs), e.g., hydroxide OH or cyanide CN anions
    Reaction example: Basic hydrolysis of an ester
    2) Bonding pi-orbitals, most notably C=C double bonds, e.g., alkene or aromatic ring
    Reaction example: Bromination of alkenes, electrophilic aromatic substitution
    3) Bonding sigma-orbitals with highly electropositive atoms, e.g., methyllithium Li-CH3
    Reaction example: Carbonyl reduction with LiAlH4, organometallics

    This should make sense. These are the only “ways” you will ever find electrons in a molecule. Either as an unbound electron, in a pi-bond, or in a sigma-bond. This corresponds to the idea of highest occupied molecular orbitals (see below).

    Level 2: Types of electrophiles

    What about electrophiles? Two categories are similar, and one is different.

    Like nucleophiles, we have pi- and sigma-bonds as acceptors (as they have empty orbitals that can be filled with electrons). However, instead of electron pairs for nucleophiles, we need to look for empty orbitals on single atoms. Think of the empty orbitals like filled purses

    types of electrophiles

    1A) Positive charges representing an empty p orbitals, e.g., proton H+
    Reaction example: Protonation of any base
    1B) Neutral molecule with empty p orbital, e.g., Lewis acids like BF3 or AlCl3
    Reaction example: Friedel-Crafts acylation
    2) Pi-bond next to electronegative/ stabilized system, e.g., carbonyl
    Reaction example: Aldehyde hydration, conjugate addition
    3) Sigma-bond to electronegative atom, e.g., methyl iodide CH3-I
    Reaction example: SN2 reaction, bromination of alkenes

    For both of these categories, I always represented the nucleophile as “Nu-” and electrophile as “E+”. But any combination of these categories works – e.g., an nucleophilic pi-bond can attack an electrophilic pi-bond!

    If you know a fair share of reactions, try to think about additional examples for each!

    Level 3: Orbitals

    Let’s get to the bottom of this (without me writing another text book on orbitals).

    Point #2 is critical: energy levels of the nucleophile and electrophile orbitals.
    The strongest stabilization comes from interacting orbitals with similar energies.

    molecular orbital energy diagram for electrophiles and nucleophiles

    All molecules have many low-energy, unfilled orbitals and high-energy, empty orbitals (illustrative grey orbitals). We can ignore all because the energy differences between them are too large. The most relevant interaction will be the one between the lowest-energy unoccupied (LUMO) and highest-energy occupied molecular orbital (HOMO).

    The higher-energy a HOMO is, the easier it can donate electrons into LUMOs.
    The lower-energy a LUMO is, the easier it can accept electrons.

    This picture explains the types of electrophiles
    1A + B) Empty orbitals can be LUMOs (neutral or positively charged atom)
    2) Pi-bonds always have an empty antibonding pi-star MO which can be a LUMO
    3) Similarly, sigma-bonds have an antibonding sigma-star MO which can be LUMO

    … and types of nucleophiles:
    1A +B) Lone pairs can be HOMOs (neutral or negatively neutral charged atom)
    2) Pi-bonds always have a filled bonding pi MO which can be a HOMO
    3) Similarly, sigma-bonds have a filled bonding sigma MO which can be a LUMO

    Recap: Nucleophile vs electrophile

    By now you should be able to identify a nucleophile vs electrophile, and know the different types that exist. As an exercise, review reactions you already know or that I discuss on my channel, or functional groups (e.g., protecting groups) to apply your learnings.

    There are more nuances and explanations which are not digestible in a single post. So, future posts will explain things like:
    – What are the most common nucleophiles and electrophiles?
    – How does conjugation to electron-donating or -withdrawing groups influence nucleophilicity or electrophilicity?

  • TBS Protecting Group: TBS Protection & Deprotection

    TBS Protecting Group: TBS Protection & Deprotection

    Conditions for protection and deprotection of the TBS protecting group (TBSOTf or TBSCl)

    This bulky silyl PG is resilient, allowing for selective/ orthogonal deprotection of similar groups like TMS.

    For silyl ethers, bigger is better!
    As they have 3 options for deprotection, they’re a nice general learning opportunity for students.


    👀 Here’s an interactive 3D model of the TBS protecting group.

    What is the TBS Protecting Group?

    TBS or TBDMS is short for tertbutyldimethylsilyl, a protecting group for alcohols.
    TBS was introduced by the legendary E. J. Corey in 1972 [1] as an evolution to simpler silyl ethers which had already been known. Note this was right around the time of Fmoc discovery, and relatively late in the history of organic synthesis.

