Aerogel: Chemistry Updates

Week #09: Inserting N-Hydroxysuccinimide & Its Functionality

Carlos Manuel Jarquín Sánchez
7 min readOct 5, 2022


Preface ✨

Hello everyone!

My intentions for writing these articles are:

  • Explain technical information about aerogels in simple terms (to the public)
  • Store information and habits for my future self and others (in <7 minutes)

Coolio? Sweet. Enjoy the series :-)

Why New Chemicals? ⚛️

The carboxylic acid groups in the sodium alginate (derived from brown seaweed) could be converted into more efficient chemical groups: amides.

Amides are functional groups (molecules) that require a carbonyl group (a carbon atom double bonded to oxygen) to bond with a nitrogen atom. The nitrogen atom will additionally bond with two hydrogen atoms (to form an amine)

Amides will allow for increased adsorption of heavy metal ions & contribute to the final structure of the MGDA-based aerogel filter. 💥

A Primary Amine; Only One “R” Group Is Present | “R” Is Most Likely An Alkyl Group (Ex: Methyl, CH3)

But this reaction can only work if the carboxyl group is deprotonated (loses a proton) to form a carboxylate.

The reaction of a carboxylic acid group & an amine would just form a salt (ammonium carboxylate salt) that would limit the aerogel filter’s usability.

There’s two ways to resolve this issue:

  • Adding heat into the reaction (to boil off the water in the solution & form the amide)
  • Insert Sodium Alginate, EDC, & N-Hydroxysuccinimide together

Why Add Heat? 🔥

A regular carboxyl group and an amine would cause deprotonation in the carboxyl group and transfer the released proton (H+) into the amine.

On The Left: Carboxyl Group + Amine | On The Right: Carobxylate (Lost Proton) & Amine (Gained Proton)

Carboxylate is now anionic (negatively charged; more electrons than protons)

Amine is now cationic (positively charged; more protons than electrons)

Another issue to worry about is:

The pKa value for a carboxylate is ~5

The pKa value for a protonated amine group is ~11

The pKa Value measures how tightly a proton is held in a molecule (Bronsted Acid). The proton is held more tightly (will not leave the molecule/functional group) if the pKa value is higher.

This is why the proton from the hydrogen atom in the carboxyl group left. It was more reactive (to transfer the proton) than an amine group.

But we still do not have the desired outcome!

The reason why is that an amide group is more reactive towards nucleophilic acyl substitution than the deprotonated carboxylic acid (carboxylate). The pKa of an amide group is ~0.5

Nucleophilic Acyl Substitution is a reaction where a nucleophile forms a new bond with the carbonyl carbon (C=O) of an acyl group with accompanying breakage of a bond between the carbonyl carbon (it went from C=O to C-O) and a leaving group (a lost substance, like evaporated water).

Acyl Group is a functional group/molecule that contains “RCO-”. “R” can be an alkyl group (ex: CH3) where “R” is bound to the main carbon atom with a single bond.

“RCO-” Is In Blue

Nucleophiles are atoms/functional groups with a pair of non-bonding electrons (two electrons) that can be shared by outside compounds.

pKa Amides: ~0.5 > pKa Carboxylates: ~5 || The Lower pKa Value Is More Reactive

A functional group that requires to go from a less reactive state/molecule to a higher reactive state/molecule needs more energy inserted into the reaction.

The solution to this dilemma is adding heat.

The leftover reaction contains 3 hydrogen atoms and an excess of one proton(H+). The oxygen atom has an excess of one electron (O-).

Two hydrogen atoms can combine with the oxygen atom to form a water molecule! This is a leftover product and can leave the reaction if we had more energy!

One must heat the functional groups by a minimum of 100°C (212°F) to boil out the water remains.

Why? The boiling point of water is 99.97°C (211.9°F)

This would be the final reaction with heat:

Number One - Number Two Is Before Heat | Number Two - Number Three Is After Heat

The symbol “Δ” is the Greek uppercase letter (Delta) & is used in chemistry to describe the addition of heat.

Heat Is Effective. But Not Energy-Efficient. Fail.❌

Using Activating Agents🔧

The energy-efficient AND effective choice is to use a functional group that creates the jump from carboxylic acid to an amide group without using heat or creating a carboxylate.

The activating agent will be EDC.

[1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride]

EDC Raw Chemistry

The reason this works is that one of the remaining products is water (from the previous example of adding heat). EDC is a compound/molecule that removes water from the reaction. This is known as a dehydrating agent.

This will allow for the leftover molecule (that will not make part of the amide functional group) to leave without ruining the final chemical and the aerogel filter!

The first step is to deprotonate (remove the proton) the hydrogen atom in the carboxyl group and transfer the proton into the EDC compound.

Carboxyl + EDC Combined | Oxygen Atom Gained 2 Electrons & Nitrogen Lost An Electron + Gained A Proton

The next step is for the top oxygen atom to bond with EDC with the carbon atom in EDC. It works because of the Lewis Acid & Base Theory.

TL;DR: A positively-charged molecule (Electron Acceptor, Lewis Acid) & a negatively-charged molecule (Electron Donor, Lewis Base) react to form a covalent bond. The Lewis Base must have two electrons to spare if a covalent bond is desired.

The oxygen atom with additional electrons (Lewis Base) will link/react with the nitrogen with additional protons (Lewis Acid) and form the covalent bond! The Lewis Base also has two electrons to spare! It works!

Note: “Nu attack” means “nucleophilic attack”; the amine group that we will use is Diethylenetriamine (DETA) functional group. Do not worry; the amine group did not appear from anywhere: it must be inserted into the reaction.

The next step involves the amine group (DETA) attacking the primary carbon atom (carbonyl group) in the carboxylic acid. This “nucleophilic” attack displaces the second double bond (pi-bond) between the oxygen and carbon atoms (C=O) and “uses it” to bond with the amine group.

This reaction creates the foundation for the final product: the amine group.

P.S. Notice where the positive & negative charges are on the developing amide group. It looks quite similar to the second photo of this article (final reaction)… Interesting pattern… 😃

Note: “Good LG” means “Good Leaving Group”; this will detach from the amide group and wander away. It is officially stable/strong (non-ionic) to leave. Think of The Space Shuttle (Amide Group) detaching from the solid rocket boosters and the liquid orange tank (Leaving Group).

The next step is to detach the leaving group from the final amide group. It is simple: The lower oxygen bond recreates a double bond with carbon (pi-bond) and breaks the covalent bond made with the higher oxygen bond. This is the detachment of the amide group and the leaving group.

The leaving group is on the left & the amide group is on the right.

But hold it! There is still an anionic (negative) & cationic (positive) charge in both the groups!

The final step is to transfer a proton from the cationic compound to the anionic compound. The amide group (NH2+) is really (NH3+):

  • A Nitrogen Atom (N)
  • Two Hydrogen Atoms (H2)
  • One Free Proton With No Electron (H+)

The anionic oxygen lacks a second covalent bond to complete its outer valence electron shell. This leads to a free electron floating around in the molecule.

Oxygen has 6 valence electrons, it needs two more valence electrons to fill its outer shell and stabilize itself.

By transferring the excess proton in (NH3+) into the free electron, you make a hydrogen atom: one proton & one electron!

The oxygen atom now has its double bond (carbonyl bond) with carbon & the nitrogen pairs both have hydrogen attached (in the leaving group). The amide group is now neutral-charged.


This Process Functions At Room Temperature With ~80% Efficiency. Success.✔️

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© 2023 by Carlos Manuel Jarquín Sánchez. All Rights Reserved.