    The research already covered protection and deprotection conditions still used today. It is one of the most cited JACS publications ever. A decade later, Corey also introduced triflate reagents for silyl ether synthesis [2].

    TBS Protection Mechanism

    TBS protection conditions (TBSCl, imidazole or TBSOTf, lutidine)

    The most common TBS protection conditions are TBS-Cl (forms hygroscopic white crystals) in DMF with imidazole or DMAP.
    Corey encountered challenges using TBS-Cl for protection of tertiary or hindered secondary alcohols. Use of TBS-OTf triflate (with 2,6-lutidine as base in solvents like dichloromethane) proved more potent for such cases.

    TBS protection mechanism with imidazole catalysis

    The classic mechanism contains generation of an imidazolium intermediate which acts as a silyl transfer reagent for the actual silylation.
    The steps might look counterintuitive. Silicon, in contrast to carbon, can have five bonds at once! Both silylations likely proceed through associative substitutions with pentavalent silicon intermediates. However, you’re likely also fine drawing a concerted step.

    Silyl ether protecting group Stability

    Many different variants of silyl ethers exist. Despite their overall similarity, they can behave quasi-orthogonal due to different lability. Below, you can see the relative stability towards acidic and basic aqueous hydrolysis.

    Silyl ether protecting groupStability to acid Stability to base
    TMS (trimethylsilyl)11
    TES (triethylsilyl)~60~10-100
    TBS (tertbutyldimethylsilyl)~20’000~20’000 (likely higher
    as basic stability > acidic)
    TIPS (triisopropylsilyl)~700’000~100’000
    Stability data from [3]

    As you can see, bigger silyl ethers are more stable than smaller ones. This stability directly shows – TBDMS ethers are stable to chromatography and survive various reaction conditions which smaller ethers do not. With different labilities, chemists can deprotect TMS or TES ethers in presence of TBS protecting groups (more below).

    TBS Deprotection Mechanisms

    There are three types of deprotection mechanisms for TBS and silyl ethers in general.

    Acidic deprotection mechanism of TBS silyl ethers

    1. Acidic hydrolysis works through protonation of the protected oxygen atom, followed by associate hydrolysis with a pentavalent silicon intermediate.

    Fluoride mediated deprotection mechanism of TBS silyl ethers

    2. Fluoride-mediated deprotection is based on nucleophilic attack onto silicon, giving a pentacoordinate siliconate intermediate that can release our deprotected product. This is like the imidazole catalysis we’ve seen during TBS protection.

    The thermodynamic driving force is the formation of the exceptionally strong Si-F bond (>30 kcal/mol stronger than Si-O) bond. For fluoride-mediated deprotection, TBAF (tetrabutylammonium fluoride) is the archetypical fluoride source. However, other sources like HF or amine-HF complexes are also commonly used.

    3. Basic hydrolysis can theoretically also occur with TBS ethers, even though have high stability towards bases. However, at very forcing basic conditions, TBS ethers can hydrolyse (e.g., excess LiOH, dioxane, EtOH, H2O, 90 °C).
    The mechanism is also based on nucleophilic addition to silicon, followed by Si-O bond breaking.

    Selective Deprotections of silyl ethers

    So, we have mentioned that selective deprotection of silyl ethers might be possible. The first category of reactions follows the steric stability we laid out above. Let’s look at some examples [4].

    Selective deprotection of TBS over TIPS

    Pyridinium p-toluene sulfonate (PPTS) in protic solvents like MeOH is the mildest system for deprotection of TBS ethers. In this example, you can see that the conditions are controlled enough so that the bulkier TIPS group does not fall off. The same would go for TBDPS (tert-butyldiphenylsilyl).

    SEM group is relatively acid resistant

    This next example is sneaky. Don’t be fooled by seeing “TMS” and thinking it will immediately be less stable than TBS! Upon close inspection, we realize that this is actually a alkyl silyl group, part of the so-called SEM protecting group. It can be removed through fluoride anions or more forcing acidic conditions.

    Welcome to chemistry, it’s sometimes random

    The second category of selective reactions does not follow any obvious rules. It’s really experimental randomness. A commonly cited example is from the synthesis of zaragozic acid C [5].

    TBS deprotection en route to Zaragozic acid C

    During this effort, it was possible to differentiate between two very similar TBS protecting groups. The use of dichloroacetic acid in MeOH was mild enough to selectively (90% yield) cleave only one of the TBS groups.

    That same synthesis actually also nicely demonstrated the concept of selective protection based on steric hindrance. After full consumption and protection of the primary alcohol with TBS-Cl, the chemists threw in TMS-Cl to protect the tertiary hydroxyl group as well.

    Selective protection of primary alcohol over tertiary alcohol

    There’s a recent example (2024) of TBS randomness [6]. In the last synthetic steps towards (+)-heilonine, the authors performed a Clemmensen reduction with Zn in HCl to reduce the ketone. It would have been nice if this one-two punch would have directly delivered the natural product. However, for no apparent reason, only one of the two TBS groups fell off. So, a separate deprotection step with TfOH was required.

    Surprising TBS removal with Lewis acids (Clemmensen reduction)

    That’s it for TBS. Learn more about other protecting groups, or watch my educational videos for advanced science content!

    TBS Protection experimental procedure [7]

    “To a solution of the diol (57.48 g, 0.354 mol) in DMF (354 mL) were added imidazole (96.52 g, 1.418 mol) and TBSCl (160.27 g, 1.063 mol) at rt. After stirring at 50 °C for 17h. H2O was added and the mixture was extracted with Et2O. The organic layer was washed with brine, dried over MgSO4, and evaporated in vacuo. The residue was purified by flash column chromatography (SiO2; n-hexane:EtOAc = 10:1) to give the diTBS ether (138.48 g, 100%).”

    TBS deprotection experimental procedure [7]

    “To a solution of the alcohol (45.2 g) in THF (350 mL) was added TBAF (1.0 M in THF, 184 mL, 0.184 mol) at rt. After stirring at rt for 18 h, the mixture was concentrated in vacuo. The residue was purified by flash column chromatography (SiO2; n-hexane:EtOAc = 4:6→EtOAc) to give diol (29.1 g, 97% yield, 2 steps).”

    TBDMS Protecting Group References

  • SN2 Reaction Explanation & Mechanism

    SN2 Reaction Explanation & Mechanism

    Do you struggle to comprehend the SN2 mechanism, or the difference between SN2 vs SN1? You are not alone! All of us need models and practice to understand what the molecules look like in their 3D structure. On my channel, you can find some more visual explanations and animations that might help.

    SN2 Mechanism: it takes two to tango

    Our first model reaction is the nucleophilic substitution of 2-bromobutane with the phenolate anion, also called a Williamson ether synthesis.

    chiral electrophile for SN2 (bimolecular nucleophilic substitution)

    2-Bromobutane is chiral as one of the carbons has four different substituents. We are looking at the (R)-enantiomer here – this will be important for the stereospecificity of the reaction. Electrophiles provide the LUMO for reactions, in this case the antibonding sigma star orbital between carbon and our leaving group. Note that bromide and iodide are particularly potent leaving groups due to high acidity of conjugate acids but also weak bonds with carbon. This is due to weak overlap of atomic orbitals, resulting in a low-energy sigma star that is accessible to our nucleophile, phenolate.

    SN2 highest occupied molecular orbital

    This electron-rich anion is completely planar due to conjugation of one of the oxygen electron pairs with the aromatic ring. Its HOMO is localized on the oxygen as you would expect – but we can also nicely see resonance with delocalization across the pi-system.

    SN2 Transition state

    To ensure decent orbital overlap, the substitution proceeds via back-side attack. Because the nucleophile needs to get pretty close to the already tetrahedral carbon, steric factors are more important for the SN2 reaction compared to SN1.

    SN2 transition state

    The SN2 mechanism proceeds in one concerted step with both electrophile and nucleophile present in the transition state – that’s why we call it 2, for bimolecular. The carbon-bromine bond is partially broken, and the carbon-oxygen bond partially formed. Remember that is just a transient energy maximum and not a real intermediate, carbons are never actually five-coordinate!

    After the transition state, the product moves to a more comfortable conformation but importantly, features the inverted stereochemistry due to back side attack. This changes the (S) enantiomer in the starting material to the (R) enantiomer product. As a good leaving group, the bromide anion enjoys its solitude and buzzes off.

    Steric effects in SN2 substitutions

    steric hindrance in SN2 reactions

    Due to the five-coordinate transition state, more sterically hindered substrates react much slower or not at all. While it’s not intuitive on paper, the model nicely visualizes that surrounding substituents can block the nucleophiles back side attack. There’s simply too much unwanted repulsion. Instead, depending on reaction conditions like solvent polarity, we would see more step-wise SN1.

    Intramolecular SN2 reaction Mechanism

    Let’s look at a slightly more advanced example. I’m TotalSynthesis, so I just had to take a cute natural product that was isolated from random tropical algae in Brazil. As fate wanted it, this also has a secondary alkyl bromide, so it fits perfectly.

    aldingenin C, a natural product

    We’re interested in this epoxide opening step as it showcases a common question on diastereoselectivity. The reaction is intramolecular but is pretty similar to a SN2-type reaction. Given our fixed starting configuration, the side chain and the nucleophilic alkoxide hover on the bottom side of the ring.

    intramolecular SN2 epoxide opening

    As you can see, the nucleophile has a perfect position for the backside attack, leading to the 1,2-anti product. The leaving group is now much worse than bromide, but relieving the strain energy present in the epoxide drives the reaction forward.

    two potential products

    Is there another potential substitution? Indeed, the other epoxide carbon is also an electrophile. However, the methyl group at this position adds some steric hindrance. Given the quaternary center, this substitution could also proceed stepwise or “asynchronous”, with C-O bond breaking being more advanced prior to addition.

    Taking the longer approach forms a 7-membered ring. Compared to the six-member ring on the right, it’s not as rapidly formed or as stable – but the pathway is still significant with 19% yield.

    After six additional reactions, a surprising twist showed that the original proposal was incorrect. It turned out this unique natural product never existed to begin with! Instead, it was a mis-assigned, already known molecule, which is even a bit cooler given it includes two bromides and even a chloride. Well, it happens to the best of us.

    I’m looking forward to explaining simple, beginner-level content in addition to my other educational videos. Let me know if this helped you!

  • Fmoc Protecting Group: Fmoc Protection & Deprotection Mechanism

    Fmoc Protecting Group: Fmoc Protection & Deprotection Mechanism

    Conditions for protection and deprotection of the Fmoc protecting group (fluroenylmethoxycarbonyl)

    This group has some similarities to other carbamates (Boc, Cbz) despite being orthogonal.

    But, have you heard of Sulfmoc or Bsmoc? We will also discuss these exotic cousins of Fmoc to learn about important organic chemistry concepts.

    👀 Can you find the acidic C-H bond in this 3D model of Fmoc?

    What is the Fmoc Protecting Group?

    Fmoc is a fluorenylmethoxycarbonyl group that forms carbamates with amines. However, as a common theme in protecting groups, alcohols and other nucleophiles can also be protected.

    Fmoc was introduced by Carpino in 1972 [1]. At that time, few base-sensitive amine protective groups were known. Chemists obviously already used protecting groups, but they were not as straight-forward. For example, the tosylethyloxycarbonyl group (base-labile with KOH/NaOEt) gave the stable carbamate salt which required a second step for decarboxylation.

    Fmoc Protection Mechanism

    The classic Fmoc protection is with Fmoc-Cl under Schotten-Baumann conditions (e.g. NaHCO3/dioxane/H2O or NaHCO3/DMF), or with anhydrous conditions (e.g. pyridine/CH2Cl2).

    If you have seen more than one protecting group, this will not surprise you:
    The mechanism is attack of the nucleophilic amine to the highly reactive 9-fluorenylmethyl chloroformate. As chloride is the leaving group, the reaction liberates HCl which is neutralized by the base.

    Fmoc-Cl can be handled easily (it’s a solid) – however, as it’s an acid chloride, is sensitive to moisture and heat. Thus (as for all protective groups), other “Fmoc+”-equivalent reagents offer more optionality.

    Fmoc-OSu is most commonly used nowadays due to the increased stability of this succinimide carbonate. It also has lower unproductive formation of oligopeptides that can occur during preparation of Fmoc amino acid derivatives.

    Additional options exist such as Fmoc-OBt or Fmoc-N3. However, you would rather deal with some harmless solids than explosive azides…

    Fmoc DeProtecTION Mechanism With Base

    Fmoc is typically deprotected with secondary amines in DMF. The mechanism has some parallels to Boc. Instead of a stabilized (tertiary) carbocation as an intermediate, Fmoc proceeds through a fluorenyl anion. But why is it stabilized? The position might not seem acidic at first sight.

    Upon closer inspection, we see the deprotonated system fulfils Hückel’s rule for n=3 (14 electrons) and is aromatic! That’s why the pKa of fluorenyl is around ~23 (DMSO). This is basically a cyclopentadiene anion (whose aromaticity you will know) sandwiched between two benzene rings.

    The intermediary carbanion can eliminate the carbamate in a E1cb mechanism, releasing dibenzofulvene. This side product lead to byproducts (e.g., reaction with nucleophilic amino acid groups) or polymers. This is why secondary amines like piperidine or morpholine are particularly handy!

    They hit two birds with one stone. They cleave Fmoc, and also form a stable adduct with the dibenzofulvene. The “secondary” part is quite important as ammonia does not add to the fulvene system [1].

    Fmoc DeProtecTION Speed

    There is another reason why piperidine is the most commonly used base to deprotect Fmoc. This table compares half-lives for Fmoc-ValOH in presence of various amine bases in DMF.

    Amine base used for Fmoc deprotectionHalf life t1/2
    20% piperidine6 seconds
    5% piperidine20 seconds
    50% morpholine1 minute
    50% dicyclohexylamine35 minutes
    50% diisopropylethylamine10 hours
    Half-life data from [2]

    Piperidine (and morpholine) deprotection is virtually instantaneous on the second-scale. In contrast, secondary or tertiary amines deprotect Fmoc more slowly (hours) and require higher amounts of base. If you wonder, going from DMF to other solvents like DCM reduces the reaction rate.

    Fmoc protecting group Orthogonality

    Fmoc is very stable towards acid and electrophiles, tolerating reactive reagents like HBr, trifluoroacetic acid, sulfuric acid and thionyl chloride. Thus, its orthogonal to Boc.

    However, it is only quasi-orthogonal to Cbz as it undergoes hydrogenolysis as well! It is less reactive than benzyl groups, so selectivity can be achieved. The reduction can occur under traditional (Pd/C, H2) or different transfer catalytic conditions. The final step of the synthesis of Enkephalin was triple-deprotection of O-Bn, CO2-Bn and N-Fmoc.

    Fmoc deprotection for enkephalin

    Fmoc Variants

    Let us again look at some more advanced concepts. There are Fmoc-related variants that are more base-labile. By attaching electron-withdrawing substituents like sulfonic acid or halides.

    What are the effects? Specifically, Sulfmoc increased proton abstraction by a factor 30 in DCM (vs. Fmoc) using 10% morpholine in DCM, or factor ~10 for 10% piperidine [3]. In specific cases, such labile groups might be pretty useful.
    By the way, Sulfmoc was introduced by Merrifield who won the Nobel Prize for inventing solid-phase peptide synthesis.

    Evidently, this comes from acidification of the fluorenyl position. The 2,7-dibromo Fmoc analog has a pKa value of 17.9 or almost 5 units lower than normal Fmoc!

    However, there’s an even cooler analog, also published by Carpino called Bsmoc. It can be cleaved under specific conditions which leave normal Fmoc in tact, but typical conditions with piperidine work as well [4].

    Fmoc in Peptide Synthesis

    Fmoc was rapidly adopted in modern peptide chemistry [5]. Compared to the established Boc, it was easy to automate: no corrosive TFA is required, and reaction monitoring is easy due to the fluorene by-product (see deprotection). Fmoc SPPS machines were less expensive and avoided use of unpleasant hydrogen fluoride (HF). The conditions themselves were more compatible with modified peptides (e.g., modification with carbohydrates, phosphorylation…).

    As another advantage, the Fmoc protecting group enables orthogonal combination of temporary and permanent protecting groups. During Boc SPPS, iterative use of TFA during each cycle leads to deprotection of small amounts of side-chain protecting groups and cleavage of peptide from polymer support.

    Bsmoc solution

    Let’s conclude with Bsmoc.

    The innovative thing is that it functions as a protecting group and scavenger in one!
    It’s introduction is analogous to normal Fmoc, using the chloroformate or H-hydroxysuccinimide ester. Instead of a deprotonation with piperidine, we have a Michael addition to the conjugated sulfone.

    The free carbamate proceeds to decarboxylate as always, but the piperidine stays on the Bsmoc group (thus, it’s a direct scavenger). You might not expect it but it’s very logical: The initial adduct rearranges after some time to the isomer where the double bond is conjugated to the benzene ring.

    The ‘quasi-orthogonal’ conditions for Bsmoc-Fmoc are tris(2-aminoethyl)amine as a base. This primary amine cleaves Bsmoc rapidly while keeping Fmoc in tact. On the flip side, use of more hindered bases like diisopropylamine do not react with Bsmoc but cleave the Fmoc group! This is a consequence of steric hindrance slowing down the nucleophilic Michael addition.

    Fmoc: ✅ check. Learn more about other protecting groups, or watch my educational videos for advanced chemistry & science content!

    Fmoc Protection experimental procedure [6]

    D-Threonine (5.00 g, 42.0 mmol) and Fmoc-succinamide (14.9 g, 44.1 mmol) were dissolved in a 2:1 v/v mixture of THF:saturated aqueous NaHCO3 (100 mL). The reaction mixture was stirred at room temperature for 16 h. The reaction was then diluted with water (50 mL) and the pH of the mixture was adjusted to pH 9 via addition of saturated aqueous NaHCO3. The mixture was extracted with diethyl ether (3 x 50 mL) and the aqueous layer was acidified to pH 1 via addition of 1 M HCl. The acidic aqueous mixture was extracted with ethyl acetate (3 x 100 mL) and the combined organic extracts were washed with brine (100 mL), dried over Na2SO4, filtered and concentrated in vacuo to afford crude Fmoc-D-Thr-OH (14.3 g) as a white foam which was deemed to be sufficiently pure and used without further purification.

    Fmoc deprotection experimental procedure [7]

    In a vial, SM (2043 mg, 2.5mmol) was added and dissolved in 60 mL of acetonitrile. Then, morpholine (647 uL, 7.5mmol) was added while stirring. The reaction was stirred at room temperature for 24 hours, formation of product and full conversion was confirmed by LC-MS. The reaction was quenched by addition of water and extracted with DCM. The organic 9 phases were combined and washed with aqueous LiCl 5%, dried with sodium sulphate and filtered. The solvent was evaporated and crude product the crude product was purified by silica gel flash chromatography (0-5% MeOH in DCM).

    Fmoc Protecting Group References

  • Cbz Protecting Group: N-Cbz Protection & Deprotection Mechanism

    Cbz Protecting Group: N-Cbz Protection & Deprotection Mechanism

    Conditions for protection and deprotection of the Cbz protecting group (benzyloxycarbonyl)

    N-Cbz is orthogonal to numerous protecting groups (stable to bases and acids). Its deprotection is unique but it does have similarities to other PGs.

    👀 You can play around with this 3D model of the Cbz group.
    Note the orientation of the phenyl ring: it’s not co-planar with the carbamate!

    What is the Cbz Protecting Group?

    Cbz is a benzyloxycarbonyl group (formerly carboxybenzyl) and protects amines as carbamates. More rarely, chemists might use Cbz to protect alcohols as their carbonates.

    Leonidas Zervas (no not the one from the movie “300”) introduced the Cbz group, thus also abbreviated as Z [1]. With this discovery, Leonidas and his advisor Bergmann spearheaded the field of controlled peptide chemistry. In the 1930s, Cbz unlocked the synthesis of previously inaccessible oligopeptides. Zervas continued to be a driving force in peptide chemistry, including development of other protecting groups.

    Cbz Protection Mechanism

    Cbz protection is typically performed with Cbz-Cl either under Schotten-Baumann conditions (carbonate base) or with an organic base. The mechanism is attack of the nucleophilic amine to the highly reactive chloroformate. As chloride is the leaving group, the reaction liberates HCl and requires some base.

    Like we’ve seen for Boc, Cbz2O or other activated agents (e.g., Cbz-OSu) can offer more optionality, depending on the system. If you are into exotic reagents, you might like reagents A or B in the next figure – basically, anything with an activated “Cbz+” synthon works.

    Cbz protecting agents

    As is common the case, we can protect amines selectively given their higher nucleophilicity. However, there have been some reports of challenging selective protection of secondary amines over secondary alcohols. As always, our rules of thumb depend on the specific system at hand.

    Cbz DeProtecTION Mechanism With Hydrogenolysis

    Hydrogenolysis deprotects Cbz protecting groups, usually in an easy and rapid manner. The mechanism is a reduction with H2, releasing toluene and the free carbamate. Consequently, decarboxylation to the deprotected amine is very much favoured (particularly at elevated temperatures).

    Besides molecular H2, it is possible to use other “H2 donors” through transfer hydrogenation reactions (e.g., see procedures below).

    Cbz protecting group Orthogonality

    Cbz is orthogonal to Boc, Trt, Fmoc and other common protecting groups. As mentioned, it was an essential part of the early days of peptide synthesis.

    But beware thinking it’s fully orthogonal! Although Cbz tolerates some acid, harsh conditions can cleave it as well (e.g., excess HCl, HBr)! This mechanism includes protonation of the carbamate and liberation through SN2 and decarboxylation.

    Beyond hydrogenation, Cbz can be susceptible to other transition metal catalysis as well, for instance Ni(0) or Pd(0). This interesting case report demonstrated selective removal of double Cbz-protected histidine [2] . Compared to heteroaromatic nitrogen atoms, originally basic amines did not engage in any reaction.

    Cbz use cases and tricks

    As always, it would be boring to just look at the simplest case of nitrogen protection and deprotection. Let’s briefly discuss three additional topics [3].

    First, Cbz protects other nucleophilic functional groups like alcohols, phenols, thiols… as well. In these cases, an organic base (not carbonate) in dichloromethane or some ether-based solvent is typically used. To increase reactivity, NaH as base allows for protection of deactivated, tertiary alcohols:

    Notably, Cbz-Cl as a reagent can activate pyridines to regioselective nucleophilic attack. The use of electrophiles for these purposes is a key concept in heterocyclic chemistry. There is a nice collection on 1-acylpyridiniums by the Baran Lab.

    Third and coolest, the Cbz group can serve as a masked N-methylamine. Treatment with LiAlH4 exhaustively reduces the carbamate to the alkane.

    ✅ That’s it for Cbz! Learn more about other protecting groups, or watch my educational videos for advanced chemistry & science content!!

    Cbz Protection experimental procedure [4]

    “To the SM (1.70 g, 2.64 mmol) in THF/H2O (2:1, 15 mL) was added NaHCO3 (443 mg, 5.27 mmol) and Cbz-Cl (0.56 mL, 3.96 mmol) at 0 °C and the solution was stirred for 20 h at the same temperature. The reaction mixture was diluted with H2O and extracted with AcOEt. The combined organic layers were washed with brine, dried over Na2SO4, and concentrated in vacuo. The resulting residue was purified by silica gel column chromatography (40% AcOEt/n-hexane) gave 20 (1.85 g, 2.38 mmol) in 90% yield as a white powder.”

    Cbz deprotection experimental procedure

    [4] Normal hydrogenolysis
    To a solution of SM (20.7 mg, 15.0 micromol) in 2 mL of MeOH were added 5% Pd-C (6.4 mg), and the mixture was stirred at 60 °C for 40 h under atmospheric pressure of H2. Then, the catalyst was filtered of on pad of celite. The filtrate was concentrated in vacuo to give a crude material containing 27, which was used without purification for the next step.


    [5] Deprotection of 5 Cbz groups in the final step via transfer hydrogenation.
    To a solution of protected caprazamycin A (32) (6.5 mg, 3.21 micromol) in EtOH/HCO2H (1.9 ml, v/v = 20:1) was added Pd black (66.5 mg, 625 micromol) at 25 °C, and the resultant mixture was stirred for 1.5 h at 25 °C. After filtration through celite, the filtrate was concentrated under reduced pressure. The resultant residue was purified by C18 reversed phase. Caprazamycin A eluted at 11-18 min as an isolated peak. The eluent was collected and concentrated under reduced pressure to give a pure caprazamycin A (3.6 mg, 98%) as a colorless powder:

    Cbz Protecting Group References

  • Boc Protecting Group: N-Boc Protection & Deprotection Mechanism

    Boc Protecting Group: N-Boc Protection & Deprotection Mechanism

    Conditions for protection and deprotection of the Boc protecting group (tert-butyloxycarbonyl)

    The N-Boc group is a key topic during chemistry courses. Why?
    It nicely exemplifies important protecting group concepts and has an interesting deprotection mechanism.

    👀 Here’s a 3D model to help you visualize the Boc protecting group.

    What is the Boc Protecting Group?

    Boc stands for tert-butyloxycarbonyl and protects amines as carbamates. More rarely, it is also used to protect alcohols as their carbonates.
    Boc is resistant to basic hydrolysis, many nucleophiles as well as catalytic hydrogenation. The fact that it can be removed with mild acid makes it orthogonal to other key protecting groups (see below).

    Boc Protection Mechanism

    Boc protecting group mechanism with Boc anhydride

    The main method of Boc protection is use of Boc anhydride. Base is not strictly needed for the reaction with Boc2O (tert-butanol formed as product). However, bases like triethylamine or NaOH (amino acids) are sometimes used, depending on the system.

    The mechanism is straight-forward: attack of the nucleophilic amine to the electrophilic anhydride. The carbonate leaving group can release CO2, providing a strong driving force for the reaction. This step is the same as for other carbamate protecting groups such as Cbz.

    As we have seen for PMB, many variants of activated agents can exist. The same is true for Boc. For instance, we can also use Boc-Cl (t-butyl chloroformate) but because it’s unstable and needs to be prepared freshly, Boc2O is much more convenient. Boc-ON is another variant; it’s an “oxyimino-nitrile” reagent.

    As a common theme for protecting groups: Remember that amines are more nucleophilicity than alcohols, so you can selectively protect them in many cases.

    Selective N-Boc protection

    Boc DeProtecTION Mechanism WITH Acid

    Reaction mechanism of Boc deprotection with acid (TFA)

    Acids like TFA, HCl… can deprotect Boc groups. Protonation of the oxygen triggers fragmentation into a stabilized tertiary cation (inductive effect). It later deprotonates to form gaseous isobutene.
    The fragmented carbamate can decarboxylate, releasing CO2 (here you have a parallel of Boc anhydride introduction and its removal) and giving the free amine.

    Given the high steric hindrance of the carbamate, the Boc group is not base-labile like methyl esters, for instance.

    A potential issue are intermolecular side reactions of the intermediary t-butyl cation. An example from peptide chemistry is alkylation of nucleophilic amino acids methionine or tryptophan. That’s why you might see conditions which employ scavengers like thiophenol, anisole, cresol… to remove the reactive intermediate.

    Boc protecting group Orthogonality

    Boc protection is a key tool for heterocycle and peptide synthesis. In solid phase peptide synthesis (SPPS), it is used as a protecting group for alpha-amino groups and amino acids lysine, tryptophan and histidine.

    Due to its acidic deprotection, it is orthogonal to other important amino acid protecting groups:

    • Fmoc (9-fluorenylmethoxycarbonyl) – removed with base
    • Cbz / Z (benzyloxycarbonyl) – removed with H2 reduction
    • Alloc (allyloxycarbonyl) – removed with transition metal catalysis (Pd)

    However, Boc is not stable to Lewis acids or oxidative conditions. We have seen that the O-PMB protecting group is removable with DDQ. In one case [1], treatment of the PMB ether did not result in any desired deprotection.

    DDQ deprotection of Boc

    Boc side reactions

    In organic chemistry, surprises wait around every corner. Don’t assume that protecting groups stay on forever, and only cleave on demand!

    Before, we have mentioned that alcohols are less nucleophilic than amines, allowing selective protections. In this example [2], the authors observed a N-O Boc transfer when preparing a chiral oxazolidinone auxiliary. Upon deprotection of the TBDMS group, the highly nucleophilic alkoxide grabs the Boc group from the nitrogen!

    Boc protecting group side reactions

    Overman et al used a more conscious Boc-participation in their synthesis towards the diazatricyclic core of sarain marine alkaloids. [3]
    Base generates the alkoxide which again attacks Boc. This time however, the group is not transferred (the negative charge would not be stabilized on the nitrogen, unlike the previous example). Instead, we see an intramolecular cyclization.

    Protecting group side reaction of Boc

    Boc in Peptide Synthesis

    As alluded to above – particularly in the early days – the Boc protecting group proved very useful for solid-phase peptide synthesis (SPPS). However, in the late 20th century, the Fmoc protecting group started to replace Boc methodology.

    Fmoc deprotection is generally milder than the moderate/ strong acidolysis steps used for Boc. More specifically, Fmoc proved more compatible with synthesis of amino acids that are susceptible to acid-catalysed side reactions.

    A good example is the synthesis of the peptide gramicidin A which contains four acid-sensitive tryptophan residues. Using Boc chemistry, yields were in the range of 5-24%. Switching to Fmoc dramatically improved the yields, in some cases to 87% [4].

    Closing Remarks

    The Boc group is pretty cool, and its deprotection mechanism is a must-know for every organic chemistry student. The orthogonality to base- or reduction-labile protecting groups make it a top pick for many total and peptide syntheses.

    However, like all protecting groups, it has its downsides. The carbamate carbon remains somewhat nucleophilic which opens avenues for surprising reactions, particularly intramolecular. Also, the acidic conditions and reactive tert-butyl-cations used can pose challenges to some systems. As always, smart planning and workarounds might be needed.

    Boc: ✅. Learn more about other protecting groups, or watch my educational videos for for advanced chemistry & science content!

    BOC Protection experimental procedure [5]

    One pot Cbz->Boc switch
    “To a solution of Cbz-carbamate SM (3.5 g, 6.81 mmol) in MeOH (25 mL) were added Pd/C (10 % w/w, 200 mg, 0.19 mmol) and Boc2O (2.17 g, 9.9 mmol) at room temperature. The reaction mixture was stirred under a hydrogen atmosphere (balloon) at room temperature for 6 h. The reaction mixture was filtered through a pad of celite, and then concentrated in vacuo. Flash column chromatography (silica gel, hexanes:EtOAc 10:1 → 7:1) afforded Boc-carbamate 42 (2.94 g, 90 %) as an oil.”

    BOC deprotection experimental procedure [6]

    “Boc-L-allo-End(Cbz)2-OtBu (597 mg, 1 mmol) was dissolved in a mixture of TFA (10 mL) and water (1.0 mL). The mixture was stirred at room temperature for 3 h, then concentrated to give a brown oil. The resulting crude oil was azeotroped with toluene (3 x 10 mL) and concentrated in vacuo to remove any residual TFA.”

    BOC Protecting Group References